diff --git a/.gitignore b/.gitignore
new file mode 100644
index 00000000..79cf0a00
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,160 @@
+# Python cache files
+__pycache__
+**/*.pyc
+
+# UI dependencies
+ui/node_modules/
+
+# UI build output
+ui/build/
+
+# UI package manager debug output
+ui/*.log
+.skiff/webapp.yaml
+
+# Docker compose env files
+.env
+
+# Ignore any files in ./skiff_files
+skiff_files/*
+
+### Python Build Related ###
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+# For a library or package, you might want to ignore these files since the code is
+# intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+# However, in case of collaboration, if having platform-specific dependencies or dependencies
+# having no cross-platform support, pipenv may install dependencies that don't work, or not
+# install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
\ No newline at end of file
diff --git a/.skiff/cloudbuild-deploy.yaml b/.skiff/cloudbuild-deploy.yaml
new file mode 100644
index 00000000..8c76f7e7
--- /dev/null
+++ b/.skiff/cloudbuild-deploy.yaml
@@ -0,0 +1,140 @@
+# This file tells Google Cloud Build how to deploy the application.
+# It can be attached to a variety of triggers, the default being whenever
+# someone merges changes to the `master` branch.
+steps:
+# Pull down the latest versions of each Docker image, so the build is faster.
+- id: 'api.pull'
+ name: 'gcr.io/cloud-builders/docker'
+ entrypoint: '/bin/bash'
+ args: [
+ '-c',
+ 'docker pull gcr.io/$PROJECT_ID/$REPO_NAME-api:latest || exit 0'
+ ]
+ waitFor: [ '-' ]
+- id: 'ui.pull'
+ name: 'gcr.io/cloud-builders/docker'
+ entrypoint: '/bin/bash'
+ args: [
+ '-c',
+ 'docker pull gcr.io/$PROJECT_ID/$REPO_NAME-ui:latest || exit 0'
+ ]
+ waitFor: [ '-' ]
+- id: 'proxy.pull'
+ name: 'gcr.io/cloud-builders/docker'
+ entrypoint: '/bin/bash'
+ args: [
+ '-c',
+ 'docker pull gcr.io/$PROJECT_ID/$REPO_NAME-proxy:latest || exit 0'
+ ]
+ waitFor: [ '-' ]
+# Build docker images for each piece of the puzzle
+- id: 'api.build'
+ name: 'gcr.io/cloud-builders/docker'
+ entrypoint: '/bin/bash'
+ args: [
+ '-c',
+ 'docker build -t gcr.io/$PROJECT_ID/$REPO_NAME-api:latest -t gcr.io/$PROJECT_ID/$REPO_NAME-api:$COMMIT_SHA --cache-from gcr.io/$PROJECT_ID/$REPO_NAME-api:latest .'
+ ]
+ waitFor: [ 'api.pull' ]
+ dir: 'api'
+- id: 'ui.build'
+ name: 'gcr.io/cloud-builders/docker'
+ args: [
+ 'build',
+ '-t', 'gcr.io/$PROJECT_ID/$REPO_NAME-ui:latest',
+ '-t', 'gcr.io/$PROJECT_ID/$REPO_NAME-ui:$COMMIT_SHA',
+ '--cache-from', 'gcr.io/$PROJECT_ID/$REPO_NAME-ui:latest',
+ '.',
+ '--build-arg', 'NODE_ENV=production',
+ '--build-arg', 'BABEL_ENV=production'
+ ]
+ waitFor: [ 'ui.pull' ]
+ dir: 'ui'
+- id: 'ui.dist.create'
+ name: 'gcr.io/cloud-builders/docker'
+ args: [
+ 'create',
+ '--name', '$REPO_NAME-ui',
+ 'gcr.io/$PROJECT_ID/$REPO_NAME-ui:$COMMIT_SHA',
+ ]
+ waitFor: [ 'ui.build' ]
+ dir: 'ui'
+- id: 'ui.dist.cp'
+ name: 'gcr.io/cloud-builders/docker'
+ args: [
+ 'cp',
+ '$REPO_NAME-ui:/usr/local/src/skiff/app/ui/build',
+ '/workspace/proxy/dist'
+ ]
+ waitFor: ['ui.dist.create']
+- id: 'proxy.build'
+ name: 'gcr.io/cloud-builders/docker'
+ args: [
+ 'build',
+ '-t', 'gcr.io/$PROJECT_ID/$REPO_NAME-proxy:latest',
+ '-t', 'gcr.io/$PROJECT_ID/$REPO_NAME-proxy:$COMMIT_SHA',
+ '--cache-from', 'gcr.io/$PROJECT_ID/$REPO_NAME-proxy:latest',
+ '.',
+ '--build-arg', 'CONF_FILE=prod.conf'
+ ]
+ waitFor: [ 'ui.dist.cp', 'proxy.pull' ]
+ dir: 'proxy'
+- id: 'api.push'
+ name: 'gcr.io/cloud-builders/docker'
+ args: [
+ 'push',
+ 'gcr.io/$PROJECT_ID/$REPO_NAME-api:$COMMIT_SHA',
+ ]
+ waitFor: [ 'api.build' ]
+- id: 'proxy.push'
+ name: 'gcr.io/cloud-builders/docker'
+ args: [
+ 'push',
+ 'gcr.io/$PROJECT_ID/$REPO_NAME-proxy:$COMMIT_SHA'
+ ]
+ waitFor: [ 'proxy.build' ]
+# Generate our Kubernetes configuration
+- id: 'config'
+ name: 'gcr.io/ai2-reviz/jsonnet'
+ args: [
+ 'eval',
+ '-y',
+ '--output-file', './webapp.yaml',
+ '--tla-str', 'env=$_ENV',
+ '--tla-str', 'apiImage=gcr.io/$PROJECT_ID/$REPO_NAME-api:$COMMIT_SHA',
+ '--tla-str', 'proxyImage=gcr.io/$PROJECT_ID/$REPO_NAME-proxy:$COMMIT_SHA',
+ '--tla-str', 'sha=$COMMIT_SHA',
+ '--tla-str', 'cause=Automated Skiff Deploy SHA:$COMMIT_SHA BUILD:$BUILD_ID',
+ '--tla-str', 'branch=$BRANCH_NAME',
+ '--tla-str', 'repo=$REPO_NAME',
+ '--tla-str', 'buildId=$BUILD_ID',
+ './webapp.jsonnet'
+ ]
+ dir: '.skiff'
+ waitFor: [ '-' ]
+# Deploy the image to Kubernetes
+- id: 'deploy'
+ name: 'gcr.io/ai2-reviz/rudder'
+ args: [
+ 'deploy',
+ '-f',
+ 'webapp.yaml'
+ ]
+ dir: '.skiff'
+ waitFor: [ 'api.push', 'proxy.push', 'config' ]
+substitutions:
+ _ENV: prod
+images: [
+ 'gcr.io/$PROJECT_ID/$REPO_NAME-api:$COMMIT_SHA',
+ 'gcr.io/$PROJECT_ID/$REPO_NAME-api:latest',
+ 'gcr.io/$PROJECT_ID/$REPO_NAME-ui:$COMMIT_SHA',
+ 'gcr.io/$PROJECT_ID/$REPO_NAME-ui:latest',
+ 'gcr.io/$PROJECT_ID/$REPO_NAME-proxy:$COMMIT_SHA',
+ 'gcr.io/$PROJECT_ID/$REPO_NAME-proxy:latest'
+]
+artifacts:
+ objects:
+ location: 'gs://skiff-archive/$REPO_NAME/$_ENV/$BUILD_ID/$COMMIT_SHA'
+ paths: ['.skiff/webapp.yaml']
+
+timeout: 900s
diff --git a/.skiff/webapp.jsonnet b/.skiff/webapp.jsonnet
new file mode 100644
index 00000000..39b56205
--- /dev/null
+++ b/.skiff/webapp.jsonnet
@@ -0,0 +1,352 @@
+/**
+ * This is a template that's compiled down to a definition of the
+ * infrastructural resources required for running your application.
+ *
+ * For more information on the JSONNET language, see:
+ * https://jsonnet.org/learning/getting_started.html
+ */
+
+// This file is generated once at template creation time and unlikely to change
+// from that point forward.
+local config = import '../skiff.json';
+
+function(
+ apiImage, proxyImage, cause, sha, env='prod', branch='', repo='',
+ buildId=''
+)
+ // We only allow registration of hostnames attached to '*.apps.allenai.org'
+ // at this point. If you need a custom domain, contact us: reviz@allenai.org.
+ local topLevelDomain = '.apps.allenai.org';
+ local hosts = [
+ if env == 'prod' then
+ config.appName + topLevelDomain
+ else
+ config.appName + '.' + env + topLevelDomain
+ ];
+
+ // In production we run two versions of your application, as to ensure that
+ // if one instance goes down or is busy, end users can still use the application.
+ // In all other environments we run a single instance to save money.
+ local replicas = (
+ if env == 'prod' then
+ 2
+ else
+ 1
+ );
+
+ // Each app gets it's own namespace.
+ local namespaceName = config.appName;
+
+ // Since we deploy resources for different environments in the same namespace,
+ // we need to give things a fully qualified name that includes the environment
+ // as to avoid unintentional collission / redefinition.
+ local fullyQualifiedName = config.appName + '-' + env;
+
+ // Every resource is tagged with the same set of labels. These labels serve the
+ // following purposes:
+ // - They make it easier to query the resources, i.e.
+ // kubectl get pod -l app=my-app,env=staging
+ // - The service definition uses them to find the pods it directs traffic to.
+ local namespaceLabels = {
+ app: config.appName,
+ contact: config.contact,
+ team: config.team
+ };
+
+ local labels = namespaceLabels + {
+ env: env
+ };
+
+ // By default multiple instances of your application could get scheduled
+ // to the same node. This means if that node goes down your application
+ // does too. We use the label below to avoid that.
+ local antiAffinityLabels = {
+ onlyOneOfPerNode: config.appName + '-' + env
+ };
+ local podLabels = labels + antiAffinityLabels;
+
+ // Annotations carry additional information about your deployment that
+ // we use for auditing, debugging and administrative purposes
+ local annotations = {
+ "apps.allenai.org/sha": sha,
+ "apps.allenai.org/branch": branch,
+ "apps.allenai.org/repo": repo,
+ "apps.allenai.org/build": buildId
+ };
+
+ // The port the NGINX proxy is bound to.
+ local proxyPort = 80;
+
+ // The port the API (Python Flask application) is bound to.
+ local apiPort = 8000;
+
+ // This is used to verify that the proxy (and thereby the UI portion of the
+ // application) is healthy. If this fails the application won't receive traffic,
+ // and may be restarted.
+ local proxyHealthCheck = {
+ port: proxyPort,
+ scheme: 'HTTP'
+ };
+
+ // This is used to verify that the API is funtional. We simply check for
+ // whether the socket is open and available.
+ local apiHealthCheck = {
+ port: apiPort,
+ scheme: 'HTTP'
+ };
+
+ local namespace = {
+ apiVersion: 'v1',
+ kind: 'Namespace',
+ metadata: {
+ name: namespaceName,
+ labels: namespaceLabels
+ }
+ };
+
+ local ingress = {
+ apiVersion: 'extensions/v1beta1',
+ kind: 'Ingress',
+ metadata: {
+ name: fullyQualifiedName,
+ namespace: namespaceName,
+ labels: labels,
+ annotations: annotations + {
+ 'cert-manager.io/cluster-issuer': 'letsencrypt-prod',
+ 'kubernetes.io/ingress.class': 'nginx',
+ 'nginx.ingress.kubernetes.io/ssl-redirect': 'true',
+ 'nginx.ingress.kubernetes.io/auth-url': 'https://google.login.apps.allenai.org/oauth2/auth',
+ 'nginx.ingress.kubernetes.io/auth-signin': 'https://google.login.apps.allenai.org/oauth2/start?rd=https://$host$request_uri',
+ 'nginx.ingress.kubernetes.io/auth-response-headers': 'X-Auth-Request-User, X-Auth-Request-Email'
+ }
+ },
+ spec: {
+ tls: [
+ {
+ secretName: fullyQualifiedName + '-tls',
+ hosts: hosts
+ }
+ ],
+ rules: [
+ {
+ host: host,
+ http: {
+ paths: [
+ {
+ backend: {
+ serviceName: fullyQualifiedName,
+ servicePort: proxyPort
+ }
+ }
+ ]
+ }
+ } for host in hosts
+ ]
+ }
+ };
+
+ local deployment = {
+ apiVersion: 'apps/v1',
+ kind: 'Deployment',
+ metadata: {
+ labels: labels,
+ name: fullyQualifiedName,
+ namespace: namespaceName,
+ annotations: annotations + {
+ 'kubernetes.io/change-cause': cause
+ }
+ },
+ spec: {
+ revisionHistoryLimit: 3,
+ replicas: replicas,
+ selector: {
+ matchLabels: labels
+ },
+ template: {
+ metadata: {
+ name: fullyQualifiedName,
+ namespace: namespaceName,
+ labels: podLabels,
+ annotations: annotations
+ },
+ spec: {
+ # This block tells the cluster that we'd like to make sure
+ # each instance of your application is on a different node. This
+ # way if a node goes down, your application doesn't:
+ # See: https://kubernetes.io/docs/concepts/configuration/assign-pod-node/#node-isolation-restriction
+ affinity: {
+ podAntiAffinity: {
+ requiredDuringSchedulingIgnoredDuringExecution: [
+ {
+ labelSelector: {
+ matchExpressions: [
+ {
+ key: labelName,
+ operator: "In",
+ values: [ antiAffinityLabels[labelName], ],
+ } for labelName in std.objectFields(antiAffinityLabels)
+ ],
+ },
+ topologyKey: "kubernetes.io/hostname"
+ },
+ ]
+ },
+ },
+ volumes: [
+ {
+ name: 'skiff-files',
+ persistentVolumeClaim: {
+ claimName: 'skiff-files-server-pawls'
+ }
+ },
+ {
+ name: "users",
+ secret: {
+ secretName: "users"
+ }
+ }
+ ],
+ containers: [
+ {
+ name: fullyQualifiedName + '-api',
+ image: apiImage,
+ env: [ { name: "IN_PRODUCTION", value: "prod" }],
+ volumeMounts: [
+ {
+ mountPath: '/skiff_files/apps/pawls',
+ name: 'skiff-files',
+ readOnly: false
+ },
+ {
+ name: 'users',
+ mountPath: '/users',
+ readOnly: true
+ }
+ ],
+ # The "probes" below allow Kubernetes to determine
+ # if your application is working properly.
+ #
+ # The readiness probe is used to determine if
+ # an instance of your application can accept live
+ # requests. The configuration below tells Kubernetes
+ # to stop sending live requests to your application
+ # if it returns 3 non 2XX responses over 30 seconds.
+ # When this happens the application instance will
+ # be taken out of rotation and given time to "catch-up".
+ # Once it returns a single 2XX, Kubernetes will put
+ # it back in rotation.
+ #
+ # The liveness probe is used to determine if an
+ # instance needs to be restarted. The configuration
+ # below tells Kubernetes to restart the application
+ # if it's unhealthy for 90 seconds. You can increase
+ # the `failureThreshold` if your API is slow.
+ #
+ # The route that's used by these probes should not
+ # depend on any external services, it should purely
+ # assess the health of your local application.
+ #
+ # Lastly, the `initialDelaySeconds` instructs
+ # Kubernetes to wait 30 seconds before starting the
+ # liveness probe. This is to give your application
+ # time to start. If your application needs more time
+ # you should increase this value and give things
+ # a little headroom, things are always a little slower
+ # in the cloud :).
+ readinessProbe: {
+ httpGet: apiHealthCheck + {
+ path: '/?check=readiness_probe'
+ },
+ periodSeconds: 10,
+ failureThreshold: 3
+ },
+ livenessProbe: {
+ httpGet: apiHealthCheck + {
+ path: '/?check=liveness_probe'
+ },
+ periodSeconds: 10,
+ failureThreshold: 9,
+ initialDelaySeconds: 30
+ },
+ # This tells Kubernetes what CPU and memory resources your API needs.
+ # We set these values low by default, as most applications receive
+ # bursts of activity and accordingly don't need dedicated resources
+ # at all times.
+ #
+ # Your application will be allowed to use more resources than what's
+ # specified below. That said your application might be killed if it
+ # uses more than what's requested. If you know you need more memory
+ # or that your workload is CPU intensive, consider increasing the
+ # values below.
+ #
+ # Currently all pods (the collection of containers defined here)
+ # cannot request more than 23.9 GB of RAM or 3.92 (3920m) CPU
+ # cycles. If you need more resources reach out to reviz@allenai.org,
+ # we can provide accomodations on a case by case basis.
+ #
+ # If your application is of high criticality and you'd like to ensure
+ # maximum availability, reach out to reviz@allenai.org for help modifying
+ # these settings.
+ #
+ # See the following for more information on these values:
+ # https://kubernetes.io/docs/concepts/configuration/manage-compute-resources-container/#how-pods-with-resource-requests-are-scheduled
+ resources: {
+ requests: {
+ cpu: '50m',
+ memory: '500Mi'
+ }
+ },
+ },
+ {
+ name: fullyQualifiedName + '-proxy',
+ image: proxyImage,
+ readinessProbe: {
+ httpGet: proxyHealthCheck + {
+ path: '/?check=rdy'
+ }
+ },
+ livenessProbe: {
+ failureThreshold: 6,
+ httpGet: proxyHealthCheck + {
+ path: '/?check=live'
+ }
+ },
+ resources: {
+ requests: {
+ cpu: '50m',
+ memory: '100Mi'
+ }
+ }
+ }
+ ]
+ }
+ }
+ }
+ };
+
+ local service = {
+ apiVersion: 'v1',
+ kind: 'Service',
+ metadata: {
+ name: fullyQualifiedName,
+ namespace: namespaceName,
+ labels: labels,
+ annotations: annotations
+ },
+ spec: {
+ selector: labels,
+ ports: [
+ {
+ port: proxyPort,
+ name: 'http'
+ }
+ ]
+ }
+ };
+
+ [
+ namespace,
+ ingress,
+ deployment,
+ service
+ ]
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 00000000..9b259bdf
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,201 @@
+ Apache License
+ Version 2.0, January 2004
+ https://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
+ and distribution as defined by Sections 1 through 9 of this document.
+
+ "Licensor" shall mean the copyright owner or entity authorized by
+ the copyright owner that is granting the License.
+
+ "Legal Entity" shall mean the union of the acting entity and all
+ other entities that control, are controlled by, or are under common
+ control with that entity. For the purposes of this definition,
+ "control" means (i) the power, direct or indirect, to cause the
+ direction or management of such entity, whether by contract or
+ otherwise, or (ii) ownership of fifty percent (50%) or more of the
+ outstanding shares, or (iii) beneficial ownership of such entity.
+
+ "You" (or "Your") shall mean an individual or Legal Entity
+ exercising permissions granted by this License.
+
+ "Source" form shall mean the preferred form for making modifications,
+ including but not limited to software source code, documentation
+ source, and configuration files.
+
+ "Object" form shall mean any form resulting from mechanical
+ transformation or translation of a Source form, including but
+ not limited to compiled object code, generated documentation,
+ and conversions to other media types.
+
+ "Work" shall mean the work of authorship, whether in Source or
+ Object form, made available under the License, as indicated by a
+ copyright notice that is included in or attached to the work
+ (an example is provided in the Appendix below).
+
+ "Derivative Works" shall mean any work, whether in Source or Object
+ form, that is based on (or derived from) the Work and for which the
+ editorial revisions, annotations, elaborations, or other modifications
+ represent, as a whole, an original work of authorship. For the purposes
+ of this License, Derivative Works shall not include works that remain
+ separable from, or merely link (or bind by name) to the interfaces of,
+ the Work and Derivative Works thereof.
+
+ "Contribution" shall mean any work of authorship, including
+ the original version of the Work and any modifications or additions
+ to that Work or Derivative Works thereof, that is intentionally
+ submitted to Licensor for inclusion in the Work by the copyright owner
+ or by an individual or Legal Entity authorized to submit on behalf of
+ the copyright owner. For the purposes of this definition, "submitted"
+ means any form of electronic, verbal, or written communication sent
+ to the Licensor or its representatives, including but not limited to
+ communication on electronic mailing lists, source code control systems,
+ and issue tracking systems that are managed by, or on behalf of, the
+ Licensor for the purpose of discussing and improving the Work, but
+ excluding communication that is conspicuously marked or otherwise
+ designated in writing by the copyright owner as "Not a Contribution."
+
+ "Contributor" shall mean Licensor and any individual or Legal Entity
+ on behalf of whom a Contribution has been received by Licensor and
+ subsequently incorporated within the Work.
+
+ 2. Grant of Copyright License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ copyright license to reproduce, prepare Derivative Works of,
+ publicly display, publicly perform, sublicense, and distribute the
+ Work and such Derivative Works in Source or Object form.
+
+ 3. Grant of Patent License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ (except as stated in this section) patent license to make, have made,
+ use, offer to sell, sell, import, and otherwise transfer the Work,
+ where such license applies only to those patent claims licensable
+ by such Contributor that are necessarily infringed by their
+ Contribution(s) alone or by combination of their Contribution(s)
+ with the Work to which such Contribution(s) was submitted. If You
+ institute patent litigation against any entity (including a
+ cross-claim or counterclaim in a lawsuit) alleging that the Work
+ or a Contribution incorporated within the Work constitutes direct
+ or contributory patent infringement, then any patent licenses
+ granted to You under this License for that Work shall terminate
+ as of the date such litigation is filed.
+
+ 4. Redistribution. You may reproduce and distribute copies of the
+ Work or Derivative Works thereof in any medium, with or without
+ modifications, and in Source or Object form, provided that You
+ meet the following conditions:
+
+ (a) You must give any other recipients of the Work or
+ Derivative Works a copy of this License; and
+
+ (b) You must cause any modified files to carry prominent notices
+ stating that You changed the files; and
+
+ (c) You must retain, in the Source form of any Derivative Works
+ that You distribute, all copyright, patent, trademark, and
+ attribution notices from the Source form of the Work,
+ excluding those notices that do not pertain to any part of
+ the Derivative Works; and
+
+ (d) If the Work includes a "NOTICE" text file as part of its
+ distribution, then any Derivative Works that You distribute must
+ include a readable copy of the attribution notices contained
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+ pertain to any part of the Derivative Works, in at least one
+ of the following places: within a NOTICE text file distributed
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+ within a display generated by the Derivative Works, if and
+ wherever such third-party notices normally appear. The contents
+ of the NOTICE file are for informational purposes only and
+ do not modify the License. You may add Your own attribution
+ notices within Derivative Works that You distribute, alongside
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+ 5. Submission of Contributions. Unless You explicitly state otherwise,
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+ of your accepting any such warranty or additional liability.
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+ END OF TERMS AND CONDITIONS
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+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
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+ Copyright {yyyy} {name of copyright owner}
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
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+
+ Unless required by applicable law or agreed to in writing, software
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diff --git a/README.md b/README.md
new file mode 100644
index 00000000..1d131e25
--- /dev/null
+++ b/README.md
@@ -0,0 +1,168 @@
+
+
+
+
+ PDF Annotations with Labels and Structure is software that makes it easy
+ to collect a series of annotations associated with a PDF document. It was written
+ specifically for annotating academic papers within the [Semantic Scholar](https://www.semanticscholar.org) corpus, but can be used with any collection of PDF documents.
+
+### Quick Start
+
+*Quick start will download some pre-processed PDFs and get the UI set up so that you can see them. If you want to pre-process your own pdfs, keep reading! If it's your first time working with PAWLS, we recommend you try the quick start first though.*
+
+First, we need to download some processed PDFs to view in the UI. PAWLS uses the PDFs themselves to render in the browser, as well as using a JSON file of extracted token bounding boxes per page, called `pdf_structure.json`. The [PAWLS CLI](cli/readme.md) can be used to do this pre-processing, but for the quick start, we have done it for you. Download them from the provided AWS S3 Bucket like so:
+
+```bash
+aws s3 sync s3://ai2-s2-pawls-public/example-data ./skiff_files/apps/pawls/papers/
+```
+
+Configuration in PAWLS is controlled by a json file, located in the [`api/config`](./api/config/configuration.json) directory. The location that we downloaded the pdfs to above corresponds to the location in the config file, where it is mounted in using [`docker-compose.yaml`](./docker-compose.yaml). So, when PAWLS starts up, the API knows where to look to serve the PDFs we want.
+
+Next, we can start the services required to use PAWLS using `docker-compose`:
+
+```
+~ docker-compose up --build
+```
+
+This process launches 4 services:
+- the `ui`, which renders the user interface that PAWLS uses
+- the `api`, which serves PDFs and saves/recieves annotations
+- a `proxy` responsible for forwarding traffic to the appropriate services.
+- A `grobid` service, running [a fork of Grobid](https://github.com/allenai/grobid). This is not actually necessary for the application, but is useful for the CLI.
+
+You'll see output from each.
+
+Once all of these have come up, navigate to `localhost:8080` in your browser and you should see the PAWLS UI! Happy annotating.
+
+
+### Getting Started
+
+In order to run a local environment, you'll need to use the [PAWLS CLI](cli/readme.md) to download the PDFs and metadata you want to serve. The PDFs should be put in `skiff_files/apps/pawls`.
+
+For instance, you can run this command to download the specified PDF:
+
+```bash
+ # Fetches pdfs from semantic scholar's S3 buckets.
+ python scripts/ai2-internal/fetch_pdfs.py skiff_files/apps/pawls/papers 34f25a8704614163c4095b3ee2fc969b60de4698 3febb2bed8865945e7fddc99efd791887bb7e14f 553c58a05e25f794d24e8db8c2b8fdb9603e6a29
+ # ensure that the papers are pre-processed with grobid so that they have token information.
+ pawls preprocess grobid skiff_files/apps/pawls/papers
+ # Assign the development user to all the papers we've downloaded.
+ pawls assign skiff_files/apps/pawls/papers development_user --all --name-file skiff_files/apps/pawls/papers/name_mapping.json
+```
+
+and then open up the UI locally by running `docker-compose up`.
+
+### Authentication and Authorization
+
+*Authentication* is simply checking that users are who they say they are. Whether
+or not these users' requests are allowed (e.g., to view a PDFs) is considerd
+*authorization*. See more about this distinction at [Skiff
+Login](https://skiff.allenai.org/login.html).
+
+#### Authentication
+
+All requests must be authenticated.
+
+* The production deployment of PAWLS uses [Skiff
+ Login](https://skiff.allenai.org/login.html) to authenticate requests. New
+ users are bounced to a Google login workflow, and redirected back to the site
+ if they authenticate with Google. Authenticated requests carry an HTTP header
+ that identifies the user.
+* For local development, there is no login workflow. Instead, all requests are
+ supplemented with a hard-coded authentication header in
+ [proxy/local.conf](proxy/local.conf) specifying that the user is
+ `development_user@example.com`.
+
+Look at the function `get_user_from_header` in [main.py](api/main.py) for
+details.
+
+#### Authorization
+
+Authorization is enforced by the PAWLS app. A file of allowed user email
+addresses is consulted on every request.
+
+* In production, this file is sourced from [the secret named
+ "users"](http://marina.apps.allenai.org/a/pawls/s/users) in Marina, which is
+ projected to `/users/allowed.txt` in the container.
+* For local development, this file is sourced from
+ [allowed_users_local_development.txt](api/config/allowed_users_local_development.txt),
+ and also projected to `/users/allowed.txt` in the Docker container.
+
+The format of the file is simply a list of allowed email addresses.
+
+There's a special case when an allowed email address in this file starts with
+"@", meaning all users in that domain are allowed. That is, an entry
+"@allenai.org" will grant access to all AI2 people.
+
+Look at the function `user_is_allowed` in [main.py](api/main.py) for details.
+
+### Python Development
+
+The Python service and Python cli are formatted using `black` and `flake8`. Currently this is run in a local environment
+using the app's `requirements.txt`. To run the linters:
+
+```
+black api/
+flake8 api/
+```
+
+
+## Prerequisites
+
+Make sure that you have the latest version of [Docker 🐳](https://www.docker.com/get-started)
+installed on your local machine.
+
+To start a version of the application locally for development purposes, run
+this command:
+
+```
+~ docker-compose up --build
+```
+
+This process launches 3 services, the `ui`, `api` and a `proxy` responsible
+for forwarding traffic to the appropriate services. You'll see output
+from each.
+
+It might take a minute or two for the application to start, particularly
+if it's the first time you've executed this command. Be patience and wait
+for a clear message indicating that all of the required services have
+started up.
+
+As you make changes the running application will be automatically updated.
+Simply refresh your browser to see them.
+
+Sometimes one portion of your application will crash due to errors in the code.
+When this occurs resolve the related issue and re-run `docker-compose up --build`
+to start things back up.
+
+## Development Tips and Tricks
+
+The skiff template contains some features which are ideal for a robust web application, but might be un-intuitive for researchers.
+Below are some small technical points that might help you if you are making substantial changes to the skiff template.
+
+* Skiff uses `sonar` to check that all parts of the application (frontend, backend) are up and running before serving requests.
+To do this, it checks that your api returns 2XX codes from its root url - if you change the server, you'll need to make sure to add
+code which returns a 2XX response from your server.
+
+* To ease development/deployment differences, skiff uses a proxy to route different urls to different containers in your application.
+The TL;DR of this is the following:
+
+| External URL | Internal URL | Container |
+|------------------------|:------------------:|:---------:|
+| `localhost:8080/*` | `localhost:3000/*` | `ui` |
+| `localhost:8080/api/*` | `localhost:8000/*` | `api` |
+
+So, in your web application, you would make a request, e.g `axios.get("/api/route", data)`, which the server recieves at `localhost:8000/route`.
+This makes it easy to develop without worrying about where apis will be hosted in production vs development, and also allows for things like
+rate limiting. The configuration for the proxy lives [here](./proxy/local.conf) for development and [here](./proxy/prod.conf) for production.
+
+For example, if you wanted to expose the `docs` route `localhost:8000/docs` from your `api` container to users of your app in production, you would add this to `prod.conf`:
+
+```
+location /docs/ {
+ limit_req zone=api;
+ proxy_pass http://api:8000/;
+}
+```
+
+PAWLS is an open-source project developed by [the Allen Institute for Artificial Intelligence (AI2)](http://www.allenai.org). AI2 is a non-profit institute with the mission to contribute to humanity through high-impact AI research and engineering.
diff --git a/api/.dockerignore b/api/.dockerignore
new file mode 100644
index 00000000..232db3d7
--- /dev/null
+++ b/api/.dockerignore
@@ -0,0 +1,8 @@
+# Python cache files
+**.pyc
+**/__pycache__
+.dockerignore
+
+# Docker artifacts
+Dockerfile
+
diff --git a/api/.flake8 b/api/.flake8
new file mode 100644
index 00000000..ebb4370f
--- /dev/null
+++ b/api/.flake8
@@ -0,0 +1,12 @@
+[flake8]
+max-line-length = 115
+
+ignore =
+ # these rules don't play well with black
+ E203 # whitespace before :
+ W503 # line break before binary operator
+
+per-file-ignores =
+ # __init__.py files are allowed to have unused imports and lines-too-long
+ */__init__.py:F401
+ */**/**/__init__.py:F401,E501
diff --git a/api/Dockerfile b/api/Dockerfile
new file mode 100644
index 00000000..905ee00c
--- /dev/null
+++ b/api/Dockerfile
@@ -0,0 +1,22 @@
+FROM python:3.7.2
+
+# Setup a spot for the api code
+WORKDIR /usr/local/src/skiff/app/api
+
+ARG GITHUB_ACCESS_TOKEN
+
+# Install Python dependencies
+RUN pip install --upgrade pip setuptools wheel
+COPY requirements.txt .
+
+RUN pip install -r requirements.txt
+
+
+# Copy over the source code
+COPY app app/
+COPY config config/
+COPY main.py main.py
+
+# Kick things off
+ENTRYPOINT [ "uvicorn" ]
+CMD ["main:app", "--host", "0.0.0.0"]
diff --git a/api/app/__init__.py b/api/app/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/api/app/annotations.py b/api/app/annotations.py
new file mode 100644
index 00000000..e4fe6d27
--- /dev/null
+++ b/api/app/annotations.py
@@ -0,0 +1,38 @@
+from typing import Optional, List
+from pydantic import BaseModel
+
+
+class Bounds(BaseModel):
+ left: float
+ top: float
+ right: float
+ bottom: float
+
+
+class Label(BaseModel):
+ text: str
+ color: str
+
+
+class TokenId(BaseModel):
+ pageIndex: int
+ tokenIndex: int
+
+
+class Annotation(BaseModel):
+ id: str
+ page: int
+ label: Label
+ bounds: Bounds
+ tokens: Optional[List[TokenId]] = None
+
+
+class RelationGroup(BaseModel):
+ sourceIds: List[str]
+ targetIds: List[str]
+ label: Label
+
+
+class PdfAnnotation(BaseModel):
+ annotations: List[Annotation]
+ relations: List[RelationGroup]
diff --git a/api/app/metadata.py b/api/app/metadata.py
new file mode 100644
index 00000000..00120c13
--- /dev/null
+++ b/api/app/metadata.py
@@ -0,0 +1,32 @@
+from typing import Optional, List
+
+from pydantic import BaseModel
+
+
+class PaperStatus(BaseModel):
+ sha: str
+ name: str
+ annotations: int
+ relations: int
+ finished: bool
+ junk: bool
+ comments: str
+ completedAt: Optional[str]
+
+ @staticmethod
+ def empty(sha: str, name: str):
+ return PaperStatus(
+ sha=sha,
+ name=name,
+ annotations=0,
+ relations=0,
+ finished=False,
+ junk=False,
+ comments="",
+ completedAt=None,
+ )
+
+
+class Allocation(BaseModel):
+ papers: List[PaperStatus]
+ hasAllocatedPapers: bool
diff --git a/api/app/pre_serve.py b/api/app/pre_serve.py
new file mode 100644
index 00000000..05962f6d
--- /dev/null
+++ b/api/app/pre_serve.py
@@ -0,0 +1,38 @@
+from typing import NamedTuple, List, Dict
+import json
+
+
+class Configuration(NamedTuple):
+ """
+ General configuration for the annotation tool.
+
+ output_directory: str, required.
+ The directory where the pdfs and
+ annotation output will be stored.
+ labels: List[Dict[str, str]], required.
+ The labels in use for annotation.
+ relations: List[Dict[str, str]], required.
+ The relations in use for annotation.
+ users_file: Name str, required
+ Filename where list of allowed users is specified.
+ """
+
+ output_directory: str
+ labels: List[Dict[str, str]]
+ relations: List[Dict[str, str]]
+ users_file: str
+
+
+def load_configuration(filepath: str) -> Configuration:
+ try:
+ blob = json.load(open(filepath))
+ return Configuration(**blob)
+ except TypeError as e:
+ print(
+ "Error loading configuration file %s, maybe you're missing a required field? Exception string: %s"
+ % (filepath, e)
+ )
+ raise e
+ except Exception as e:
+ print("Error loading configuration file %s" % filepath)
+ raise e
diff --git a/api/app/utils.py b/api/app/utils.py
new file mode 100644
index 00000000..c343d893
--- /dev/null
+++ b/api/app/utils.py
@@ -0,0 +1,20 @@
+from pythonjsonlogger import jsonlogger
+
+
+class StackdriverJsonFormatter(jsonlogger.JsonFormatter):
+ """
+ Custom log JSON log formatter that adds the severity member, allowing
+ end users to filter logs by the level of the log message emitted.
+
+ TODO: Parse request logs and add fields for each request element (user-agent
+ processing time, etc)
+
+ TODO:Add a timestamp that's used in place of Stackdriver's records (which
+ reflect the time the log was written to Stackdriver, I think).
+ """
+
+ def add_fields(self, log_record, record, message_dict):
+ super(StackdriverJsonFormatter, self).add_fields(
+ log_record, record, message_dict
+ )
+ log_record["severity"] = record.levelname
diff --git a/api/config/allowed_users_local_development.txt b/api/config/allowed_users_local_development.txt
new file mode 100644
index 00000000..2fd6bacb
--- /dev/null
+++ b/api/config/allowed_users_local_development.txt
@@ -0,0 +1 @@
+development_user@example.com
diff --git a/api/config/configuration.json b/api/config/configuration.json
new file mode 100644
index 00000000..8422e566
--- /dev/null
+++ b/api/config/configuration.json
@@ -0,0 +1,87 @@
+{
+ "output_directory": "/skiff_files/apps/pawls/papers/",
+ "labels": [
+ {
+ "text": "Title",
+ "color": "#70DDBA"
+ },
+ {
+ "text": "Author",
+ "color": "#B8DE6F"
+ },
+ {
+ "text": "Abstract",
+ "color": "#A8DDA8"
+ },
+ {
+ "text": "Keywords",
+ "color": "#64ED96"
+ },
+ {
+ "text": "Section",
+ "color": "#FFDA77"
+ },
+ {
+ "text": "Paragraph",
+ "color": "#D9E4DD"
+ },
+ {
+ "text": "ListItem",
+ "color": "#CEEBFC"
+ },
+ {
+ "text": "BibItem",
+ "color": "#C6CC82"
+ },
+ {
+ "text": "Default",
+ "color": "#BFBFBF"
+ },
+ {
+ "text": "Equation",
+ "color": "#D6D2C4"
+ },
+ {
+ "text": "Figure",
+ "color": "#EFDDF5"
+ },
+ {
+ "text": "Table",
+ "color": "#C7C2EB"
+ },
+ {
+ "text": "Algorithm",
+ "color": "#CFD4DF"
+ },
+ {
+ "text": "Caption",
+ "color": "#2F85F7"
+ },
+ {
+ "text": "Footer",
+ "color": "#FFB2A7"
+ },
+ {
+ "text": "Header",
+ "color": "#FFB2A7"
+ },
+ {
+ "text": "Author/Name",
+ "color": "#F5A25D"
+ },
+ {
+ "text": "Author/Affiliation",
+ "color": "#28ABB9"
+ },
+ {
+ "text": "Author/Email",
+ "color": "#706897"
+ },
+ {
+ "text": "Paper/Venue",
+ "color": "#34626C"
+ }
+ ],
+ "relations": [],
+ "users_file": "/users/allowed.txt"
+}
diff --git a/api/main.py b/api/main.py
new file mode 100644
index 00000000..ef251db8
--- /dev/null
+++ b/api/main.py
@@ -0,0 +1,321 @@
+from typing import List, Optional, Dict, Any
+import logging
+import os
+import json
+import glob
+
+from fastapi import FastAPI, HTTPException, Header, Response, Body
+from fastapi.responses import FileResponse
+from fastapi.encoders import jsonable_encoder
+
+from app.metadata import PaperStatus, Allocation
+from app.annotations import Annotation, RelationGroup, PdfAnnotation
+from app.utils import StackdriverJsonFormatter
+from app import pre_serve
+
+IN_PRODUCTION = os.getenv("IN_PRODUCTION", "dev")
+
+CONFIGURATION_FILE = os.getenv(
+ "PAWLS_CONFIGURATION_FILE", "/usr/local/src/skiff/app/api/config/configuration.json"
+)
+
+handlers = None
+
+if IN_PRODUCTION == "prod":
+ json_handler = logging.StreamHandler()
+ json_handler.setFormatter(StackdriverJsonFormatter())
+ handlers = [json_handler]
+
+logging.basicConfig(
+ level=os.environ.get("LOG_LEVEL", default=logging.INFO), handlers=handlers
+)
+logger = logging.getLogger("uvicorn")
+
+# boto3 logging is _super_ verbose.
+logging.getLogger("boto3").setLevel(logging.CRITICAL)
+logging.getLogger("botocore").setLevel(logging.CRITICAL)
+logging.getLogger("nose").setLevel(logging.CRITICAL)
+logging.getLogger("s3transfer").setLevel(logging.CRITICAL)
+
+# The annotation app requires a bit of set up.
+configuration = pre_serve.load_configuration(CONFIGURATION_FILE)
+
+app = FastAPI()
+
+
+def get_user_from_header(user_email: Optional[str]) -> Optional[str]:
+ """
+ Call this function with the X-Auth-Request-Email header value. This must
+ include an "@" in its value.
+
+ * In production, this is provided by Skiff after the user authenticates.
+ * In development, it is provided in the NGINX proxy configuration file local.conf.
+
+ If the value isn't well formed, or the user isn't allowed, an exception is
+ thrown.
+ """
+ if "@" not in user_email:
+ raise HTTPException(403, "Forbidden")
+
+ if not user_is_allowed(user_email):
+ raise HTTPException(403, "Forbidden")
+
+ return user_email
+
+
+def user_is_allowed(user_email: str) -> bool:
+ """
+ Return True if the user_email is in the users file, False otherwise.
+ """
+ try:
+ with open(configuration.users_file) as file:
+ for line in file:
+ entry = line.strip()
+ if user_email == entry:
+ return True
+ # entries like "@allenai.org" mean anyone in that domain @allenai.org is granted access
+ if entry.startswith("@") and user_email.endswith(entry):
+ return True
+ except FileNotFoundError:
+ logger.warning("file not found: %s", configuration.users_file)
+ pass
+
+ return False
+
+
+def all_pdf_shas() -> List[str]:
+ pdfs = glob.glob(f"{configuration.output_directory}/*/*.pdf")
+ return [p.split("/")[-2] for p in pdfs]
+
+
+def update_status_json(status_path: str, sha: str, data: Dict[str, Any]):
+
+ with open(status_path, "r+") as st:
+ status_json = json.load(st)
+ status_json[sha] = {**status_json[sha], **data}
+ st.seek(0)
+ json.dump(status_json, st)
+ st.truncate()
+
+
+@app.get("/", status_code=204)
+def read_root():
+ """
+ Skiff's sonar, and the Kubernetes health check, require
+ that the server returns a 2XX response from it's
+ root URL, so it can tell the service is ready for requests.
+ """
+ return Response(status_code=204)
+
+
+@app.get("/api/doc/{sha}/pdf")
+async def get_pdf(sha: str):
+ """
+ Fetches a PDF.
+
+ sha: str
+ The sha of the pdf to return.
+ """
+ pdf = os.path.join(configuration.output_directory, sha, f"{sha}.pdf")
+ pdf_exists = os.path.exists(pdf)
+ if not pdf_exists:
+ raise HTTPException(status_code=404, detail=f"pdf {sha} not found.")
+
+ return FileResponse(pdf, media_type="application/pdf")
+
+
+@app.get("/api/doc/{sha}/title")
+async def get_pdf_title(sha: str) -> Optional[str]:
+ """
+ Fetches a PDF's title.
+
+ sha: str
+ The sha of the pdf title to return.
+ """
+ pdf_info = os.path.join(configuration.output_directory, "pdf_metadata.json")
+
+ with open(pdf_info, "r") as f:
+ info = json.load(f)
+
+ data = info.get("sha", None)
+
+ if data is None:
+ return None
+
+ return data.get("title", None)
+
+
+@app.post("/api/doc/{sha}/comments")
+def set_pdf_comments(
+ sha: str, comments: str = Body(...), x_auth_request_email: str = Header(None)
+):
+ user = get_user_from_header(x_auth_request_email)
+ status_path = os.path.join(configuration.output_directory, "status", f"{user}.json")
+ exists = os.path.exists(status_path)
+
+ if not exists:
+ # Not an allocated user. Do nothing.
+ return {}
+
+ update_status_json(status_path, sha, {"comments": comments})
+ return {}
+
+
+@app.post("/api/doc/{sha}/junk")
+def set_pdf_junk(
+ sha: str, junk: bool = Body(...), x_auth_request_email: str = Header(None)
+):
+ user = get_user_from_header(x_auth_request_email)
+ status_path = os.path.join(configuration.output_directory, "status", f"{user}.json")
+ exists = os.path.exists(status_path)
+ if not exists:
+ # Not an allocated user. Do nothing.
+ return {}
+
+ update_status_json(status_path, sha, {"junk": junk})
+ return {}
+
+
+@app.post("/api/doc/{sha}/finished")
+def set_pdf_finished(
+ sha: str, finished: bool = Body(...), x_auth_request_email: str = Header(None)
+):
+ user = get_user_from_header(x_auth_request_email)
+ status_path = os.path.join(configuration.output_directory, "status", f"{user}.json")
+ exists = os.path.exists(status_path)
+ if not exists:
+ # Not an allocated user. Do nothing.
+ return {}
+
+ update_status_json(status_path, sha, {"finished": finished})
+ return {}
+
+
+@app.get("/api/doc/{sha}/annotations")
+def get_annotations(
+ sha: str, x_auth_request_email: str = Header(None)
+) -> PdfAnnotation:
+ user = get_user_from_header(x_auth_request_email)
+ annotations = os.path.join(
+ configuration.output_directory, sha, f"{user}_annotations.json"
+ )
+ exists = os.path.exists(annotations)
+
+ if exists:
+ with open(annotations) as f:
+ blob = json.load(f)
+
+ return blob
+
+ else:
+ return {"annotations": [], "relations": []}
+
+
+@app.post("/api/doc/{sha}/annotations")
+def save_annotations(
+ sha: str,
+ annotations: List[Annotation],
+ relations: List[RelationGroup],
+ x_auth_request_email: str = Header(None),
+):
+ """
+ sha: str
+ PDF sha to save annotations for.
+ annotations: List[Annotation]
+ A json blob of the annotations to save.
+ relations: List[RelationGroup]
+ A json blob of the relations between the annotations to save.
+ x_auth_request_email: str
+ This is a header sent with the requests which specifies the user login.
+ For local development, this will be None, because the authentication
+ is controlled by the Skiff Kubernetes cluster.
+ """
+ # Update the annotations in the annotation json file.
+ user = get_user_from_header(x_auth_request_email)
+ annotations_path = os.path.join(
+ configuration.output_directory, sha, f"{user}_annotations.json"
+ )
+ json_annotations = [jsonable_encoder(a) for a in annotations]
+ json_relations = [jsonable_encoder(r) for r in relations]
+
+ # Update the annotation counts in the status file.
+ status_path = os.path.join(configuration.output_directory, "status", f"{user}.json")
+ exists = os.path.exists(status_path)
+ if not exists:
+ # Not an allocated user. Do nothing.
+ return {}
+
+ with open(annotations_path, "w+") as f:
+ json.dump({"annotations": json_annotations, "relations": json_relations}, f)
+
+ update_status_json(
+ status_path, sha, {"annotations": len(annotations), "relations": len(relations)}
+ )
+
+ return {}
+
+
+@app.get("/api/doc/{sha}/tokens")
+def get_tokens(sha: str):
+ """
+ sha: str
+ PDF sha to retrieve tokens for.
+ """
+ pdf_tokens = os.path.join(configuration.output_directory, sha, "pdf_structure.json")
+ if not os.path.exists(pdf_tokens):
+ raise HTTPException(status_code=404, detail="No tokens for pdf.")
+ with open(pdf_tokens, "r") as f:
+ response = json.load(f)
+
+ return response
+
+
+@app.get("/api/annotation/labels")
+def get_labels() -> List[Dict[str, str]]:
+ """
+ Get the labels used for annotation for this app.
+ """
+ return configuration.labels
+
+
+@app.get("/api/annotation/relations")
+def get_relations() -> List[Dict[str, str]]:
+ """
+ Get the relations used for annotation for this app.
+ """
+ return configuration.relations
+
+
+@app.get("/api/annotation/allocation/info")
+def get_allocation_info(x_auth_request_email: str = Header(None)) -> Allocation:
+
+ # In development, the app isn't passed the x_auth_request_email header,
+ # meaning this would always fail. Instead, to smooth local development,
+ # we always return all pdfs, essentially short-circuiting the allocation
+ # mechanism.
+ user = get_user_from_header(x_auth_request_email)
+
+ status_dir = os.path.join(configuration.output_directory, "status")
+ status_path = os.path.join(status_dir, f"{user}.json")
+ exists = os.path.exists(status_path)
+
+ if not exists:
+ # If the user doesn't have allocated papers, they can see all the
+ # pdfs but they can't save anything.
+ papers = [PaperStatus.empty(sha, sha) for sha in all_pdf_shas()]
+ response = Allocation(
+ papers=papers,
+ hasAllocatedPapers=False
+ )
+
+ else:
+ with open(status_path) as f:
+ status_json = json.load(f)
+
+ papers = []
+ for sha, status in status_json.items():
+ papers.append(PaperStatus(**status))
+
+ response = Allocation(papers=papers, hasAllocatedPapers=True)
+
+ return response
diff --git a/api/pytest.ini b/api/pytest.ini
new file mode 100644
index 00000000..9e65da02
--- /dev/null
+++ b/api/pytest.ini
@@ -0,0 +1,4 @@
+[pytest]
+env =
+ D:PAWLS_CONFIGURATION_FILE=test/fixtures/config/configuration.json
+ D:PAWLS_ANNOTATORS_FILE=test/fixtures/config/annotators.json
\ No newline at end of file
diff --git a/api/requirements.txt b/api/requirements.txt
new file mode 100644
index 00000000..19f8fc28
--- /dev/null
+++ b/api/requirements.txt
@@ -0,0 +1,21 @@
+
+# Skiff logging
+python-json-logger==0.1.10
+
+# Server
+fastapi
+uvicorn
+
+# used for testing/formatting
+pytest
+pytest-env
+flake8
+black==20.8b1
+requests
+
+# used for form parsing
+python-multipart
+
+# Allows us to use FastAPI's FileResponse for serving pdfs.
+aiofiles
+
diff --git a/api/test/__init__.py b/api/test/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/api/test/fixtures/config/configuration.json b/api/test/fixtures/config/configuration.json
new file mode 100644
index 00000000..f919909f
--- /dev/null
+++ b/api/test/fixtures/config/configuration.json
@@ -0,0 +1,24 @@
+{
+ "output_directory": "test/fixtures/tmp",
+ "labels": [
+ {
+ "text": "Figure Text",
+ "color": "#70DDBA"
+ },
+ {
+ "text": "Section Header",
+ "color": "#FFD45D"
+ }
+ ],
+ "relations": [
+ {
+ "text": "Caption Of",
+ "color": "#70DDBA"
+ },
+ {
+ "text": "Definition",
+ "color": "#FFD45D"
+ }
+ ],
+ "users_file": "test/fixtures/users/allowed.txt"
+}
diff --git a/api/test/fixtures/data/3febb2bed8865945e7fddc99efd791887bb7e14f/3febb2bed8865945e7fddc99efd791887bb7e14f.pdf b/api/test/fixtures/data/3febb2bed8865945e7fddc99efd791887bb7e14f/3febb2bed8865945e7fddc99efd791887bb7e14f.pdf
new file mode 100644
index 00000000..fd49db4e
Binary files /dev/null and b/api/test/fixtures/data/3febb2bed8865945e7fddc99efd791887bb7e14f/3febb2bed8865945e7fddc99efd791887bb7e14f.pdf differ
diff --git a/api/test/fixtures/data/3febb2bed8865945e7fddc99efd791887bb7e14f/pdf_structure.json b/api/test/fixtures/data/3febb2bed8865945e7fddc99efd791887bb7e14f/pdf_structure.json
new file mode 100644
index 00000000..bb23a28a
--- /dev/null
+++ b/api/test/fixtures/data/3febb2bed8865945e7fddc99efd791887bb7e14f/pdf_structure.json
@@ -0,0 +1 @@
+[{"page": {"width": 595.276, "height": 841.89, "index": 0}, "tokens": [{"text": "Proceedings", "x": 202.544, "y": 793.155, "width": 44.4195, "height": 10.7059}, {"text": "of", "x": 249.205, "y": 793.155, "width": 6.97586, "height": 10.7059}, {"text": "NAACL", "x": 258.423, "y": 793.155, "width": 25.91288888888889, "height": 10.7059}, {"text": "-", "x": 284.3358888888889, "y": 793.155, "width": 5.1825777777777775, "height": 10.7059}, {"text": "HLT", "x": 289.51846666666665, "y": 793.155, "width": 15.547733333333333, "height": 10.7059}, {"text": "2018", "x": 307.307, "y": 793.155, "width": 16.138560000000002, "height": 10.7059}, {"text": ",", "x": 323.44556, "y": 793.155, "width": 4.0346400000000004, "height": 10.7059}, {"text": "pages", "x": 329.722, "y": 793.155, "width": 20.4165, "height": 10.8045}, {"text": "2227", "x": 352.38, "y": 793.155, "width": 17.932799999999997, "height": 10.8045}, {"text": "-", "x": 370.3128, "y": 793.155, "width": 4.483199999999999, "height": 10.8045}, {"text": "2237", "x": 374.796, "y": 793.155, "width": 17.932799999999997, "height": 10.8045}, {"text": "New", "x": 129.748, "y": 804.493, "width": 16.7044, "height": 10.8045}, {"text": "Orleans", "x": 148.694, "y": 804.493, "width": 26.3612125, "height": 10.8045}, {"text": ",", "x": 175.05521249999998, "y": 804.493, "width": 3.7658875, "height": 10.8045}, {"text": "Louisiana", "x": 181.063, "y": 804.493, "width": 33.844590000000004, "height": 10.8045}, {"text": ",", "x": 214.90759, "y": 804.493, "width": 3.76051, "height": 10.8045}, {"text": "June", "x": 220.909, "y": 804.493, "width": 16.4354, "height": 10.8045}, {"text": "1", "x": 239.586, "y": 804.493, "width": 4.4832, "height": 10.8045}, {"text": "-", "x": 246.311, "y": 804.493, "width": 2.98581, "height": 10.8045}, {"text": "6", "x": 251.539, "y": 804.493, "width": 3.3624, "height": 10.8045}, {"text": ",", "x": 254.9014, "y": 804.493, "width": 3.3624, "height": 10.8045}, {"text": "2018", "x": 260.505, "y": 804.493, "width": 16.13952, "height": 10.8045}, {"text": ".", "x": 276.64452, "y": 804.493, "width": 4.03488, "height": 10.8045}, {"text": "c", "x": 286.075, "y": 804.223, "width": 3.98108, "height": 10.8045}, {"text": "2018", "x": 292.673, "y": 804.493, "width": 17.9328, "height": 10.8045}, {"text": "Association", "x": 312.847, "y": 804.493, "width": 42.3393, "height": 10.8045}, {"text": "for", "x": 357.428, "y": 804.493, "width": 10.4548, "height": 10.8045}, {"text": "Computational", "x": 370.125, "y": 804.493, "width": 53.3052, "height": 10.8045}, {"text": "Linguistics", "x": 425.672, "y": 804.493, "width": 39.8556, "height": 10.8045}, {"text": "Deep", "x": 182.273, "y": 94.885, "width": 28.3473, "height": 17.0267}, {"text": "contextualized", "x": 213.893, "y": 94.885, "width": 80.6969, "height": 17.0267}, {"text": "word", "x": 297.861, "y": 94.885, "width": 28.9493, "height": 17.0267}, {"text": "representations", "x": 330.083, "y": 94.885, "width": 86.0366, "height": 17.0267}, {"text": "Matthew", 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10.9516}, {"text": "Kevin", "x": 198.438, "y": 704.553, "width": 21.7577, "height": 10.9516}, {"text": "Gimpel", "x": 222.313, "y": 704.553, "width": 25.31777142857143, "height": 10.9516}, {"text": ",", "x": 247.63077142857142, "y": 704.553, "width": 4.219628571428571, "height": 10.9516}, {"text": "and", "x": 253.996, "y": 704.553, "width": 13.1237, "height": 10.9516}, {"text": "Karen", "x": 269.237, "y": 704.553, "width": 22.2031, "height": 10.9516}, {"text": "Livescu", "x": 102.273, "y": 714.55, "width": 26.847275, "height": 10.9516}, {"text": ".", "x": 129.120275, "y": 714.55, "width": 3.835325, "height": 10.9516}, {"text": "2016", "x": 135.846, "y": 714.55, "width": 16.3592, "height": 10.9516}, {"text": ".", "x": 152.2052, "y": 714.55, "width": 4.0898, "height": 10.9516}, {"text": "Charagram", "x": 161.548, "y": 714.55, "width": 38.61585, "height": 10.9516}, {"text": ":", "x": 200.16385, "y": 714.55, "width": 4.29065, "height": 10.9516}, {"text": "Embedding", "x": 208.508, "y": 714.55, "width": 41.9068, "height": 10.9516}, {"text": "words", "x": 253.305, "y": 714.55, "width": 22.1213, "height": 10.9516}, {"text": "and", "x": 278.316, "y": 714.55, "width": 13.1237, "height": 10.9516}, {"text": "sentences", "x": 102.273, "y": 724.547, "width": 34.8269, "height": 10.9516}, {"text": "via", "x": 139.372, "y": 724.547, "width": 11.1061, "height": 10.9516}, {"text": "character", "x": 152.75, "y": 724.547, "width": 33.3, "height": 10.9516}, {"text": "n", "x": 188.323, "y": 724.547, "width": 4.0068625, "height": 10.9516}, {"text": "-", "x": 192.32986250000002, "y": 724.547, "width": 4.0068625, "height": 10.9516}, {"text": "grams", "x": 196.336725, "y": 724.547, "width": 20.034312500000002, "height": 10.9516}, {"text": ".", "x": 216.3710375, "y": 724.547, "width": 4.0068625, "height": 10.9516}, {"text": "In", "x": 223.649, "y": 724.547, "width": 7.57067, "height": 10.9516}, {"text": "EMNLP", "x": 233.491, "y": 724.547, "width": 26.71966666666667, "height": 10.8516}, {"text": ".", "x": 260.21066666666667, "y": 724.547, "width": 5.343933333333333, "height": 10.8516}, {"text": "Sam", "x": 306.953, "y": 95.8219, "width": 16.1592, "height": 10.9516}, {"text": "Wiseman", "x": 327.602, "y": 95.8219, "width": 31.698187500000003, "height": 10.9516}, {"text": ",", "x": 359.3001875, "y": 95.8219, "width": 4.5283125, "height": 10.9516}, {"text": "Alexander", "x": 368.873, "y": 95.8219, "width": 37.717, "height": 10.9516}, {"text": "M", "x": 411.079, "y": 95.8219, "width": 5.17585, "height": 10.9516}, {"text": ".", "x": 416.25485000000003, "y": 95.8219, "width": 5.17585, "height": 10.9516}, {"text": "Rush", "x": 425.912, "y": 95.8219, "width": 16.76632, "height": 10.9516}, {"text": ",", "x": 442.67832, "y": 95.8219, "width": 4.19158, "height": 10.9516}, {"text": "and", "x": 451.914, "y": 95.8219, "width": 13.1237, "height": 10.9516}, {"text": "Stuart", "x": 469.518, "y": 95.8219, "width": 21.7123, "height": 10.9516}, {"text": "M", "x": 495.72, "y": 95.8219, "width": 5.17585, "height": 10.9516}, {"text": ".", "x": 500.89585000000005, "y": 95.8219, "width": 5.17585, "height": 10.9516}, {"text": "Shieber", "x": 316.905, "y": 105.819, "width": 25.845225000000003, "height": 10.9516}, {"text": ".", "x": 342.750225, "y": 105.819, "width": 3.692175, "height": 10.9516}, {"text": "2016", "x": 349.687, "y": 105.819, "width": 16.3592, "height": 10.9516}, {"text": ".", "x": 366.0462, "y": 105.819, "width": 4.0898, "height": 10.9516}, {"text": "Learning", "x": 376.516, "y": 105.819, "width": 32.8093, "height": 10.9516}, {"text": "global", "x": 412.561, "y": 105.819, "width": 22.7211, "height": 10.9516}, {"text": "features", "x": 438.526, "y": 105.819, "width": 28.7649, "height": 10.9516}, {"text": "for", "x": 470.536, "y": 105.819, "width": 10.5971, "height": 10.9516}, {"text": "coref", "x": 484.378, "y": 105.819, "width": 18.078416666666666, "height": 10.9516}, {"text": "-", "x": 502.45641666666666, "y": 105.819, "width": 3.615683333333333, "height": 10.9516}, {"text": "erence", "x": 316.905, "y": 115.817, "width": 23.7117, "height": 10.9516}, {"text": "resolution", "x": 342.889, "y": 115.817, "width": 35.11445454545454, "height": 10.9516}, {"text": ".", "x": 378.00345454545453, "y": 115.817, "width": 3.5114454545454548, "height": 10.9516}, {"text": "In", "x": 384.787, "y": 115.817, "width": 7.57067, "height": 10.9516}, {"text": "HLT", "x": 394.628, "y": 115.817, "width": 14.67144, "height": 10.8516}, {"text": "-", "x": 409.29944, "y": 115.817, "width": 4.89048, "height": 10.8516}, {"text": "NAACL", "x": 414.18992, "y": 115.817, "width": 24.4524, "height": 10.8516}, {"text": ".", "x": 438.64232, "y": 115.817, "width": 4.89048, "height": 10.8516}, {"text": "Matthew", "x": 306.953, "y": 133.993, "width": 32.0822, "height": 10.9516}, {"text": "D", "x": 341.071, "y": 133.993, "width": 4.41698, "height": 10.9516}, {"text": ".", "x": 345.48798000000005, "y": 133.993, "width": 4.41698, "height": 10.9516}, {"text": "Zeiler", "x": 351.95, "y": 133.993, "width": 20.121771428571428, "height": 10.9516}, {"text": ".", "x": 372.0717714285714, "y": 133.993, "width": 3.353628571428571, "height": 10.9516}, {"text": "2012", "x": 377.461, "y": 133.993, "width": 16.3592, "height": 10.9516}, {"text": ".", "x": 393.8202, "y": 133.993, "width": 4.0898, "height": 10.9516}, {"text": "Adadelta", "x": 401.228, "y": 133.993, "width": 31.409599999999998, "height": 10.9516}, {"text": ":", "x": 432.6376, "y": 133.993, "width": 3.9261999999999997, "height": 10.9516}, {"text": "An", "x": 439.263, "y": 133.993, "width": 11.1061, "height": 10.9516}, {"text": "adaptive", "x": 452.405, "y": 133.993, "width": 30.4281, "height": 10.9516}, {"text": "learn", "x": 484.878, "y": 133.993, "width": 17.661833333333334, "height": 10.9516}, {"text": "-", "x": 502.5398333333333, "y": 133.993, "width": 3.5323666666666664, "height": 10.9516}, {"text": "ing", "x": 316.905, "y": 143.991, "width": 11.615, "height": 10.9516}, {"text": "rate", "x": 330.792, "y": 143.991, "width": 13.6236, "height": 10.9516}, {"text": "method", "x": 346.688, "y": 143.991, "width": 25.31777142857143, "height": 10.9516}, {"text": ".", "x": 372.0057714285714, "y": 143.991, "width": 4.219628571428571, "height": 10.9516}, {"text": "CoRR", "x": 379.497, "y": 143.991, "width": 21.7123, "height": 10.8516}, {"text": "abs", "x": 403.481, "y": 143.991, "width": 11.901299999999999, "height": 10.9516}, {"text": "/", "x": 415.3823, "y": 143.991, "width": 3.9671, "height": 10.9516}, {"text": "1212", "x": 419.3494, "y": 143.991, "width": 15.8684, "height": 10.9516}, {"text": ".", "x": 435.2178, "y": 143.991, "width": 3.9671, "height": 10.9516}, {"text": "5701", "x": 439.18489999999997, "y": 143.991, "width": 15.8684, "height": 10.9516}, {"text": ".", "x": 455.0533, "y": 143.991, "width": 3.9671, "height": 10.9516}, {"text": "Jie", "x": 306.953, "y": 162.167, "width": 10.0973, "height": 10.9516}, {"text": "Zhou", "x": 320.404, "y": 162.167, "width": 19.1857, "height": 10.9516}, {"text": "and", "x": 342.943, "y": 162.167, "width": 13.1237, "height": 10.9516}, {"text": "Wei", "x": 359.43, "y": 162.167, "width": 14.4143, "height": 10.9516}, {"text": "Xu", "x": 377.198, "y": 162.167, "width": 8.9188, "height": 10.9516}, {"text": ".", "x": 386.11679999999996, "y": 162.167, "width": 4.4594, "height": 10.9516}, {"text": "2015", "x": 393.93, "y": 162.167, "width": 16.3592, "height": 10.9516}, {"text": ".", "x": 410.2892, "y": 162.167, "width": 4.0898, "height": 10.9516}, {"text": "End", "x": 421.113, "y": 162.167, "width": 12.26667, "height": 10.9516}, {"text": "-", "x": 433.37967, "y": 162.167, "width": 4.08889, "height": 10.9516}, {"text": "to", "x": 437.46856, "y": 162.167, "width": 8.17778, "height": 10.9516}, {"text": "-", "x": 445.64634, "y": 162.167, "width": 4.08889, "height": 10.9516}, {"text": "end", "x": 449.73523, "y": 162.167, "width": 12.26667, "height": 10.9516}, {"text": "learning", "x": 465.356, "y": 162.167, "width": 29.7828, "height": 10.9516}, {"text": "of", "x": 498.501, "y": 162.167, "width": 7.57067, "height": 10.9516}, {"text": "semantic", "x": 316.905, "y": 172.165, "width": 32.3094, "height": 10.9516}, {"text": "role", "x": 353.231, "y": 172.165, "width": 14.1325, "height": 10.9516}, {"text": "labeling", "x": 371.381, "y": 172.165, "width": 29.2829, "height": 10.9516}, {"text": "using", "x": 404.681, "y": 172.165, "width": 19.6946, "height": 10.9516}, {"text": "recurrent", "x": 428.393, "y": 172.165, "width": 32.8002, "height": 10.9516}, {"text": "neural", "x": 465.21, "y": 172.165, "width": 22.712, "height": 10.9516}, {"text": "net", "x": 491.939, "y": 172.165, "width": 10.599375, "height": 10.9516}, {"text": "-", "x": 502.53837500000003, "y": 172.165, "width": 3.533125, "height": 10.9516}, {"text": "works", "x": 316.905, "y": 182.162, "width": 20.327833333333334, "height": 10.9516}, {"text": ".", "x": 337.2328333333333, "y": 182.162, "width": 4.065566666666666, "height": 10.9516}, {"text": "In", "x": 344.57, "y": 182.162, "width": 7.57067, "height": 10.9516}, {"text": "ACL", "x": 354.412, "y": 182.162, "width": 14.02155, "height": 10.8516}, {"text": ".", "x": 368.43354999999997, "y": 182.162, "width": 4.67385, "height": 10.8516}, {"text": "Peng", "x": 306.953, "y": 200.34, "width": 18.1769, "height": 10.9516}, {"text": "Zhou", "x": 328.066, "y": 200.34, "width": 17.16624, "height": 10.9516}, {"text": ",", "x": 345.23224, "y": 200.34, "width": 4.29156, "height": 10.9516}, {"text": "Zhenyu", "x": 352.623, "y": 200.34, "width": 27.6288, "height": 10.9516}, {"text": "Qi", "x": 383.178, "y": 200.34, "width": 7.573666666666666, "height": 10.9516}, {"text": ",", "x": 390.75166666666667, "y": 200.34, "width": 3.786833333333333, "height": 10.9516}, {"text": "Suncong", "x": 397.638, "y": 200.34, "width": 31.8095, "height": 10.9516}, {"text": "Zheng", "x": 432.383, "y": 200.34, "width": 21.24425, "height": 10.9516}, {"text": ",", "x": 453.62725, "y": 200.34, "width": 4.248849999999999, "height": 10.9516}, {"text": "Jiaming", "x": 460.975, "y": 200.34, "width": 28.7831, "height": 10.9516}, {"text": "Xu", "x": 492.694, "y": 200.34, "width": 8.9188, "height": 10.9516}, {"text": ",", "x": 501.6128, "y": 200.34, "width": 4.4594, "height": 10.9516}, {"text": "Hongyun", "x": 316.905, "y": 210.336, "width": 33.8272, "height": 10.9516}, {"text": "Bao", "x": 353.068, "y": 210.336, "width": 12.685199999999998, "height": 10.9516}, {"text": ",", "x": 365.7532, "y": 210.336, "width": 4.2284, "height": 10.9516}, {"text": "and", "x": 372.335, "y": 210.336, "width": 13.1237, "height": 10.9516}, {"text": "Bo", "x": 387.795, "y": 210.336, "width": 10.6062, "height": 10.9516}, {"text": "Xu", "x": 400.737, "y": 210.336, "width": 8.9188, "height": 10.9516}, {"text": ".", "x": 409.6558, "y": 210.336, "width": 4.4594, "height": 10.9516}, {"text": "2016", "x": 416.46, "y": 210.336, "width": 16.3592, "height": 10.9516}, {"text": ".", "x": 432.81919999999997, "y": 210.336, "width": 4.0898, "height": 10.9516}, {"text": "Text", "x": 440.39, "y": 210.336, "width": 15.8866, "height": 10.9516}, {"text": "classification", "x": 458.612, "y": 210.336, "width": 47.4598, "height": 10.9516}, {"text": "improved", "x": 316.905, "y": 220.334, "width": 34.5633, "height": 10.9516}, {"text": "by", "x": 353.459, "y": 220.334, "width": 9.08844, "height": 10.9516}, {"text": "integrating", "x": 364.538, "y": 220.334, "width": 39.2439, "height": 10.9516}, {"text": "bidirectional", "x": 405.772, "y": 220.334, "width": 45.942, "height": 10.9516}, {"text": "lstm", "x": 453.704, "y": 220.334, "width": 15.6594, "height": 10.9516}, {"text": "with", "x": 471.354, "y": 220.334, "width": 16.1592, "height": 10.9516}, {"text": "two", "x": 489.504, "y": 220.334, "width": 12.42615, "height": 10.9516}, {"text": "-", "x": 501.93015, "y": 220.334, "width": 4.14205, "height": 10.9516}, {"text": "dimensional", "x": 316.905, "y": 230.331, "width": 44.4334, "height": 10.9516}, {"text": "max", "x": 363.61, "y": 230.331, "width": 15.6503, "height": 10.9516}, {"text": "pooling", "x": 381.533, "y": 230.331, "width": 26.290599999999998, "height": 10.9516}, {"text": ".", "x": 407.8236, "y": 230.331, "width": 3.7558, "height": 10.9516}, {"text": "In", "x": 414.851, "y": 230.331, "width": 7.57067, "height": 10.9516}, {"text": "COLING", "x": 424.693, "y": 230.331, "width": 30.51308571428571, "height": 10.8516}, {"text": ".", "x": 455.2060857142857, "y": 230.331, "width": 5.085514285714285, "height": 10.8516}, {"text": "2237", "x": 287.863, "y": 775.563, "width": 21.8182, "height": 13.1455}]}]
\ No newline at end of file
diff --git a/api/test/fixtures/status/example@gmail.com.json b/api/test/fixtures/status/example@gmail.com.json
new file mode 100644
index 00000000..40b34c47
--- /dev/null
+++ b/api/test/fixtures/status/example@gmail.com.json
@@ -0,0 +1,12 @@
+{
+ "3febb2bed8865945e7fddc99efd791887bb7e14f": {
+ "sha": "3febb2bed8865945e7fddc99efd791887bb7e14f",
+ "name": "3febb2bed8865945e7fddc99efd791887bb7e14f",
+ "annotations": 0,
+ "relations": 0,
+ "finished": false,
+ "junk": false,
+ "comments": "",
+ "completedAt": null
+ }
+}
\ No newline at end of file
diff --git a/api/test/fixtures/users/allowed.txt b/api/test/fixtures/users/allowed.txt
new file mode 100644
index 00000000..b7eb2b03
--- /dev/null
+++ b/api/test/fixtures/users/allowed.txt
@@ -0,0 +1,2 @@
+example@gmail.com
+example2@gmail.com
\ No newline at end of file
diff --git a/api/test/test_app.py b/api/test/test_app.py
new file mode 100644
index 00000000..48286f7c
--- /dev/null
+++ b/api/test/test_app.py
@@ -0,0 +1,174 @@
+import os
+import shutil
+from unittest import TestCase
+
+from fastapi.testclient import TestClient
+
+from main import app
+
+
+def copy_and_overwrite(from_path: str, to_path: str):
+ if os.path.exists(to_path):
+ shutil.rmtree(to_path)
+ shutil.copytree(from_path, to_path)
+
+
+class TestApp(TestCase):
+ def setUp(self):
+ super().setUp()
+
+ self.client = TestClient(app)
+ self.TEST_DIR = "test/fixtures/tmp/"
+ copy_and_overwrite("test/fixtures/data/", self.TEST_DIR)
+ copy_and_overwrite(
+ "test/fixtures/status/", os.path.join(self.TEST_DIR, "status")
+ )
+ self.pdf_sha = "3febb2bed8865945e7fddc99efd791887bb7e14f"
+
+ def tearDown(self):
+ shutil.rmtree(self.TEST_DIR)
+
+ def test_root(self):
+ response = self.client.get("/")
+ assert response.status_code == 204
+
+ def test_get_bad_pdf(self):
+
+ response = self.client.get("/api/doc/not_a_pdf/pdf")
+ assert response.status_code == 404
+
+ def test_get_labels(self):
+ response = self.client.get("/api/annotation/labels")
+ assert response.json() == [
+ {"text": "Figure Text", "color": "#70DDBA"},
+ {"text": "Section Header", "color": "#FFD45D"},
+ ]
+
+ def test_get_relations(self):
+ response = self.client.get("/api/annotation/relations")
+ assert response.json() == [
+ {"text": "Caption Of", "color": "#70DDBA"},
+ {"text": "Definition", "color": "#FFD45D"},
+ ]
+
+ def test_set_pdf_comments(self):
+
+ self.client.post(
+ f"/api/doc/{self.pdf_sha}/comments",
+ json="hello this is a comment.",
+ headers={"X-Auth-Request-Email": "example@gmail.com"},
+ )
+ response = self.client.get(
+ "/api/annotation/allocation/info",
+ headers={"X-Auth-Request-Email": "example@gmail.com"},
+ )
+ assert response.json()["papers"][0]["comments"] == "hello this is a comment."
+
+ def test_set_pdf_finished(self):
+
+ self.client.post(
+ f"/api/doc/{self.pdf_sha}/finished",
+ json=True,
+ headers={"X-Auth-Request-Email": "example@gmail.com"},
+ )
+ response = self.client.get(
+ "/api/annotation/allocation/info",
+ headers={"X-Auth-Request-Email": "example@gmail.com"},
+ )
+ assert response.json()["papers"][0]["finished"] is True
+
+ def test_set_pdf_junk(self):
+
+ self.client.post(
+ f"/api/doc/{self.pdf_sha}/junk",
+ json=True,
+ headers={"X-Auth-Request-Email": "example@gmail.com"},
+ )
+ response = self.client.get(
+ "/api/annotation/allocation/info",
+ headers={"X-Auth-Request-Email": "example@gmail.com"},
+ )
+ assert response.json()["papers"][0]["junk"] is True
+
+ def test_get_allocation_info(self):
+
+ response = self.client.get(
+ "/api/annotation/allocation/info",
+ headers={"X-Auth-Request-Email": "example@gmail.com"},
+ )
+
+ gold = {
+ "papers": [
+ {
+ "sha": "3febb2bed8865945e7fddc99efd791887bb7e14f",
+ "name": "3febb2bed8865945e7fddc99efd791887bb7e14f",
+ "annotations": 0,
+ "relations": 0,
+ "finished": False,
+ "junk": False,
+ "comments": "",
+ "completedAt": None,
+ }
+ ],
+ "hasAllocatedPapers": True
+ }
+ assert response.json() == gold
+
+ # Now check that authorized but un-allocated users see all pdfs,
+ # but have hasAllocatedPapers set to false:
+ response = self.client.get(
+ "/api/annotation/allocation/info",
+ headers={"X-Auth-Request-Email": "example2@gmail.com"},
+ )
+
+ assert response.json()["papers"] == gold["papers"]
+ assert response.json()["hasAllocatedPapers"] == False
+
+ def test_get_tokens(self):
+
+ response = self.client.get(f"/api/doc/{self.pdf_sha}/tokens")
+
+ data = response.json()
+ assert len(data) == 11
+
+ # Wrong pdf sha should return 404
+ response = self.client.get(f"/api/doc/not_a_pdf_sha/tokens")
+ assert response.status_code == 404
+
+ def test_get_annotations(self):
+ # All requests in this test are authenticated as this user.
+ headers = {"X-Auth-Request-Email": "example@gmail.com"}
+
+ # Initially there are no annotations
+ response = self.client.get(
+ f"/api/doc/{self.pdf_sha}/annotations", headers=headers
+ )
+ assert response.json() == {"annotations": [], "relations": []}
+
+ # Now, post an annotation
+ annotation = {
+ "id": "this-is-an-id",
+ "page": 1,
+ "label": {"text": "label1", "color": "red"},
+ "bounds": {"left": 1.0, "top": 4.3, "right": 5.1, "bottom": 2.5},
+ "tokens": None,
+ }
+ self.client.post(
+ f"/api/doc/{self.pdf_sha}/annotations",
+ json={"annotations": [annotation], "relations": []},
+ headers=headers,
+ )
+
+ # And now, the annotation should be there
+ response = self.client.get(
+ f"/api/doc/{self.pdf_sha}/annotations", headers=headers
+ )
+ assert response.json() == {"annotations": [annotation], "relations": []}
+
+ # and the status should have been updated with the annotation count:
+ response = self.client.get(
+ "/api/annotation/allocation/info",
+ headers={"X-Auth-Request-Email": "example@gmail.com"},
+ )
+
+ assert response.json()["papers"][0]["annotations"] == 1
diff --git a/bin/kubeconf b/bin/kubeconf
new file mode 100755
index 00000000..b1b395c1
--- /dev/null
+++ b/bin/kubeconf
@@ -0,0 +1,70 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import json
+from os import path, getlogin, devnull
+from argparse import ArgumentParser
+from subprocess import check_call, check_output
+
+def configure(env, api, proxy, message, silent = False):
+ builder_image = "gcr.io/ai2-reviz/jsonnet"
+ stdout = open(devnull) if silent == True else None
+ check_call(["docker", "pull", builder_image ], stdout=stdout)
+ root = path.abspath(path.join(path.dirname(__file__), ".."))
+ sha = check_output([ "git", "rev-parse", "HEAD" ]).decode("utf-8").strip()
+ branch = check_output([ "git", "rev-parse", "--abbrev-ref", "HEAD" ]).decode("utf-8").strip()
+ cmd = [
+ "docker",
+ "run",
+ "--rm",
+ "-it",
+ "-v", "%s:/workspace" % root,
+ builder_image,
+ "eval",
+ "-y",
+ "--output-file", "/workspace/.skiff/webapp.yaml",
+ "--tla-str", "proxyImage=%s" % proxy,
+ "--tla-str", "apiImage=%s" % api,
+ "--tla-str", "cause=%s" % message,
+ "--tla-str", "env=%s" % env,
+ "--tla-str", "sha=%s" % sha,
+ "--tla-str", "branch=%s" % branch,
+ "/workspace/.skiff/webapp.jsonnet"
+ ]
+ # The docker run command needs a valid stdout to write to, which means
+ # if the silent flag is enabled we need to capture and discard the output
+ if silent == True:
+ check_output(cmd)
+ else:
+ check_call(cmd)
+ config = path.abspath(path.join(root, ".skiff", "webapp.yaml"))
+ return config
+
+if __name__ == "__main__":
+ parser = ArgumentParser(prog="kubeconf",
+ description="Utility for generating the kubernetes manifest for a given environment")
+ parser.add_argument("--env", "-e", default="staging", type=str,
+ help="The value of the $_ENV cloudbuild variable")
+ parser.add_argument("--api", "-a", type=str,
+ help="The target API image.", required=True)
+ parser.add_argument("--proxy", "-p", type=str,
+ help="The target Proxy image.", required=True)
+ parser.add_argument("--message", "-m", type=str,
+ help="The reason behind the deployment", required=True)
+ formats = set([ "text", "json" ])
+ parser.add_argument("--output", "-o", type=str, choices=formats,
+ help="The output format.", default="text")
+ parser.add_argument("-s", "--silent", action="store_true", default=False,
+ help="If specified verbose output is disabled.")
+ args = parser.parse_args()
+ output = configure(
+ args.env,
+ args.api,
+ args.proxy,
+ args.message,
+ args.silent
+ )
+ if args.output == "text":
+ print("✨ successfully wrote %s" % output)
+ else:
+ print(json.dumps(output))
diff --git a/bin/sh b/bin/sh
new file mode 100755
index 00000000..4fecb601
--- /dev/null
+++ b/bin/sh
@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from argparse import ArgumentParser
+from subprocess import check_call
+from os import path
+
+def start_shell():
+ """
+ Starts a shell session in the target container.
+ """
+
+ # TODO: We could parse these from the `docker-compose.yaml` file instead
+ # of hard-coding them, but for now this is easier.
+ services = [ 'api', 'ui', 'proxy' ]
+
+ arg_parser = ArgumentParser(
+ description='A utility that opens a shell session in the specified web application container.',
+ prog='sh')
+ arg_parser.add_argument('service', type=str, help='The service container',
+ choices=list(services))
+ args = arg_parser.parse_args()
+
+ check_call(
+ [ 'docker-compose', 'exec', '--user', 'root', args.service, '/bin/sh' ],
+ cwd=path.realpath(path.dirname(__file__)))
+
+if __name__ == '__main__':
+ start_shell()
diff --git a/cli/__init__.py b/cli/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/cli/pawls/__init__.py b/cli/pawls/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/cli/pawls/__main__.py b/cli/pawls/__main__.py
new file mode 100644
index 00000000..d8fb7b1f
--- /dev/null
+++ b/cli/pawls/__main__.py
@@ -0,0 +1,31 @@
+import click
+import logging
+from pawls import commands
+
+
+logger = logging.getLogger(__name__)
+
+
+@click.group(context_settings={"help_option_names": ["--help", "-h"]})
+@click.option("--verbose", "-v", is_flag=True, help="Set log level to DEBUG.")
+def pawls_cli(verbose):
+ """An interface for managing PDFs for PAWLS."""
+ log_level = logging.DEBUG if verbose else logging.INFO
+ logger.setLevel(log_level)
+
+
+subcommands = [
+ commands.preprocess,
+ commands.assign,
+ commands.export,
+ commands.status,
+ commands.preannotate,
+ commands.metric
+]
+
+for subcommand in subcommands:
+ pawls_cli.add_command(subcommand)
+
+
+if __name__ == "__main__":
+ pawls_cli()
diff --git a/cli/pawls/commands/__init__.py b/cli/pawls/commands/__init__.py
new file mode 100644
index 00000000..56f754e7
--- /dev/null
+++ b/cli/pawls/commands/__init__.py
@@ -0,0 +1,6 @@
+from pawls.commands.preprocess import preprocess
+from pawls.commands.preannotate import preannotate
+from pawls.commands.assign import assign
+from pawls.commands.export import export
+from pawls.commands.status import status
+from pawls.commands.metric import metric
diff --git a/cli/pawls/commands/assign.py b/cli/pawls/commands/assign.py
new file mode 100644
index 00000000..6ffc3cf9
--- /dev/null
+++ b/cli/pawls/commands/assign.py
@@ -0,0 +1,132 @@
+import os
+from typing import Tuple
+
+import click
+from click import UsageError, BadArgumentUsage
+import json
+import glob
+import re
+
+
+@click.command(context_settings={"help_option_names": ["--help", "-h"]})
+@click.argument("path", type=click.Path(exists=True, file_okay=False))
+@click.argument("annotator", type=str)
+@click.argument("shas", type=str, nargs=-1)
+@click.option(
+ "--sha-file",
+ "-f",
+ type=click.Path(exists=True, file_okay=True, dir_okay=False),
+ help="A path to a file containing shas.",
+)
+@click.option(
+ "--name-file",
+ "-f",
+ type=click.Path(exists=True, file_okay=True, dir_okay=False),
+ help="A path to a json file mapping shas to file names.",
+)
+@click.option(
+ "--all",
+ "-a",
+ is_flag=True,
+ type=bool,
+ default=False,
+ help="A flag to assign all current pdfs in a pawls project to an annotator.",
+)
+def assign(
+ path: click.Path,
+ annotator: str,
+ shas: Tuple[str],
+ sha_file: click.Path = None,
+ name_file: click.Path = None,
+ all: bool = False,
+):
+ """
+ Assign pdfs and annotators for a project.
+
+ Use assign to assign annotators to a project, or assign them
+ pdfs in the specified directory.
+
+ Annotators must be assigned a username corresponding
+ to a gmail email address, such as `markn@gmail.com`.
+
+ Add an annotator:
+
+ `pawls assign markn@gmail.com`
+
+ To assign all current pdfs in the project to an annotator, use:
+
+ `pawls assign --all`
+ """
+ shas = set(shas)
+
+ pdfs = glob.glob(os.path.join(path, "*/*.pdf"))
+ project_shas = {p.split("/")[-2] for p in pdfs}
+ if all:
+ # If --all flag, we use all pdfs in the current project.
+ shas.update(project_shas)
+
+ if sha_file is not None:
+ extra_ids = [x.strip("\n") for x in open(sha_file, "r")]
+ shas.extend(extra_ids)
+
+ diff = shas.difference(project_shas)
+ if diff:
+ error = f"Found shas which are not present in path {path} .\n"
+ error = (
+ error
+ + f"Add pdf files in the specified directory, one per sub-directory."
+ )
+ for sha in diff:
+ error = error + f"{sha}\n"
+ raise UsageError(error)
+
+ if all:
+ # If --all flag, we use all pdfs in the current project.
+ shas.update(project_shas)
+
+ if sha_file is not None:
+ extra_ids = [x.strip("\n") for x in open(sha_file, "r")]
+ shas.extend(extra_ids)
+
+ result = re.match(r"(^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$)", annotator)
+
+ if not result or result.group(0) != annotator:
+ raise BadArgumentUsage("Provided annotator was not a valid email.")
+
+ status_dir = os.path.join(path, "status")
+ os.makedirs(status_dir, exist_ok=True)
+
+ status_path = os.path.join(status_dir, f"{annotator}.json")
+
+ pdf_status = {}
+ if os.path.exists(status_path):
+ pdf_status = json.load(open(status_path))
+
+ name_mapping = {}
+ if name_file is not None:
+ name_mapping = json.load(open(name_file))
+ else:
+ print("Warning: --name-file was not provided, using shas as pdf names.")
+
+ for sha in shas:
+ if sha in pdf_status:
+ continue
+ else:
+
+ name = name_mapping.get(sha, None)
+ if name is None:
+ name = sha
+
+ pdf_status[sha] = {
+ "sha": sha,
+ "name": name,
+ "annotations": 0,
+ "relations": 0,
+ "finished": False,
+ "junk": False,
+ "comments": "",
+ "completedAt": None,
+ }
+
+ with open(status_path, "w+") as out:
+ json.dump(pdf_status, out)
diff --git a/cli/pawls/commands/export.py b/cli/pawls/commands/export.py
new file mode 100644
index 00000000..b5299706
--- /dev/null
+++ b/cli/pawls/commands/export.py
@@ -0,0 +1,394 @@
+import os
+import json
+from typing import List, NamedTuple, Union, Dict, Any
+
+import click
+import pandas as pd
+from tqdm import tqdm
+from pdf2image import convert_from_path
+
+from pawls.commands.utils import (
+ load_json,
+ get_pdf_sha,
+ get_pdf_pages_and_sizes,
+ LabelingConfiguration,
+ AnnotationFolder,
+ AnnotationFiles,
+)
+
+ALL_SUPPORTED_EXPORT_TYPE = ["coco", "token"]
+
+
+def _convert_bounds_to_coco_bbox(bounds: Dict[str, Union[int, float]]):
+ x1, y1, x2, y2 = bounds["left"], bounds["top"], bounds["right"], bounds["bottom"]
+ return x1, y1, x2 - x1, y2 - y1
+
+
+class COCOBuilder:
+ class CategoryTemplate(NamedTuple):
+ id: int
+ name: str
+ supercategory: str = None
+
+ class PaperTemplate(NamedTuple):
+ id: int
+ paper_sha: str
+ pages: int
+
+ class ImageTemplate(NamedTuple):
+ id: int
+ file_name: str
+ height: Union[float, int]
+ width: Union[float, int]
+ paper_id: int
+ page_number: int
+
+ class AnnoTemplate(NamedTuple):
+ id: int
+ bbox: List
+ image_id: int
+ category_id: int
+ area: Union[float, int]
+ iscrowd: bool = False
+
+ def __init__(self, categories: List, save_path: str):
+ """COCOBuilder generates the coco-format dataset based on
+ source annotation files.
+
+ It will create a COCO-format annotation json file for every
+ annotated page and convert all the labeled pdf pages into
+ images, which is stored in `/images/_.jpg`.
+
+ Args:
+ categories (List):
+ All the labeling categories in the dataset
+ save_path (str):
+ The folder for saving all the annotation files.
+
+ Examples::
+ >>> anno_files = AnnotationFiles(**configs) # Initialize anno_files based on configs
+ >>> coco_builder = COCOBuilder(["title", "abstract"], "export_path")
+ >>> coco_builder.build_annotations(anno_files)
+ >>> coco_builder.export()
+ """
+ # Create Paths
+ self.save_path = save_path
+ self.save_path_image = f"{self.save_path}/images"
+ os.makedirs(self.save_path, exist_ok=True)
+ os.makedirs(self.save_path_image, exist_ok=True)
+
+ # Internal COCO information storage
+ self._categories = self._create_coco_categories(categories)
+ self._name2catid = {ele["name"]: ele["id"] for ele in self._categories}
+ self._images = []
+ self._papers = []
+
+ def get_image_data(self, paper_sha: str, page_id: int):
+ """Find the image data with the given paper_sha and page_id."""
+ filename = self._create_pdf_page_image_filename(paper_sha, page_id)
+ for data in self._images:
+ if data["file_name"] == filename:
+ return data
+
+ def _create_pdf_page_image_filename(self, paper_sha: str, page_id: int) -> str:
+ return f"{paper_sha}_{page_id}.jpg"
+
+ def _create_coco_categories(self, categories: List) -> List[str]:
+ return [
+ self.CategoryTemplate(idx, category)._asdict()
+ for idx, category in enumerate(categories)
+ ]
+
+ def create_paper_data(
+ self, annotation_folder: AnnotationFolder, save_images: bool = True
+ ):
+
+ _papers = []
+ _images = []
+ pbar = tqdm(annotation_folder.all_pdf_paths)
+ for pdf_path in pbar:
+ paper_sha = get_pdf_sha(pdf_path)
+ pbar.set_description(f"Working on {paper_sha[:10]}...")
+
+ num_pages, page_sizes = get_pdf_pages_and_sizes(pdf_path)
+ pdf_page_images = convert_from_path(pdf_path)
+
+ # Add paper information
+ paper_id = len(_papers) # Start from zero
+ paper_info = self.PaperTemplate(
+ paper_id,
+ paper_sha,
+ pages=num_pages,
+ )
+
+ current_images = []
+ previous_image_id = len(_images) # Start from zero
+
+ for page_id, page_size in enumerate(page_sizes):
+ image_filename = self._create_pdf_page_image_filename(
+ paper_sha, page_id
+ )
+ width, height = page_size
+ current_images.append(
+ self.ImageTemplate(
+ id=previous_image_id + len(current_images),
+ file_name=image_filename,
+ height=height,
+ width=width,
+ paper_id=paper_id,
+ page_number=page_id,
+ )._asdict()
+ )
+ if save_images and not os.path.exists(
+ f"{self.save_path_image}/{image_filename}"
+ ):
+ pdf_page_images[page_id].resize((width, height)).save(
+ f"{self.save_path_image}/{image_filename}"
+ )
+
+ _papers.append(paper_info._asdict())
+ _images.extend(current_images)
+
+ self._papers = _papers
+ self._images = _images
+
+ def create_annotation_for_annotator(self, anno_files: AnnotationFiles) -> None:
+ """Create the annotations for the given annotation files"""
+
+ _annotations = []
+ anno_id = 0
+ pbar = tqdm(anno_files)
+ for anno_file in pbar:
+
+ paper_sha = anno_file["paper_sha"]
+
+ pbar.set_description(f"Working on {paper_sha[:10]}...")
+ pawls_annotations = load_json(anno_file["annotation_path"])["annotations"]
+
+ for anno in pawls_annotations:
+ page_id = anno["page"]
+ category = anno["label"]["text"]
+
+ # Skip if current category is not in the specified categories
+ cat_id = self._name2catid.get(category, None)
+ if cat_id is None:
+ continue
+
+ image_data = self.get_image_data(paper_sha, page_id)
+ width, height = image_data["width"], image_data["height"]
+
+ x, y, w, h = _convert_bounds_to_coco_bbox(anno["bounds"])
+
+ _annotations.append(
+ self.AnnoTemplate(
+ id=anno_id,
+ bbox=[x, y, w, h],
+ category_id=cat_id,
+ image_id=image_data["id"],
+ area=w * h,
+ )._asdict()
+ )
+ anno_id += 1
+
+ return _annotations
+
+ def create_combined_json_for_annotations(
+ self, annotations: List[Dict]
+ ) -> Dict[str, Any]:
+ return {
+ "papers": self._papers,
+ "images": self._images,
+ "annotations": annotations,
+ "categories": self._categories,
+ }
+
+ def build_annotations(self, anno_files: AnnotationFiles) -> None:
+
+ annotations = self.create_annotation_for_annotator(anno_files)
+ coco_json = self.create_combined_json_for_annotations(annotations)
+ self.export(coco_json, f"{anno_files.annotator}.json")
+
+ def export(self, coco_json: Dict, annotation_name="annotations.json") -> None:
+
+ with open(f"{self.save_path}/{annotation_name}", "w") as fp:
+
+ json.dump(coco_json, fp)
+
+
+class TokenTableBuilder:
+ def __init__(self, categories, save_path: str):
+
+ self.categories = categories
+ self.save_path = save_path
+
+ def create_paper_data(self, annotation_folder: AnnotationFolder):
+
+ all_page_token_data = {}
+ for pdf in annotation_folder.all_pdfs:
+ all_page_tokens = annotation_folder.get_pdf_tokens(pdf)
+
+ # Get page token data
+ page_token_data = []
+ for page_tokens in all_page_tokens:
+ token_data = [
+ (page_tokens.page.index, idx, token.text)
+ for idx, token in enumerate(page_tokens.tokens)
+ ]
+ df = pd.DataFrame(token_data, columns=["page_index", "index", "text"])
+ df = df.set_index(["page_index", "index"])
+ page_token_data.append(df)
+ page_token_data = pd.concat(page_token_data)
+
+ all_page_token_data[get_pdf_sha(pdf)] = page_token_data
+
+ self.all_page_token_data = all_page_token_data
+
+ def create_annotation_for_annotator(self, anno_files: AnnotationFiles) -> None:
+
+ # Firstly initialize the annotation tables with the annotator name
+ annotator = anno_files.annotator
+ for token_data in self.all_page_token_data.values():
+ token_data[annotator] = None
+
+ pbar = tqdm(anno_files)
+
+ for anno_file in pbar:
+ paper_sha = anno_file["paper_sha"]
+ df = self.all_page_token_data[paper_sha]
+
+ pawls_annotations = load_json(anno_file["annotation_path"])["annotations"]
+ for anno in pawls_annotations:
+ if anno["tokens"] is None:
+ continue
+
+ # Skip if current category is not in the specified categories
+ label = anno["label"]["text"]
+ if label not in self.categories:
+ continue
+
+ anno_token_indices = [
+ (ele["pageIndex"], ele["tokenIndex"]) for ele in anno["tokens"]
+ ]
+
+ df.loc[anno_token_indices, annotator] = label
+
+ def export(self):
+
+ for pdf, df in self.all_page_token_data.items():
+ df["pdf"] = pdf
+
+ df = (
+ pd.concat(self.all_page_token_data.values())
+ .reset_index()
+ .set_index(["pdf", "page_index", "index"])
+ )
+
+ df.to_csv(self.save_path)
+ return df
+
+
+@click.command(context_settings={"help_option_names": ["--help", "-h"]})
+@click.argument("path", type=click.Path(exists=True, file_okay=False))
+@click.argument("config", type=str)
+@click.argument("output", type=click.Path(file_okay=True))
+@click.argument("format", type=click.Path(file_okay=False))
+@click.option(
+ "--annotator",
+ "-u",
+ multiple=True,
+ help="Export annotations of the specified annotator.",
+)
+@click.option(
+ "--categories",
+ "-c",
+ multiple=True,
+ help="Export specified categories in the annotations.",
+)
+@click.option(
+ "--include-unfinished",
+ "-i",
+ is_flag=True,
+ help="A flag to export all annotation by the specified annotator including unfinished ones.",
+)
+@click.option(
+ "--export-images/--no-export-images",
+ default=True,
+ help="A flag to not to export images of PDFs",
+)
+def export(
+ path: click.Path,
+ config: click.File,
+ output: click.Path,
+ format: str,
+ annotator: List,
+ categories: List,
+ include_unfinished: bool = False,
+ export_images: bool = True,
+):
+ """
+ Export the COCO annotations for an annotation project.
+
+ To export all annotations of a project of all annotators, use:
+ `pawls export `
+
+ To export only finished annotations of from specified annotators, e.g. markn and shannons, use:
+ `pawls export -u markn -u shannons`.
+
+ To export all annotations of from a given annotator, use:
+ `pawls export -u markn --include-unfinished`.
+ """
+
+ assert (
+ format in ALL_SUPPORTED_EXPORT_TYPE
+ ), f"Invalid export format {format}. Should be one of {ALL_SUPPORTED_EXPORT_TYPE}."
+ print(f"Export the annotations to the {format} format.")
+
+ config = LabelingConfiguration(config)
+ annotation_folder = AnnotationFolder(path)
+
+ if len(annotator) == 0:
+ all_annotators = annotation_folder.all_annotators
+ print(f"Export annotations from all available annotators {all_annotators}")
+ else:
+ all_annotators = annotator
+
+ if len(categories) == 0:
+ categories = config.categories
+ print(f"Export annotations from all available categories {categories}")
+
+ if format == "coco":
+
+ coco_builder = COCOBuilder(categories, output)
+ print(f"Creating paper data for annotation folder {annotation_folder.path}")
+ coco_builder.create_paper_data(annotation_folder, save_images=export_images)
+
+ for annotator in all_annotators:
+ print(f"Export annotations from annotators {annotator}")
+
+ anno_files = AnnotationFiles(path, annotator, include_unfinished)
+
+ coco_builder.build_annotations(anno_files)
+
+ print(
+ f"Successfully exported {len(anno_files)} annotations of annotator {annotator} to {output}."
+ )
+
+ elif format == "token":
+
+ if not output.endswith(".csv"):
+ output = f"{output}.csv"
+ token_builder = TokenTableBuilder(categories, output)
+
+ print(f"Creating paper data for annotation folder {annotation_folder.path}")
+ token_builder.create_paper_data(annotation_folder)
+
+ for annotator in all_annotators:
+
+ # print(f"Export annotations from annotators {annotator}")
+ anno_files = AnnotationFiles(path, annotator, include_unfinished)
+ token_builder.create_annotation_for_annotator(anno_files)
+
+ df = token_builder.export()
+ print(
+ f"Successfully exported annotations for {len(df)} tokens from annotators {all_annotators} to {output}."
+ )
\ No newline at end of file
diff --git a/cli/pawls/commands/metric.py b/cli/pawls/commands/metric.py
new file mode 100644
index 00000000..c0d6a2dc
--- /dev/null
+++ b/cli/pawls/commands/metric.py
@@ -0,0 +1,365 @@
+import os
+import sys
+import tempfile
+from glob import glob
+from copy import deepcopy
+from collections import defaultdict
+from typing import List, NamedTuple, Union, Dict, Any, Set, Tuple
+
+import click
+import pandas as pd
+import numpy as np
+from tabulate import tabulate
+from pycocotools.coco import COCO
+from pycocotools.cocoeval import COCOeval
+
+from pawls.commands.export import export
+
+
+def get_unique_image_ids(coco: COCO) -> Set[int]:
+ return set([anno["image_id"] for anno in coco.dataset["annotations"]])
+
+
+def get_mutually_annotated_image_ids(coco1: COCO, coco2: COCO) -> Set[int]:
+ return get_unique_image_ids(coco1).intersection(get_unique_image_ids(coco2))
+
+
+def filter_annotation_with_image_ids(coco: COCO, image_ids: Set[int]) -> COCO:
+ coco = deepcopy(coco)
+ coco.dataset["annotations"] = [
+ anno for anno in coco.dataset["annotations"] if anno["image_id"] in image_ids
+ ]
+ coco.dataset["images"] = [
+ image for image in coco.dataset["images"] if image["id"] in image_ids
+ ]
+ return coco
+
+
+def print_results(calculation_method_msg, df: pd.DataFrame):
+
+ print(calculation_method_msg)
+ print("-" * 45)
+ print(
+ "The (i,j)-th element in the table is calculated by treating the annotations from\n"
+ "i as the 'ground-truth's, and those from j are considered as 'predictions'."
+ )
+ print(
+ tabulate(
+ df[sorted(df.columns)].loc[sorted(df.columns)],
+ headers="keys",
+ tablefmt="psql",
+ )
+ )
+ print("\n")
+
+
+class PythonLiteralOption(click.Option):
+ """Used for parsing list-like stings from the input.
+
+ A technique adapted from https://stackoverflow.com/a/47730333
+ """
+
+ def type_cast_value(self, ctx, value):
+ try:
+ return [ele.strip() for ele in value.split(",")]
+ except:
+ raise click.BadParameter(value)
+
+
+class HiddenPrints:
+ """Used for hiding unnecessary prints of COCO Eval
+ A trick learned from https://stackoverflow.com/a/45669280
+ """
+
+ def __enter__(self):
+ self._original_stdout = sys.stdout
+ sys.stdout = open(os.devnull, "w")
+
+ def __exit__(self, exc_type, exc_val, exc_tb):
+ sys.stdout.close()
+ sys.stdout = self._original_stdout
+
+
+class COCOEvaluator:
+
+ COCO_METRICS = ["AP", "AP50", "AP75", "APs", "APm", "APl"]
+
+ def __init__(self, coco_save_path: str, class_names: List[str] = None):
+
+ all_cocos = {}
+ annotators = []
+ for userfile in sorted(glob(f"{coco_save_path}/*.json")):
+ with HiddenPrints():
+ username = userfile.split("/")[-1].replace(".json", "")
+ annotators.append(username)
+ all_cocos[username] = COCO(userfile)
+
+ # A hack to make use of the current COCOEval API
+ for coco in all_cocos.values():
+ for ele in coco.dataset["annotations"]:
+ ele["score"] = 1
+
+ self.all_cocos = all_cocos
+ self.annotators = annotators
+
+ self.class_names = class_names or [
+ val["name"] for _, val in all_cocos[annotators[0]].cats.items()
+ ]
+
+ def calculate_scores_for_two_cocos(
+ self, coco1: COCO, coco2: COCO, class_names: List[str]
+ ) -> Tuple[Dict, Dict]:
+
+ coco_eval = COCOeval(coco1, coco2, iouType="bbox")
+ with HiddenPrints():
+ coco_eval.evaluate()
+ coco_eval.accumulate()
+ coco_eval.summarize()
+
+ results = {
+ metric: float(
+ coco_eval.stats[idx] * 100 if coco_eval.stats[idx] >= 0 else "nan"
+ )
+ for idx, metric in enumerate(self.COCO_METRICS)
+ }
+ precisions = coco_eval.eval["precision"]
+
+ results_per_category = []
+ for idx, name in enumerate(class_names):
+ # area range index 0: all area ranges
+ # max dets index -1: typically 100 per image
+ precision = precisions[:, :, idx, 0, -1]
+ precision = precision[precision > -1]
+ ap = np.mean(precision) if precision.size else float("nan")
+ results_per_category.append(("{}".format(name), float(ap * 100)))
+
+ results_per_category = {name: ap for name, ap in results_per_category}
+ return results, results_per_category
+
+ def calculate_ap_scores(self) -> Tuple[Dict, Dict]:
+
+ coco_results = defaultdict(dict)
+ coco_category_results = defaultdict(dict)
+
+ for name1, coco1 in self.all_cocos.items():
+ for name2, coco2 in self.all_cocos.items():
+
+ image_ids = get_mutually_annotated_image_ids(coco1, coco2)
+ coco1 = filter_annotation_with_image_ids(coco1, image_ids)
+ coco2 = filter_annotation_with_image_ids(coco2, image_ids)
+
+ results, results_per_category = self.calculate_scores_for_two_cocos(
+ coco1, coco2, self.class_names
+ )
+ coco_results[name1][name2] = results
+ coco_category_results[name1][name2] = results_per_category
+
+ return coco_results, coco_category_results
+
+ def show_results(self, results: Dict, metric_names: List[str] = None):
+ """Show COCO Eval results for the given metric names.
+
+ Args:
+ results (Dict):
+ The coco_results dict generated by `COCOEvaluator.calculate_ap_scores`.
+
+ metric_names (List[str], optional):
+ Metric report of the specified `metric_names` will be displayed.
+ If not set, all metrics in `COCOEvaluator.COCO_METRICS` will be displayed.
+ """
+ if metric_names is None:
+ metric_names = self.COCO_METRICS
+
+ for metric_name in metric_names:
+ df = pd.DataFrame(results).applymap(
+ lambda ele: ele.get(metric_name) if not pd.isna(ele) else ele
+ )
+ print_results(
+ f"Inter-annotator agreement based on {metric_name} scores.", df
+ )
+
+ def show_category_results(self, results: Dict, class_names: List[str] = None):
+ """Show COCO Eval results for the given class_names.
+
+ Args:
+ results (Dict):
+ The coco_category_results dict generated by `COCOEvaluator.calculate_ap_scores`.
+
+ class_names (List[str], optional):
+ Metric report of the specified `class_names` will be displayed.
+ If not set, all classes in `self.class_names` will be displayed.
+ """
+ if class_names is None:
+ class_names = self.class_names
+
+ for class_name in class_names:
+ df = pd.DataFrame(results).applymap(
+ lambda ele: ele.get(class_name) if not pd.isna(ele) else ele
+ )
+
+ print_results(
+ f"Inter-annotator agreement of the {class_name} class based on AP scores.",
+ df,
+ )
+
+
+class TokenEvaluator:
+
+ PDF_FEATURES_IN_SAVED_TABLES = ["pdf", "page_index", "index", "text"]
+
+ def __init__(self, token_save_path: str):
+
+ self.df = pd.read_csv(token_save_path)
+ self.annotators = list(
+ self.df.columns[len(self.PDF_FEATURES_IN_SAVED_TABLES) :]
+ )
+ # Assuming all users are stored in email address
+
+ def calculate_scores_for_two_annotators(
+ self, annotator_gt: str, annotator_pred: str
+ ):
+
+ cur_df = self.df[[annotator_gt, annotator_pred]].fillna(-1)
+ acc = (cur_df[annotator_gt] == cur_df[annotator_pred]).mean()
+
+ return acc
+
+ def calculate_token_accuracy(self):
+ table = defaultdict(dict)
+
+ for i, annotator_gt in enumerate(self.annotators):
+ for j, annotator_pred in enumerate(self.annotators):
+
+ if j <= i: # Skip the diagonal
+ continue
+
+ # The token_acc table is symmetric
+ table[annotator_pred][annotator_gt] = table[annotator_gt][
+ annotator_pred
+ ] = self.calculate_scores_for_two_annotators(
+ annotator_gt, annotator_pred
+ )
+
+ return table
+
+ @staticmethod
+ def show_results(results: Dict):
+
+ df = pd.DataFrame(results)
+
+ calculation_method_msg = (
+ "The token accuracy is calculated by simply comparing"
+ "the compatibility of tokens labels agasin two annotators."
+ )
+
+ print_results(calculation_method_msg, df)
+
+
+@click.command(context_settings={"help_option_names": ["--help", "-h"]})
+@click.argument("path", type=click.Path(exists=True, file_okay=False))
+@click.argument("config", type=str)
+@click.option(
+ "--annotator",
+ "-u",
+ multiple=True,
+ help="Export annotations of the specified annotator.",
+)
+@click.option(
+ "--textual-categories",
+ cls=PythonLiteralOption,
+ help="The annotations of textual categories will be evaluated based on token accuracy.",
+)
+@click.option(
+ "--non-textual-categories",
+ cls=PythonLiteralOption,
+ help="The annotations of non-textual categories will be evaluated based on AP scores based on box overlapping.",
+)
+@click.option(
+ "--include-unfinished",
+ "-i",
+ is_flag=True,
+ help="A flag to export all annotation by the specified annotator including unfinished ones.",
+)
+@click.option(
+ "--verbose",
+ "-v",
+ is_flag=True,
+ help="A flag to show detailed reports.",
+)
+@click.pass_context
+def metric(
+ ctx,
+ path: click.Path,
+ config: str,
+ annotator: List,
+ textual_categories: List,
+ non_textual_categories: List,
+ include_unfinished: bool = False,
+ verbose: bool = False,
+):
+ """Calculate the inter-annotator agreement for the annotation project for both textual-categories
+
+ Usage:
+
+ Run evaluation for textual-categories cat1 and cat2, and for non-textual-categories cat3 and cat4:
+
+ pawls metric --textual-categories cat1,cat2 --non-textual-categories cat3,cat4
+
+
+ Specifying annotators for evaluation, and include any unfinished annotations:
+
+ pawls metric -u annotator1 -u annotator2 --textual-categories cat1,cat2 --non-textual-categories cat3,cat4 --include-unfinished
+
+ Generating detailed reports:
+
+ pawls metric --textual-categories cat1,cat2 --non-textual-categories cat3,cat4 --verbose
+
+ """
+
+ invoke_export = lambda tempdir, format, categories: ctx.invoke(
+ export,
+ path=path,
+ config=config,
+ output=tempdir,
+ format=format,
+ annotator=annotator,
+ categories=categories,
+ include_unfinished=include_unfinished,
+ export_images=False,
+ )
+
+ if len(non_textual_categories) > 0:
+ print(
+ f"Generating Accuracy report for non-textual categories {non_textual_categories}"
+ )
+
+ with tempfile.TemporaryDirectory() as tempdir:
+
+ invoke_export(
+ tempdir=tempdir, format="coco", categories=non_textual_categories
+ )
+
+ coco_eval = COCOEvaluator(tempdir)
+ coco_results, coco_category_results = coco_eval.calculate_ap_scores()
+
+ if verbose:
+ coco_eval.show_results(coco_results)
+ coco_eval.show_category_results(coco_category_results)
+ else:
+ coco_eval.show_results(coco_results, ["AP"])
+
+ if len(textual_categories) > 0:
+ print(f"Generating Accuracy report for textual categories {textual_categories}")
+
+ with tempfile.TemporaryDirectory() as tempdir:
+
+ tempdir = os.path.join(tempdir, "annotation.csv")
+
+ invoke_export(
+ tempdir=tempdir, format="token", categories=textual_categories
+ )
+
+ token_eval = TokenEvaluator(tempdir)
+ token_results = token_eval.calculate_token_accuracy()
+
+ token_eval.show_results(token_results)
\ No newline at end of file
diff --git a/cli/pawls/commands/preannotate.py b/cli/pawls/commands/preannotate.py
new file mode 100644
index 00000000..4bb9d95d
--- /dev/null
+++ b/cli/pawls/commands/preannotate.py
@@ -0,0 +1,233 @@
+import os
+import json
+import logging
+from glob import glob
+from typing import List, NamedTuple, Union, Dict, Iterable, Any, Optional
+
+import click
+from tqdm import tqdm
+
+from pawls.commands.utils import LabelingConfiguration, load_json, AnnotationFolder
+from pawls.preprocessors.model import Page, Block, PageInfo, union_boxes
+
+logger = logging.getLogger(__name__)
+
+PADDING_FOR_SEARCHING_TOKEN_INSIDE_BOX = {"top": 3, "left": 3, "bottom": 3, "right": 3}
+PADDING_FOR_RECTIFYING_BLOCK_BOX = {"top": 2, "left": 2, "bottom": 2, "right": 2}
+
+
+class ModelPredictions:
+ """A class for loading model predictions.
+
+ It supports loading predictions directly from a JSON file with the following format:
+
+ {".pdf":
+ [
+ {
+ "page": {"height": xx, "width": xx, "index": 0},
+ "blocks": [
+ [x, y, w, h, "category"]
+ ]
+ },
+ ....
+ ],
+ }
+
+ Or you could load predictions from a folder of json files, each with the name of
+ .json. And the json format is:
+
+ [
+ {
+ "page": {"height": xx, "width": xx, "index": 0},
+ "blocks": [
+ [x, y, w, h, "category"]
+ ]
+ },
+ ....
+ ]
+
+ """
+
+ def __init__(self, pred_file: str):
+
+ if os.path.isfile(pred_file):
+ self.pdf_preds = load_json(pred_file)
+ elif os.path.isdir(pred_file):
+ self.pdf_preds = self.load_directory(pred_file)
+
+ def load_directory(self, pred_dir: str) -> Dict[str, Dict]:
+
+ pdf_preds = {}
+
+ for pred_json in glob(f"{pred_dir}/*.json"):
+
+ filename = os.path.basename(pred_json).replace(".json", ".pdf")
+ self.pdf_preds[filename] = load_json(pred_json)
+
+ return pdf_preds
+
+ @property
+ def all_pdfs(self) -> List[str]:
+ """Obtain all pdfs in the ModelPredictions"""
+ return list(self.pdf_preds.keys())
+
+ def get_pdf_annotations_per_page(self, pdf_name: str) -> Iterable[Page]:
+ """For a given pdf_name, return a iterator yielding block annotations for each page."""
+
+ pdf_pred = self.pdf_preds[pdf_name]
+
+ for page_pred in pdf_pred:
+
+ # Create a pseudo "page", where tokens are actually blocks.
+ yield Page(
+ page=PageInfo(**page_pred["page"]),
+ tokens=self.load_page_blocks(page_pred["blocks"]),
+ )
+
+ @staticmethod
+ def load_page_blocks(boxes: List[Any]) -> List[Block]:
+ return [
+ Block(x=x, y=y, width=w, height=h, label=label)
+ for (x, y, w, h, label) in boxes
+ ]
+
+
+def find_token_data(all_token_data: List[Page], index: int) -> Optional[Page]:
+ """Find the token_data with the given page index.
+
+ Args:
+ all_token_data (List[Page]):
+ A list of Page, contating the token data.
+ index (int):
+ The index of the target page.
+
+ Returns:
+ Optional[Page]:
+ Return the Page with the designated index when found.
+ Otherwise return None.
+ """
+ for token_data in all_token_data:
+ if token_data.page.index == index:
+ return token_data
+
+ return None
+
+
+@click.command(context_settings={"help_option_names": ["--help", "-h"]})
+@click.argument("path", type=click.Path(exists=True, file_okay=False))
+@click.argument("config", type=click.File("r"))
+@click.argument("pred_file", type=click.Path(file_okay=True))
+@click.option(
+ "--annotator",
+ "-u",
+ multiple=True,
+ help="Preannotate for the specified annotator."
+)
+@click.option(
+ "--all",
+ "-a",
+ is_flag=True,
+ type=bool,
+ default=False,
+ help="Whether to preannotate for all annotators."
+)
+def preannotate(
+ path: click.Path, config: click.File, pred_file: click.Path, annotator: List,
+ all: bool=False
+):
+ """
+ Preannotate the PDFs with model prediction results.
+
+ Firstly, you need to generate the region bounding box predictions using some models.
+ And it should be stored in a format that's compatible with the ModelPredictions format.
+
+ We've provided a exemplar script for generating predictions for PDF files in
+ https://github.com/allenai/pawls/tree/master/scripts/generate_pdf_layouts.py .
+
+ You also need to preprocess the PDFs in the use the `pawls preprocess` command.
+
+ To prepopulate predictions for PDFs in the for some annotator, you could use:
+
+ pawls preannoate -u markn
+
+ To prepopulate predictions for PDFs all annotators, you can use:
+
+ pawls preannoate --all
+ """
+
+ anno_folder = AnnotationFolder(path)
+ if all:
+ all_annotators = anno_folder.all_annotators
+ else:
+ all_annotators = annotator
+ for annotator in all_annotators:
+ assert annotator in anno_folder.all_annotators, f"Invalid Annotator {annotator}"
+
+ model_pred = ModelPredictions(pred_file)
+ config_labels = LabelingConfiguration(config).get_labels()
+
+ for annotator in all_annotators:
+ print(f"Adding annotations for the annotator {annotator}")
+
+ pbar = tqdm(model_pred.all_pdfs)
+
+ for pdf_name in pbar:
+
+ pbar.set_description(f"{pdf_name[:10]}...")
+
+ if pdf_name not in anno_folder.all_pdfs:
+ logger.warning(
+ f"The {pdf_name} is not in the annotation folder. Skipped"
+ )
+
+ source_token_data = anno_folder.get_pdf_tokens(pdf_name)
+ annotation_file = anno_folder.create_annotation_file(pdf_name, annotator)
+
+ anno_count = 0
+ for page_blocks in model_pred.get_pdf_annotations_per_page(pdf_name):
+
+ page_index = page_blocks.page.index
+ page_tokens = find_token_data(source_token_data, page_index)
+
+ if page_tokens is None:
+ logger.warning(
+ f"There's no token data for page {page_index} in {pdf_name}. Skipped"
+ )
+ continue
+
+ page_blocks.scale_like(page_tokens) # Ensure they have the same size
+
+ for block_id, block in enumerate(page_blocks.tokens):
+
+ if block.label not in config_labels:
+ logger.warning(
+ f"The {block_id}-th block in page {page_index} of {pdf_name} has labels which are not present in the configuration file. Add all labels produced by your model to the config file to include them. Skipping."
+ )
+ continue
+
+ contained_tokens = page_tokens.filter_tokens_by(
+ block, soft_margin=PADDING_FOR_SEARCHING_TOKEN_INSIDE_BOX
+ )
+
+ token_indices = contained_tokens.keys()
+ contained_tokens = contained_tokens.values()
+
+ # Rectify the block based on the contained tokens
+ if len(contained_tokens) >= 1:
+ rectified_block = union_boxes(contained_tokens)
+ else:
+ # Sometimes a valid block does not include any tokens (e.g., figure).
+ # So we just use the block itself as the rectified_block.
+ rectified_block = block.copy()
+ rectified_block.pad(**PADDING_FOR_RECTIFYING_BLOCK_BOX)
+
+ annotation_file.add_annotation(
+ page_index=page_index,
+ label=config_labels[block.label],
+ bounds=rectified_block.as_bounds(),
+ token_indices=token_indices,
+ )
+ anno_count += 1
+
+ annotation_file.save()
+ logger.info(f"Successfully stored {anno_count} annotations for {pdf_name}.")
diff --git a/cli/pawls/commands/preprocess.py b/cli/pawls/commands/preprocess.py
new file mode 100644
index 00000000..b11b8a5f
--- /dev/null
+++ b/cli/pawls/commands/preprocess.py
@@ -0,0 +1,49 @@
+import os
+from pathlib import Path
+import json
+
+from tqdm import tqdm
+import click
+import glob
+
+from pawls.preprocessors.grobid import process_grobid
+from pawls.preprocessors.pdfplumber import process_pdfplumber
+
+@click.command(context_settings={"help_option_names": ["--help", "-h"]})
+@click.argument("preprocessor", type=str)
+@click.argument("path", type=click.Path(exists=True, file_okay=True, dir_okay=True))
+def preprocess(preprocessor: str, path: click.Path):
+ """
+ Run a pre-processor on a pdf/directory of pawls pdfs and
+ write the resulting token information to the pdf location.
+
+ Current preprocessor options are: "grobid".
+
+ To send all pawls structured pdfs in the current directory for processing:
+
+ `pawls preprocess grobid ./`
+ """
+ print(f"Processing using the {preprocessor} preprocessor...")
+
+ if os.path.isdir(path):
+ in_glob = os.path.join(path, "*/*.pdf")
+ pdfs = glob.glob(in_glob)
+ else:
+ if not str(path).endswith(".pdf"):
+ raise ValueError("Path is not a directory, but also not a pdf.")
+ pdfs = [str(path)]
+
+ pbar = tqdm(pdfs)
+
+ for p in pbar:
+ path = Path(p)
+ sha = path.name.strip(".pdf")
+ pbar.set_description(f"Processing {sha[:10]}...")
+ if preprocessor == "grobid":
+ data = process_grobid(str(path))
+ elif preprocessor == "pdfplumber":
+ data = process_pdfplumber(str(path))
+ with open(path.parent / "pdf_structure.json", "w+") as f:
+
+ json.dump(data, f)
+
diff --git a/cli/pawls/commands/status.py b/cli/pawls/commands/status.py
new file mode 100644
index 00000000..40f009ea
--- /dev/null
+++ b/cli/pawls/commands/status.py
@@ -0,0 +1,111 @@
+import os
+from glob import glob
+import click
+from typing import Tuple
+
+import pandas as pd
+from tabulate import tabulate
+
+from pawls.commands.utils import load_json, get_pdf_pages_and_sizes
+
+
+def get_labeling_status(target_dir: str) -> Tuple[pd.DataFrame, pd.DataFrame]:
+
+ all_json_records = glob(f"{target_dir}/status/*.json")
+
+ all_record = []
+ for record in all_json_records:
+ name = os.path.splitext(os.path.basename(record))[0]
+ all_annotations = load_json(record)
+ cur_record = pd.DataFrame(all_annotations).T
+ cur_record["annotator"] = name
+ all_record.append(cur_record)
+
+ all_record = pd.concat(all_record)
+ pdf_pages = {
+ sha: get_pdf_pages_and_sizes(f"{target_dir}/{sha}/{sha}.pdf")[0]
+ for sha in set(all_record.index)
+ }
+ all_record = all_record.reset_index()
+ all_record["page_num"] = all_record["index"].map(pdf_pages)
+
+ all_record["junk_or_finished"] = all_record["finished"] | all_record["junk"]
+ # used for calculating the unfinished tasks
+
+ all_record["valid_page_num"] = all_record.apply(
+ lambda row: row["page_num"] if row["finished"] else 0, axis=1
+ )
+ all_record["valid_annotations"] = all_record.apply(
+ lambda row: row["annotations"] if row["finished"] else 0, axis=1
+ )
+
+ status = all_record.groupby("annotator").agg(
+ {
+ "index": ["count"],
+ "finished": ["sum"],
+ "valid_annotations": ["sum", "max", "min"],
+ "junk": ["sum"],
+ "junk_or_finished": ["sum"],
+ "valid_page_num": ["sum"],
+ }
+ )
+
+ status.columns = status.columns.map("_".join)
+ status = status.rename(
+ columns={
+ "index_count": "total_tasks",
+ "finished_sum": "total_finished",
+ "junk_sum": "total_junks",
+ "junk_or_finished_sum": "junk_or_finished",
+ "valid_page_num_sum": "page_num",
+ "valid_annotations_sum": "anno_sum",
+ "valid_annotations_max": "anno_max",
+ }
+ )
+
+ status["total_unfinished"] = status["total_tasks"] - status["junk_or_finished"]
+
+ status["avg_anno_per_page"] = status["anno_sum"] / status["page_num"]
+ display_status = status[
+ [
+ "total_tasks",
+ "total_finished",
+ "avg_anno_per_page",
+ "page_num",
+ "anno_sum",
+ "anno_max",
+ ]
+ ].copy()
+
+ display_status.loc["AGGREGATION", :] = display_status.sum()
+ display_status.loc["AGGREGATION", "avg_anno_per_page"] = (
+ display_status.loc["AGGREGATION", "anno_sum"]
+ / display_status.loc["AGGREGATION", "page_num"]
+ )
+
+ return display_status.fillna(0.0), all_record.rename(columns={"index": "sha"})
+
+
+@click.command(context_settings={"help_option_names": ["--help", "-h"]})
+@click.argument("path", type=click.Path(exists=True, file_okay=False))
+@click.option("--output", help="Path to save the export data", type=click.Path())
+def status(
+ path: click.Path,
+ output: click.Path,
+):
+ """
+ Checking the labeling status for some annotation project
+
+ To check the labeling status for some PAWLS annotation folder, use:
+ `pawls status `
+
+ To save the labeling record table for some PAWLS annotation folder, use:
+ `pawls status --output record.csv`
+ """
+
+ labeling_status, all_record = get_labeling_status(path)
+ print(tabulate(labeling_status, headers="keys", tablefmt="psql"))
+
+ if output is not None:
+ all_record.to_csv(output, index=None)
+ print(f"Saved the annotation record table to {output}")
diff --git a/cli/pawls/commands/utils.py b/cli/pawls/commands/utils.py
new file mode 100644
index 00000000..fd2a15fb
--- /dev/null
+++ b/cli/pawls/commands/utils.py
@@ -0,0 +1,252 @@
+import json
+from typing import List, Dict, Iterable
+from glob import glob
+import os
+import uuid
+
+import click
+from pdfminer.pdfparser import PDFParser
+from pdfminer.pdfdocument import PDFDocument
+from pdfminer.pdfpage import PDFPage
+from pdfminer.pdfinterp import resolve1
+
+from pawls.preprocessors.model import load_tokens_from_file
+
+
+DEVELOPMENT_USER = "development_user@example.com"
+
+
+def load_json(filename: str):
+ with open(filename, "r") as fp:
+ return json.load(fp)
+
+
+def get_pdf_pages_and_sizes(filename: str):
+ """Ref https://stackoverflow.com/a/47686921"""
+ with open(filename, "rb") as fp:
+ parser = PDFParser(fp)
+ document = PDFDocument(parser)
+ num_pages = resolve1(document.catalog["Pages"])["Count"]
+ page_sizes = [
+ (int(page.mediabox[2]), int(page.mediabox[3]))
+ for page in PDFPage.create_pages(document)
+ ]
+ return num_pages, page_sizes
+
+
+def get_pdf_sha(pdf_file_name: str) -> str:
+ return os.path.basename(pdf_file_name).replace(".pdf", "")
+
+
+class LabelingConfiguration:
+ def __init__(self, config: str):
+ """LabelingConfiguration handles parsing the configuration file.
+
+ Args:
+ config (str): The config file path.
+ """
+
+ self.config = load_json(config)
+
+ @property
+ def categories(self) -> List[str]:
+ """Returns all labeling category names in the config file."""
+ return [l["text"] for l in self.config["labels"]]
+
+ @property
+ def relations(self):
+ raise NotImplementedError
+
+ def get_labels(self) -> Dict[str, Dict]:
+ """Returns a dictionary for category name, label pairs in the config file."""
+ return {l["text"]: l for l in self.config["labels"]}
+
+
+class AnnotationFolder:
+ DEFAULT_PDF_STRUCTURE_NAME = "pdf_structure.json"
+
+ def __init__(self, path, pdf_structure_name=None):
+
+ self.path = path
+ self.pdf_structure_name = pdf_structure_name or self.DEFAULT_PDF_STRUCTURE_NAME
+
+ self.all_pdf_paths = [pdf_path for pdf_path in glob(f"{self.path}/*/*.pdf")]
+ self.all_pdfs = [os.path.basename(pdf_path) for pdf_path in self.all_pdf_paths]
+
+ @property
+ def all_annotators(self) -> List[str]:
+ """Fetch all annotators in the labeling folder,
+ including the default DEVELOPMENT_USER.
+ """
+
+ return [DEVELOPMENT_USER] + [
+ os.path.splitext(e)[0] for e in os.listdir(f"{self.path}/status")
+ ]
+
+ def get_pdf_tokens(self, pdf_name: str) -> str:
+ """Get the pdf tokens for a pdf name by loading from the corresponding pdf_structure file.
+
+ Args:
+ pdf_name (str): the name of the pdf file, e.g., xxx.pdf
+
+ Raises:
+ FileNotFoundError:
+ When the pdf_structure is not found for this pdf_name, raise a FileNotFoundError.
+
+ Returns:
+ str: the pdf_structure file path for this pdf file.
+ """
+
+ sha = get_pdf_sha(pdf_name)
+ pdf_structure_path = f"{self.path}/{sha}/{self.pdf_structure_name}"
+
+ if os.path.exists(pdf_structure_path):
+ return load_tokens_from_file(pdf_structure_path)
+ else:
+ raise FileNotFoundError(
+ f"pdf_structure is not found for {sha}.Did you forget run the following command?\n pawls preprocess {self.path}/{sha}/{pdf_name}"
+ )
+
+ def create_annotation_file(self, pdf_name: str, annotator: str) -> "AnnotationFile":
+ """Create an annotation file for the given pdf name and annotator.
+
+ Returns:
+ AnnotationFile:
+ An AnnotationFile object that used for creating annotations.
+ """
+ sha = get_pdf_sha(pdf_name)
+ annotation_file_path = f"{self.path}/{sha}/{annotator}_annotations.json"
+
+ return AnnotationFile(annotation_file_path)
+
+
+class AnnotationFile:
+ def __init__(self, filepath: str):
+ """Annotation file is used to help creating the annotation
+ files manually.
+
+ Args:
+ filepath (str): the path to store the annotation file.
+ """
+ self.filepath = filepath
+ self.data = {"annotations": [], "relations": []}
+
+ def add_annotation(
+ self,
+ page_index: int,
+ label: Dict[str, str],
+ bounds: Dict[str, int],
+ token_indices: List[int] = [],
+ ):
+ """Add an annotation to the given paper.
+
+ Args:
+ page_index (int):
+ The page index of this annotation.
+ label (Dict[str, str]):
+ The label (text and color) of this annotation.
+ bounds (Dict[str, int]):
+ The bounding box coordinates of the block.
+ token_indices (List[int], optional):
+ A list of the indices of the contained tokens.
+ Defaults to [].
+ """
+ annotation = {
+ "id": str(uuid.uuid4()),
+ "page": page_index,
+ "label": label,
+ "bounds": bounds,
+ "tokens": [
+ {"pageIndex": page_index, "tokenIndex": token_id}
+ for token_id in token_indices
+ ],
+ }
+
+ self.data["annotations"].append(annotation)
+
+ def add_relations(self):
+ raise NotImplementedError()
+
+ def save(self):
+ """Save the annotation file in the designated filepath"""
+ if os.path.exists(self.filepath):
+ while True:
+ overwrite = input(
+ f"Overwrite existing annotations {self.filepath}? [Y/N]\n"
+ ).lower()
+ if overwrite in ["y", "n"]:
+ if overwrite == "n":
+ return None
+ break
+ print("Please enter Y or N.")
+
+ with open(self.filepath, "w") as fp:
+ json.dump(self.data, fp)
+
+
+class AnnotationFiles:
+ def __init__(
+ self, labeling_folder: str, annotator: str, include_unfinished: bool = True
+ ):
+ """AnnotationFiles is an iterator for selected annotation files
+ given the selected annotators and configurations.
+
+ Args:
+ labeling_folder (str):
+ The folder to save the pdf annotation files, e.g.,
+ `./skiff_files/apps/pawls/papers`.
+ annotator (str, optional):
+ The name of the annotator.
+ If not set, then changed to the default user
+ `AnnotationFiles.DEVELOPMENT_USER`.
+ include_unfinished (bool, optional):
+ Whether output unfinished annotations of the given user.
+ Defaults to True.
+ """
+ self.labeling_folder = labeling_folder
+
+ self.annotator = annotator
+ self.include_unfinished = include_unfinished
+
+ if self.include_unfinished:
+ self._files = self.get_all_annotation_files()
+ else:
+ self._files = self.get_finished_annotation_files()
+
+ def get_all_annotation_files(self) -> List[str]:
+ return glob(
+ os.path.join(f"{self.labeling_folder}/*/{self.annotator}_annotations.json")
+ )
+
+ def get_finished_annotation_files(self) -> List[str]:
+
+ user_assignment_file = f"{self.labeling_folder}/status/{self.annotator}.json"
+ if not os.path.exists(user_assignment_file):
+ print(
+ "Warning:",
+ f"The user annotation file does not exist: {user_assignment_file}",
+ )
+ return self.get_all_annotation_files()
+
+ user_assignment = load_json(user_assignment_file)
+ return [
+ f"{self.labeling_folder}/{pdf_sha}/{self.annotator}_annotations.json"
+ for pdf_sha, assignment in user_assignment.items()
+ if (assignment["finished"] and not assignment["junk"])
+ ]
+
+ def __iter__(self) -> Iterable[Dict]:
+
+ for _file in self._files:
+ paper_sha = _file.split("/")[-2]
+ pdf_path = f"{self.labeling_folder}/{paper_sha}/{paper_sha}.pdf"
+
+ yield dict(
+ paper_sha=paper_sha,
+ pdf_path=pdf_path,
+ annotation_path=_file,
+ )
+
+ def __len__(self):
+
+ return len(self._files)
\ No newline at end of file
diff --git a/cli/pawls/preprocessors/__init__.py b/cli/pawls/preprocessors/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/cli/pawls/preprocessors/grobid.py b/cli/pawls/preprocessors/grobid.py
new file mode 100644
index 00000000..6f6e9611
--- /dev/null
+++ b/cli/pawls/preprocessors/grobid.py
@@ -0,0 +1,63 @@
+import json
+from typing import List
+import requests
+
+from pawls.preprocessors.model import Page
+
+
+def fetch_grobid_structure(pdf_file: str, grobid_host: str = "http://localhost:8070"):
+ files = {
+ "input": (pdf_file, open(pdf_file, "rb"), "application/pdf", {"Expires": "0"})
+ }
+ url = "{}/api/processPdfStructure".format(grobid_host)
+ resp = requests.post(url, files=files)
+ if resp.status_code == 200:
+ return json.loads(resp.text)
+ else:
+ raise Exception("Grobid returned status code {}".format(resp.status_code))
+
+
+def parse_annotations(grobid_structure) -> List[Page]:
+ pages = []
+ for grobid_page in grobid_structure["tokens"]["pages"]:
+ tokens = []
+ for token in grobid_page["tokens"]:
+ tokens.append(
+ dict(
+ text=token["text"],
+ x=token["x"],
+ y=token["y"],
+ width=token["width"],
+ height=token["height"],
+ )
+ )
+ page = dict(
+ page=dict(
+ width=grobid_page["page"]["width"],
+ height=grobid_page["page"]["height"],
+ index=grobid_page["page"]["pageNumber"] - 1,
+ ),
+ tokens=tokens,
+ )
+ pages.append(page)
+
+ return pages
+
+def process_grobid(
+ pdf_file: str,
+ grobid_host: str = "http://localhost:8070"
+):
+ """
+ Integration for importing annotations from grobid.
+ Depends on a grobid API built from our fork https://github.com/allenai/grobid.
+ Fetches a PDF by sha, sends it to the Grobid API and returns them.
+
+ pdf_file: str
+ The path to the pdf file to process.
+ grobid_host: str (optional, default="http://localhost:8070")
+ The forked grobid API which we use to produce the annotations.
+ """
+ grobid_structure = fetch_grobid_structure(pdf_file, grobid_host)
+ annotations = parse_annotations(grobid_structure)
+
+ return annotations
diff --git a/cli/pawls/preprocessors/model.py b/cli/pawls/preprocessors/model.py
new file mode 100644
index 00000000..d1e97ed1
--- /dev/null
+++ b/cli/pawls/preprocessors/model.py
@@ -0,0 +1,198 @@
+import json
+from dataclasses import dataclass # enables inheritance
+from typing import NamedTuple, List, Tuple, Dict, Union
+
+
+def union_boxes(boxes: List["Box"]) -> "Box":
+ """Find the outside boundary of the given boxes.
+
+ Args:
+ boxes (List[Box]):
+ A list of Box-like instances
+
+ Returns:
+ Box: the unioned box.
+ """
+ left, top, right, bottom = float("inf"), float("inf"), float("-inf"), float("-inf")
+ for box in boxes:
+ l, t, r, b = box.coordinates
+ left = min(left, l)
+ top = min(top, t)
+ right = max(right, r)
+ bottom = max(bottom, b)
+ return Box(left, top, right - left, bottom - top)
+
+
+@dataclass
+class Box:
+
+ x: float
+ y: float
+ width: float
+ height: float
+
+ @property
+ def center(self) -> Tuple[float, float]:
+ """Return the center of the token box"""
+ return self.x + self.width / 2, self.y + self.height / 2
+
+ @property
+ def coordinates(self) -> Tuple[float, float, float, float, float]:
+ """Returns the left, top, right, bottom coordinates of the box"""
+ return (self.x, self.y, self.x + self.width, self.y + self.height)
+
+ def is_in(self, other: "Box", soft_margin: Dict = None) -> bool:
+ """Determines whether the center of this box is contained
+ inside another box with a soft margin.
+
+ Args:
+ other (Box):
+ The other box object.
+ soft_margin (Dict, optional):
+ Alllowing soft margin of the box boundaries. If set, enlarge
+ the outside box (other) by the coordinates.
+ Defaults to {}.
+ """
+ other = other.copy()
+
+ x, y = self.center
+ if soft_margin is not None:
+ other.pad(**soft_margin)
+ xa, ya, xb, yb = other.coordinates
+
+ return xa <= x <= xb and ya <= y <= yb
+
+ def pad(self, left=0, top=0, bottom=0, right=0):
+ """Change the boundary positions of the box"""
+
+ self.x -= left
+ self.y -= top
+ self.width += left + right
+ self.height += top + bottom
+
+ def copy(self):
+ """Create a copy of the box"""
+ return self.__class__(**vars(self))
+
+ def scale(self, scale_factor: Union[float, Tuple[float, float]]):
+ """Scale the box according to the given scale factor.
+
+ Args:
+ scale_factor (Union[float, Tuple[float, float]]):
+ it can be either a float, indicating the same scale factor
+ for the two axes, or a two-element tuple for x and y axis
+ scaling factor, respectively.
+
+ """
+
+ if isinstance(scale_factor, float):
+ self.x *= scale_factor
+ self.y *= scale_factor
+ self.width *= scale_factor
+ self.height *= scale_factor
+
+ elif isinstance(scale_factor, tuple):
+ scale_x, scale_y = scale_factor
+ self.x *= scale_x
+ self.y *= scale_y
+ self.width *= scale_x
+ self.height *= scale_y
+
+ def as_bounds(self) -> Dict[str, float]:
+ """Convert the box into a the bounds format."""
+ return {
+ "left": self.x,
+ "top": self.y,
+ "right": self.x + self.width,
+ "bottom": self.y + self.height,
+ }
+
+
+@dataclass
+class Token(Box):
+ text: str
+
+
+@dataclass
+class Block(Box):
+ label: str
+
+
+@dataclass
+class PageInfo:
+ width: float
+ height: float
+ index: int
+
+ def scale(self, scale_factor: Union[float, Tuple[float, float]]):
+ """Scale the page box according to the given scale factor
+
+ Args:
+ scale_factor (Union[float, Tuple[float, float]]):
+ it can be either a float, indicating the same scale factor
+ for the two axes, or a two-element tuple for x and y axis
+ scaling factor, respectively.
+ """
+
+ if isinstance(scale_factor, float):
+ self.width *= scale_factor
+ self.height *= scale_factor
+ elif isinstance(scale_factor, tuple):
+ scale_x, scale_y = scale_factor
+ self.width *= scale_x
+ self.height *= scale_y
+
+
+@dataclass
+class Page:
+ page: PageInfo
+ tokens: List[Union[Token, Block]]
+
+ def scale(self, scale_factor: Union[float, Tuple[float, float]]):
+ """Scale the page according to the given scale factor.
+
+ Args:
+ scale_factor (Union[float, Tuple[float, float]]):
+ it can be either a float, indicating the same scale factor
+ for the two axes, or a two-element tuple for x and y axis
+ scaling factor, respectively.
+ """
+ self.page.scale(scale_factor)
+ for token in self.tokens:
+ token.scale(scale_factor)
+
+ def scale_like(self, other: "Page"):
+ """Scale the page based on the other page."""
+
+ scale_x = other.page.width / self.page.width
+ scale_y = other.page.height / self.page.height
+
+ self.scale((scale_x, scale_y))
+
+ def filter_tokens_by(self, box: Box, soft_margin: Dict = None) -> Dict[int, Token]:
+ """Select tokens in the Page that inside the input box"""
+ return {
+ idx: token
+ for idx, token in enumerate(self.tokens)
+ if token.is_in(box, soft_margin)
+ }
+
+
+def load_tokens_from_file(filename: str) -> List[Page]:
+ """Load tokens files into the data model
+
+ Returns:
+ List[Page]:
+ A list of `Page` object for eac page.
+ """
+
+ with open(filename, "r") as fp:
+ source_data = json.load(fp)
+
+ return [
+ Page(
+ page=PageInfo(**page_data["page"]),
+ tokens=[Token(**token) for token in page_data["tokens"]],
+ )
+ for page_data in source_data
+ ]
\ No newline at end of file
diff --git a/cli/pawls/preprocessors/pdfplumber.py b/cli/pawls/preprocessors/pdfplumber.py
new file mode 100644
index 00000000..3b9ae442
--- /dev/null
+++ b/cli/pawls/preprocessors/pdfplumber.py
@@ -0,0 +1,98 @@
+from typing import List
+
+import pandas as pd
+import pdfplumber
+
+from pawls.preprocessors.model import Page, Token
+
+
+class PDFPlumberTokenExtractor:
+
+ @staticmethod
+ def convert_to_pagetoken(row: pd.Series) -> Token:
+ """Convert a row in a DataFrame to pagetoken"""
+ return dict(
+ text=row["text"],
+ x=row["x0"],
+ width=row["width"],
+ y=row["top"],
+ height=row["height"],
+ )
+
+ def extract(self, pdf_path: str) -> List[Page]:
+ """Extracts token text, positions, and style information from a PDF file.
+
+ Args:
+ pdf_path (str): the path to the pdf file.
+ include_lines (bool, optional): Whether to include line tokens. Defaults to False.
+
+ Returns:
+ PdfAnnotations: A `PdfAnnotations` containing all the paper token information.
+ """
+ plumber_pdf_object = pdfplumber.open(pdf_path)
+
+ pages = []
+ for page_id in range(len(plumber_pdf_object.pages)):
+ cur_page = plumber_pdf_object.pages[page_id]
+
+ tokens = self.obtain_word_tokens(cur_page)
+
+ page = dict(
+ page=dict(
+ width=float(cur_page.width),
+ height=float(cur_page.height),
+ index=page_id
+ ),
+ tokens=tokens
+ )
+ pages.append(page)
+
+ return pages
+
+ def obtain_word_tokens(self, cur_page: pdfplumber.page.Page) -> List[Token]:
+ """Obtain all words from the current page.
+ Args:
+ cur_page (pdfplumber.page.Page):
+ the pdfplumber.page.Page object with PDF token information
+
+ Returns:
+ List[PageToken]:
+ A list of page tokens stored in PageToken format.
+ """
+ words = cur_page.extract_words(
+ x_tolerance=1.5,
+ y_tolerance=3,
+ keep_blank_chars=False,
+ use_text_flow=False,
+ horizontal_ltr=True,
+ vertical_ttb=True,
+ extra_attrs=["fontname", "size"],
+ )
+
+ df = pd.DataFrame(words)
+
+ # Avoid boxes outside the page
+ df[["x0", "x1"]] = (
+ df[["x0", "x1"]].clip(lower=0, upper=int(cur_page.width)).astype("float")
+ )
+ df[["top", "bottom"]] = (
+ df[["top", "bottom"]].clip(lower=0, upper=int(cur_page.height)).astype("float")
+ )
+
+ df["height"] = df["bottom"] - df["top"]
+ df["width"] = df["x1"] - df["x0"]
+
+ word_tokens = df.apply(self.convert_to_pagetoken, axis=1).tolist()
+ return word_tokens
+
+
+def process_pdfplumber(pdf_file: str):
+ """
+ Integration for importing annotations from pdfplumber.
+ pdf_file: str
+ The path to the pdf file to process.
+ """
+ pdf_extractors = PDFPlumberTokenExtractor()
+ annotations = pdf_extractors.extract(pdf_file)
+
+ return annotations
diff --git a/cli/readme.md b/cli/readme.md
new file mode 100644
index 00000000..ee447ab8
--- /dev/null
+++ b/cli/readme.md
@@ -0,0 +1,62 @@
+## PAWLS CLI
+
+The PAWLS CLI helps manage annotation tasks based on PDFs.
+
+### Installation
+
+1. Install dependencies
+
+ ```bash
+ cd pawls/cli
+ python setup.py install
+ ```
+
+2. Install poppler, the PDF renderer, which is used to export the annotations into a COCO-format Dataset by converting the PDF pages to images.
+Please follow the [instructions here](https://github.com/Belval/pdf2image#windows).
+
+### Usage
+
+1. Download PDFs based on s into the (e.g., `skiff_files/apps/pawls/papers` ). If you work at AI2, see the internal usage script for doing this [here](../../scripts/ai2-internal). Otherwise, pdfs are expected to be in a directory structure with a single pdf per folder, where each folder's name is a unique id corresponding to that pdf. For example:
+```
+ top_level/
+ ├───pdf1/
+ │ └───pdf1.pdf
+ └───pdf2/
+ └───pdf2.pdf
+```
+By default, pawls will use the name of the containing directory to refer to the pdf in the ui.
+
+2. Process the token information for each PDF document with the given PDF preprocessor `grobid/pdfplumber`. *Note: to use the grobid preprocessor, you need to run `docker-compose up` in a separate shell, because grobid needs to be running as a service.*:
+ ```bash
+ pawls preprocess grobid skiff_files/apps/pawls/papers
+ ```
+At this point, you will be able to view a UI by running `docker-compose up` at the root of the repository and navigating to `localhost:8080`.
+
+3. Assign annotation tasks (s) to specific users :
+ ```bash
+ pawls assign ./skiff_files/apps/pawls/papers
+ ```
+ Optionally at this stage, you can provide a `--name-file` argument to `pawls assign`,
+ which allows you to specify a name for a given pdf (for example the title of a paper).
+ This file should be a json file containing `sha:name` mappings.
+4. (optional) Create pre-annotations for the PDFs based on some model predictions `anno.json`:
+ ```bash
+ pawls preannotate anno.json -u
+ ```
+ You could find an example for generating the pre-annotations in `scripts/generate_pdf_layouts.py`.
+5. Export the annotated dataset to the COCO format:
+
+ 1. Export all annotations of a project of the default annotator (development_user):
+ ```bash
+ pawls export
+ ```
+
+ 2. Export only finished annotations of from a given annotator, e.g. markn:
+ ```bash
+ pawls export -u markn
+ ```
+
+ 3. Export all annotations of from a given annotator:
+ ```bash
+ pawls export -u markn --all
+ ```
\ No newline at end of file
diff --git a/cli/requirements.txt b/cli/requirements.txt
new file mode 100644
index 00000000..7fe94c1f
--- /dev/null
+++ b/cli/requirements.txt
@@ -0,0 +1,21 @@
+click>=6.7
+tqdm
+pdfminer
+pdf2image
+pandas
+tabulate
+
+# S3 access
+boto3
+
+# Grobid integration
+requests
+
+# used for testing
+pytest
+
+# Used for pdf-token extraction
+pdfplumber
+
+# Used for calculating scores
+pycocotools
\ No newline at end of file
diff --git a/cli/setup.py b/cli/setup.py
new file mode 100644
index 00000000..c3908359
--- /dev/null
+++ b/cli/setup.py
@@ -0,0 +1,37 @@
+from setuptools import setup, find_packages
+
+with open("readme.md", "r") as readme_file:
+ readme = readme_file.read()
+
+
+setup(
+ name="pawls",
+ version="0.0.1",
+ description="PAWLS (PDF Annotation with Labels and Structure)",
+ packages=find_packages(),
+ long_description=readme,
+ url="http://github.com/allenai/pawls",
+ author="Mark Neumann",
+ author_email="markn@allenai.org",
+ keywords="",
+ classifiers=[
+ "Development Status :: 3 - Alpha",
+ "Programming Language :: Python :: 3.6",
+ "License :: OSI Approved :: Apache Software License",
+ "Intended Audience :: Developers",
+ "Intended Audience :: Science/Research",
+ "Topic :: Scientific/Engineering :: Artificial Intelligence",
+ ],
+ license="Apache 2.0",
+ install_requires=[
+ "click>=6.7",
+ "requests",
+ "boto3",
+ "tqdm",
+ "pdf2image==1.14.0",
+ "pdfminer"
+ ],
+ python_requires=">=3.6",
+ entry_points={"console_scripts": ["pawls=pawls.__main__:pawls_cli"]},
+ zip_safe=False,
+)
diff --git a/cli/test/__init__.py b/cli/test/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/cli/test/assign_test.py b/cli/test/assign_test.py
new file mode 100644
index 00000000..f91b4d8c
--- /dev/null
+++ b/cli/test/assign_test.py
@@ -0,0 +1,96 @@
+import os
+import unittest
+import tempfile
+import json
+import shutil
+
+from click.testing import CliRunner
+
+from pawls.commands import assign
+
+
+class TestAssign(unittest.TestCase):
+ def test_assign_annotator(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+ result = runner.invoke(assign, [tempdir, "mark@example.org"])
+ assert result.exit_code == 0
+ assert os.path.exists(os.path.join(tempdir, "status", "mark@example.org.json"))
+
+ def test_assign_annotator_with_bad_name(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+ result = runner.invoke(assign, [tempdir, "mark!!! ABC"])
+ assert result.exit_code == 2
+ assert "Provided annotator was not a valid email." in result.output
+
+ def test_assign_unfetched_pdfs(self):
+ runner = CliRunner()
+ sha = "34f25a8704614163c4095b3ee2fc969b60de4698"
+ with tempfile.TemporaryDirectory() as tempdir:
+ result = runner.invoke(assign, [tempdir, "mark@example.org", sha])
+ assert result.exit_code == 2
+ assert "Found shas which are not present" in result.output
+
+ def test_assign_pdfs(self):
+ runner = CliRunner()
+ sha = "34f25a8704614163c4095b3ee2fc969b60de4698"
+ with tempfile.TemporaryDirectory() as tempdir:
+
+ # Copy the fixture in, as though it was there already.
+ sub_temp_dir = os.path.join(tempdir, "pdfs")
+ shutil.copytree(f"test/fixtures/pawls/", sub_temp_dir)
+ result = runner.invoke(assign, [sub_temp_dir, "mark@example.org", sha])
+ assert result.exit_code == 0
+ status_path = os.path.join(sub_temp_dir, "status", "mark@example.org.json")
+
+ annotator_json = json.load(open(status_path))
+ assert annotator_json == {
+ sha: {
+ "sha": sha,
+ "name": sha,
+ "annotations": 0,
+ "relations": 0,
+ "finished": False,
+ "junk": False,
+ "comments": "",
+ "completedAt": None,
+ }
+ }
+
+ def test_assign_pdfs_with_name_file(self):
+ runner = CliRunner()
+ sha = "34f25a8704614163c4095b3ee2fc969b60de4698"
+ with tempfile.TemporaryDirectory() as tempdir:
+
+ # Copy the fixture in, as though it was there already.
+ sub_temp_dir = os.path.join(tempdir, "pdfs")
+ shutil.copytree(f"test/fixtures/pawls/", sub_temp_dir)
+ # This time we pass a file containing the name mapping,
+ # so we should find the name in the resulting status.
+ result = runner.invoke(
+ assign,
+ [
+ sub_temp_dir,
+ "mark@example.org",
+ sha,
+ "--name-file",
+ "test/fixtures/pawls/name_mapping.json",
+ ],
+ )
+ assert result.exit_code == 0
+ status_path = os.path.join(sub_temp_dir, "status", "mark@example.org.json")
+
+ annotator_json = json.load(open(status_path))
+ assert annotator_json == {
+ sha: {
+ "sha": sha,
+ "name": "Dropout: a simple way to prevent neural networks from overfitting",
+ "annotations": 0,
+ "relations": 0,
+ "finished": False,
+ "junk": False,
+ "comments": "",
+ "completedAt": None,
+ }
+ }
diff --git a/cli/test/export_test.py b/cli/test/export_test.py
new file mode 100644
index 00000000..df27d622
--- /dev/null
+++ b/cli/test/export_test.py
@@ -0,0 +1,228 @@
+import os
+import unittest
+import tempfile
+import json
+
+import pandas as pd
+from click.testing import CliRunner
+
+from pawls.commands import export
+
+"""
+Details of annotations in test/fixtures/pawls/
+
+There are three task:
+0. 3febb2bed8865945e7fddc99efd791887bb7e14f
+1. 34f25a8704614163c4095b3ee2fc969b60de4698
+2. 553c58a05e25f794d24e8db8c2b8fdb9603e6a29
+
+* Development user has annotations for all images
+* markn is assigned to task 0 and task 1
+* markn finishes task 1 but not task 0
+* shannons is assigned to task 1 and task 2
+* shannons finishes neither of the tasks
+* shannons does not have any annotations for task 1
+"""
+
+
+def _load_json(filename: str):
+ with open(filename, "r") as fp:
+ return json.load(fp)
+
+
+class TestExportCOCO(unittest.TestCase):
+ def setUp(self):
+ super().setUp()
+ self.TEST_ANNO_DIR = "test/fixtures/pawls/"
+ self.TEST_CONFIG_FILE = "test/fixtures/configuration.json"
+ self.TEST_SELECTED_CATEGORY = "Figure Text"
+ self.PDF_SHAS = [
+ "3febb2bed8865945e7fddc99efd791887bb7e14f",
+ "34f25a8704614163c4095b3ee2fc969b60de4698",
+ "553c58a05e25f794d24e8db8c2b8fdb9603e6a29",
+ ]
+ self.USERS = ["markn@example.com", "shannons@example.com"]
+ self.DEFAULT_USER = "development_user@example.com"
+
+ def test_export_annotation_from_all_annotators(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+ result = runner.invoke(
+ export, [self.TEST_ANNO_DIR, self.TEST_CONFIG_FILE, tempdir, "coco"]
+ )
+ assert result.exit_code == 0
+
+ assert os.path.exists(os.path.join(tempdir, self.USERS[0] + ".json"))
+ assert os.path.exists(os.path.join(tempdir, self.USERS[1] + ".json"))
+ assert os.path.exists(os.path.join(tempdir, self.DEFAULT_USER + ".json"))
+ assert os.path.exists(os.path.join(tempdir, "images"))
+
+ def test_export_annotation_from_multiple_annotators(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+ result = runner.invoke(
+ export,
+ [
+ self.TEST_ANNO_DIR,
+ self.TEST_CONFIG_FILE,
+ tempdir,
+ "coco",
+ "-u",
+ self.USERS[0],
+ "-u",
+ self.USERS[1],
+ ],
+ )
+ assert result.exit_code == 0
+
+ assert os.path.exists(os.path.join(tempdir, self.USERS[0] + ".json"))
+ assert os.path.exists(os.path.join(tempdir, self.USERS[1] + ".json"))
+ assert not os.path.exists(
+ os.path.join(tempdir, self.DEFAULT_USER + ".json")
+ )
+ assert os.path.exists(os.path.join(tempdir, "images"))
+
+ def test_export_annotation_with_all_annotators_annotations(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+ result = runner.invoke(
+ export,
+ [
+ self.TEST_ANNO_DIR,
+ self.TEST_CONFIG_FILE,
+ tempdir,
+ "coco",
+ "-u",
+ self.USERS[0],
+ "--include-unfinished",
+ ],
+ )
+ assert result.exit_code == 0
+
+ anno = _load_json(os.path.join(tempdir, f"{self.USERS[0]}.json"))
+ paper_shas = [ele["paper_sha"] for ele in anno["papers"]]
+
+ assert self.PDF_SHAS[1] in paper_shas
+ assert self.PDF_SHAS[0] in paper_shas
+
+ def test_export_annotation_with_missing_annotation_file(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+ result = runner.invoke(
+ export,
+ [
+ self.TEST_ANNO_DIR,
+ self.TEST_CONFIG_FILE,
+ tempdir,
+ "coco",
+ "-u",
+ self.USERS[1],
+ "--include-unfinished",
+ ],
+ )
+ assert result.exit_code == 0
+
+ anno_file = _load_json(os.path.join(tempdir, f"{self.USERS[1]}.json"))
+ paper_sha_map = {ele["id"]: ele["paper_sha"] for ele in anno_file["papers"]}
+ image_paper_map = {
+ ele["id"]: ele["paper_id"] for ele in anno_file["images"]
+ }
+ all_paper_shas = [
+ paper_sha_map[image_paper_map[anno["image_id"]]]
+ for anno in anno_file["annotations"]
+ ]
+
+ assert self.PDF_SHAS[2] in all_paper_shas
+ assert self.PDF_SHAS[1] not in all_paper_shas
+
+ def test_export_annotation_with_specific_category(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+ result = runner.invoke(
+ export,
+ [
+ self.TEST_ANNO_DIR,
+ self.TEST_CONFIG_FILE,
+ tempdir,
+ "coco",
+ "-u",
+ self.USERS[0],
+ "-c",
+ self.TEST_SELECTED_CATEGORY,
+ "--include-unfinished",
+ ],
+ )
+ assert result.exit_code == 0
+
+ anno = _load_json(os.path.join(tempdir, f"{self.USERS[0]}.json"))
+
+ assert len(anno["categories"]) == 1
+ assert anno["categories"][0]['name'] == self.TEST_SELECTED_CATEGORY
+
+class TestExportToken(TestExportCOCO):
+ def test_export_annotation_from_all_annotators(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+ saved_path = f"{tempdir}/annotations.csv"
+ result = runner.invoke(
+ export, [self.TEST_ANNO_DIR, self.TEST_CONFIG_FILE, saved_path, "token"]
+ )
+ assert result.exit_code == 0
+ assert os.path.exists(saved_path)
+
+ df = pd.read_csv(saved_path)
+ for annotator in self.USERS + [self.DEFAULT_USER]:
+ assert annotator in df.columns
+
+ def test_export_annotation_from_multiple_annotators(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+ saved_path = f"{tempdir}/annotations.csv"
+ result = runner.invoke(
+ export,
+ [
+ self.TEST_ANNO_DIR,
+ self.TEST_CONFIG_FILE,
+ saved_path,
+ "token",
+ "-u",
+ self.USERS[0],
+ "-u",
+ self.USERS[1],
+ ],
+ )
+ assert result.exit_code == 0
+ assert os.path.exists(saved_path)
+
+ df = pd.read_csv(saved_path)
+ for annotator in self.USERS:
+ assert annotator in df.columns
+
+ def test_export_annotation_with_specific_category(self):
+
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+ saved_path = f"{tempdir}/annotations.csv"
+ result = runner.invoke(
+ export,
+ [
+ self.TEST_ANNO_DIR,
+ self.TEST_CONFIG_FILE,
+ saved_path,
+ "token",
+ "-u",
+ self.USERS[0],
+ "-c",
+ self.TEST_SELECTED_CATEGORY
+ ]
+ )
+ assert result.exit_code == 0
+
+ df = pd.read_csv(saved_path)
+
+ all_exported_labels = df[self.USERS[0]].dropna().unique()
+ assert len(all_exported_labels) == 1
+ assert self.TEST_SELECTED_CATEGORY in all_exported_labels[0]
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/cli/test/fixtures/anno.json b/cli/test/fixtures/anno.json
new file mode 100644
index 00000000..a49feb5f
--- /dev/null
+++ b/cli/test/fixtures/anno.json
@@ -0,0 +1 @@
+{"34f25a8704614163c4095b3ee2fc969b60de4698.pdf": [{"page": {"height": 2200, "width": 1700, "index": 0}, "blocks": [[304.4071960449219, 983.696533203125, 1086.7208557128906, 425.0955810546875, "Paragraph"], [263.661865234375, 277.7256164550781, 1167.4327392578125, 95.8544921875, "Title"], [254.3060760498047, 1509.86474609375, 248.92869567871094, 40.469482421875, "Title"], [301.1861877441406, 1424.7691650390625, 973.2588806152344, 29.2496337890625, "Paragraph"], [779.6166381835938, 927.0107421875, 141.23779296875, 35.60723876953125, "Title"], [246.0847625732422, 1573.96923828125, 1214.5631866455078, 349.32421875, "Paragraph"], [253.85147094726562, 430.34661865234375, 252.85003662109375, 28.61700439453125, "Paragraph"], [250.72097778320312, 828.7415161132812, 287.9336853027344, 31.045166015625, "Paragraph"], [1132.7159423828125, 432.1298522949219, 317.59716796875, 25.765625, "Paragraph"], [1115.92822265625, 470.7099304199219, 330.2562255859375, 28.31591796875, "Paragraph"], [1103.119384765625, 427.45819091796875, 347.607666015625, 182.48101806640625, "Paragraph"], [249.61415100097656, 619.4379272460938, 456.6027069091797, 139.534912109375, "Paragraph"], [257.3518371582031, 1586.2822265625, 1194.3912048339844, 28.0361328125, "Paragraph"], [249.4932098388672, 466.64874267578125, 253.4733123779297, 33.150604248046875, "Paragraph"], [247.40536499023438, 581.2354736328125, 343.2471618652344, 30.5, "Paragraph"], [252.739990234375, 1625.4619140625, 1201.5587158203125, 26.0260009765625, "Paragraph"], [1147.1180419921875, 510.5416564941406, 297.58740234375, 25.902496337890625, "Paragraph"]]}, {"page": {"height": 2200, "width": 1700, "index": 1}, "blocks": [[407.94305419921875, 237.52598571777344, 866.1150512695312, 470.8246612548828, "Figure"], [240.72796630859375, 1579.490478515625, 1214.1228637695312, 384.177978515625, "Paragraph"], [259.76971435546875, 730.9132080078125, 1198.3634643554688, 97.400634765625, "Paragraph"], [242.04164123535156, 1117.4981689453125, 1211.0069427490234, 444.34228515625, "Paragraph"], [242.8494110107422, 908.4478759765625, 1218.1410675048828, 187.4547119140625, "Paragraph"], [291.11126708984375, 1594.3514404296875, 1160.2783813476562, 26.7987060546875, "Paragraph"], [291.1940002441406, 1125.6890869140625, 1157.5503845214844, 26.4952392578125, "Paragraph"], [247.4609375, 1820.71044921875, 1203.7481689453125, 26.491943359375, "Paragraph"], [255.13800048828125, 959.9430541992188, 1187.4738159179688, 26.91046142578125, "Paragraph"], [255.80886840820312, 922.5955810546875, 1192.2190856933594, 26.49310302734375, "Paragraph"], [259.77386474609375, 1465.7420654296875, 1185.5353393554688, 26.0477294921875, "Paragraph"], [256.8460693359375, 1429.583984375, 1192.2890625, 25.6339111328125, "Paragraph"], [248.71449279785156, 1669.8092041015625, 1218.3140716552734, 25.21435546875, "Paragraph"]]}, {"page": {"height": 2200, "width": 1700, "index": 2}, "blocks": [[239.04869079589844, 1019.4091796875, 1209.9354400634766, 453.4656982421875, "Paragraph"], [312.39410400390625, 229.8026123046875, 998.3040161132812, 280.151123046875, "Figure"], [242.19558715820312, 715.2112426757812, 1212.1612243652344, 300.15460205078125, "Paragraph"], [244.28616333007812, 1656.9310302734375, 1208.5232849121094, 304.8026123046875, "Paragraph"], [249.11001586914062, 1472.42431640625, 1210.2438659667969, 182.5247802734375, "Paragraph"], [343.6832275390625, 533.3347778320312, 1098.5809326171875, 133.21649169921875, "Paragraph"], [301.4703063964844, 536.64794921875, 1144.3846740722656, 132.60247802734375, "ListItem"], [246.86575317382812, 802.7789306640625, 1203.0116882324219, 26.06475830078125, "Paragraph"], [284.2173767089844, 1028.026123046875, 1169.4703674316406, 26.40625, "Paragraph"], [249.42330932617188, 1105.4908447265625, 1202.7772521972656, 25.3375244140625, "Paragraph"], [251.68838500976562, 1707.7322998046875, 1212.9600524902344, 25.3546142578125, "Paragraph"], [283.4576721191406, 1668.940673828125, 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diff --git a/cli/test/fixtures/pawls/34f25a8704614163c4095b3ee2fc969b60de4698/pdf_structure.json b/cli/test/fixtures/pawls/34f25a8704614163c4095b3ee2fc969b60de4698/pdf_structure.json
new file mode 100644
index 00000000..3b256c72
--- /dev/null
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6.608}, {"text": "to", "x": 429.806, "y": 359.53, "width": 6.223, "height": 6.608}, {"text": "determine", "x": 439.057, "y": 359.53, "width": 30.338, "height": 6.608}, {"text": "the", "x": 472.423, "y": 359.53, "width": 9.723, "height": 6.608}, {"text": "prevalence", "x": 485.175, "y": 359.53, "width": 32.277, "height": 6.608}, {"text": "of", "x": 520.48, "y": 359.53, "width": 6.223, "height": 6.608}, {"text": "se", "x": 529.731, "y": 359.53, "width": 5.9639999999999995, "height": 6.608}, {"text": "-", "x": 535.695, "y": 359.53, "width": 2.9819999999999998, "height": 6.608}, {"text": "lected", "x": 363.174, "y": 368.03, "width": 17.885, "height": 6.608}, {"text": "diseases", "x": 384.088, "y": 368.03, "width": 24.115, "height": 6.608}, {"text": "(", "x": 411.231, "y": 368.03, "width": 3.2676000000000003, "height": 6.608}, {"text": "198", "x": 414.4986, "y": 368.03, "width": 9.8028, "height": 6.608}, {"text": ")", "x": 424.3014, "y": 368.03, "width": 3.2676000000000003, "height": 6.608}, {"text": "*", "x": 45.1761, "y": 387.182, "width": 4.17, "height": 7.08}, {"text": "Systems", "x": 51.2211, "y": 387.4, "width": 22.9725, "height": 6.9975}, {"text": "whose", "x": 76.6311, "y": 387.4, "width": 17.85, "height": 6.9975}, {"text": "evaluations", "x": 96.9186, "y": 387.4, "width": 32.1975, "height": 6.9975}, {"text": "have", "x": 131.554, "y": 387.4, "width": 13.1025, "height": 6.9975}, {"text": "been", "x": 147.094, "y": 387.4, "width": 13.6275, "height": 6.9975}, {"text": "published", "x": 163.159, "y": 387.4, "width": 28.245, "height": 6.9975}, {"text": "in", "x": 193.841, "y": 387.4, "width": 5.865, "height": 6.9975}, {"text": "peer", "x": 202.144, "y": 387.4, "width": 12.297692307692309, "height": 6.9975}, {"text": "-", "x": 214.4416923076923, "y": 387.4, "width": 3.074423076923077, "height": 6.9975}, {"text": "reviewed", "x": 217.5161153846154, "y": 387.4, "width": 24.595384615384617, "height": 6.9975}, {"text": "reports", "x": 244.549, "y": 387.4, "width": 19.2478125, "height": 6.9975}, {"text": ".", "x": 263.7968125, "y": 387.4, "width": 2.7496875, "height": 6.9975}, {"text": " ", "x": 45.1761, "y": 395.182, "width": 2.085, "height": 7.08}, {"text": "\u2020", "x": 47.2611, "y": 395.182, "width": 2.085, "height": 7.08}, {"text": "The", "x": 51.2211, "y": 395.4, "width": 11.7825, "height": 6.9975}, {"text": "number", "x": 65.4411, "y": 395.4, "width": 22.89, "height": 6.9975}, {"text": "of", "x": 90.7686, "y": 395.4, "width": 5.82, "height": 6.9975}, {"text": "references", "x": 99.0261, "y": 395.4, "width": 28.395, "height": 6.9975}, {"text": "often", "x": 129.859, "y": 395.4, "width": 15.03, "height": 6.9975}, {"text": "exceeds", "x": 147.326, "y": 395.4, "width": 21.39, "height": 6.9975}, {"text": "the", "x": 171.154, "y": 395.4, "width": 9.135, "height": 6.9975}, {"text": "number", "x": 182.726, "y": 395.4, "width": 22.89, "height": 6.9975}, {"text": "of", "x": 208.054, "y": 395.4, "width": 5.82, "height": 6.9975}, {"text": "systems", "x": 216.311, "y": 395.4, "width": 21.7275, "height": 6.9975}, {"text": "because", "x": 240.476, "y": 395.4, "width": 21.9825, "height": 6.9975}, {"text": "systems", "x": 264.896, "y": 395.4, "width": 21.7275, "height": 6.9975}, {"text": "were", "x": 289.061, "y": 395.4, "width": 13.38, "height": 6.9975}, {"text": "often", "x": 304.879, "y": 395.4, "width": 15.03, "height": 6.9975}, {"text": "described", "x": 322.346, "y": 395.4, "width": 27.165, "height": 6.9975}, {"text": "in", "x": 351.949, "y": 395.4, "width": 5.865, "height": 6.9975}, {"text": "several", "x": 360.251, "y": 395.4, "width": 18.975, "height": 6.9975}, {"text": "reports", "x": 381.664, "y": 395.4, "width": 19.2478125, "height": 6.9975}, {"text": ".", "x": 400.9118125, "y": 395.4, "width": 2.7496875, "height": 6.9975}, {"text": "W", "x": 45.1761, "y": 745.43, "width": 4.30325, "height": 6.244}, {"text": "-", "x": 49.47935, "y": 745.43, "width": 4.30325, "height": 6.244}, {"text": "46", "x": 53.7826, "y": 745.43, "width": 8.6065, "height": 6.244}, {"text": "1", "x": 66.2386, "y": 745.731, "width": 3.5, "height": 6.531}, {"text": "June", "x": 72.7668, "y": 745.731, "width": 12.446, "height": 6.531}, {"text": "2004", "x": 88.241, "y": 745.731, "width": 14.0, "height": 6.531}, {"text": "Annals", "x": 106.236, "y": 745.731, "width": 18.529, "height": 6.531}, {"text": "of", "x": 126.515, "y": 745.731, "width": 5.432, "height": 6.531}, {"text": "Internal", "x": 133.697, "y": 745.731, "width": 21.518, "height": 6.531}, {"text": "Medicine", "x": 156.965, "y": 745.731, "width": 25.564, "height": 6.531}, {"text": "Volume", "x": 186.494, "y": 745.731, "width": 21.728, "height": 6.531}, {"text": "140", "x": 211.251, "y": 745.731, "width": 10.5, "height": 6.531}, {"text": "\u2022", "x": 223.501, "y": 745.731, "width": 2.716, "height": 6.531}, {"text": "Number", "x": 227.967, "y": 745.731, "width": 23.17, "height": 6.531}, {"text": "11", "x": 254.165, "y": 745.731, "width": 7.0, "height": 6.531}, {"text": "www", "x": 509.175, "y": 745.318, "width": 8.58, "height": 6.244}, {"text": ".", "x": 517.755, "y": 745.318, "width": 2.86, "height": 6.244}, {"text": "annals", "x": 520.615, "y": 745.318, "width": 17.16, "height": 6.244}, {"text": ".", "x": 537.775, "y": 745.318, "width": 2.86, "height": 6.244}, {"text": "org", "x": 540.635, "y": 745.318, "width": 8.58, "height": 6.244}]}]
\ No newline at end of file
diff --git a/cli/test/fixtures/pawls/553c58a05e25f794d24e8db8c2b8fdb9603e6a29/shannons@example.com_annotations.json b/cli/test/fixtures/pawls/553c58a05e25f794d24e8db8c2b8fdb9603e6a29/shannons@example.com_annotations.json
new file mode 100644
index 00000000..a4e7912b
--- /dev/null
+++ b/cli/test/fixtures/pawls/553c58a05e25f794d24e8db8c2b8fdb9603e6a29/shannons@example.com_annotations.json
@@ -0,0 +1 @@
+{"annotations": [{"id": "92a5ef67-cc23-41c3-bd41-33ecdfb328be", "page": 0, "label": {"text": "Figure Text", "color": "#70DDBA"}, "bounds": {"left": 40.175899505615234, "top": 186.57899475097656, "right": 290.20291328430176, "bottom": 226.92900562286377}, "tokens": [{"pageIndex": 0, "tokenIndex": 106}, {"pageIndex": 0, "tokenIndex": 107}, {"pageIndex": 0, "tokenIndex": 108}, {"pageIndex": 0, "tokenIndex": 109}, {"pageIndex": 0, "tokenIndex": 110}, {"pageIndex": 0, "tokenIndex": 111}, {"pageIndex": 0, "tokenIndex": 112}, {"pageIndex": 0, "tokenIndex": 113}, {"pageIndex": 0, "tokenIndex": 114}, {"pageIndex": 0, "tokenIndex": 115}, {"pageIndex": 0, "tokenIndex": 116}, {"pageIndex": 0, "tokenIndex": 117}, {"pageIndex": 0, "tokenIndex": 118}, {"pageIndex": 0, "tokenIndex": 119}, {"pageIndex": 0, "tokenIndex": 120}, {"pageIndex": 0, "tokenIndex": 121}, {"pageIndex": 0, "tokenIndex": 122}, {"pageIndex": 0, "tokenIndex": 123}, {"pageIndex": 0, "tokenIndex": 124}, {"pageIndex": 0, "tokenIndex": 126}, {"pageIndex": 0, "tokenIndex": 127}]}, {"id": "837a8fe3-c540-4b83-bf50-5c2bdecb4613", "page": 0, "label": {"text": "Figure Text", "color": "#70DDBA"}, "bounds": {"left": 304.1759948730469, "top": 291.8059997558594, "right": 554.2253875732422, "bottom": 375.8599901199341}, "tokens": [{"pageIndex": 0, "tokenIndex": 385}, {"pageIndex": 0, "tokenIndex": 386}, {"pageIndex": 0, "tokenIndex": 387}, {"pageIndex": 0, "tokenIndex": 388}, {"pageIndex": 0, "tokenIndex": 389}, {"pageIndex": 0, "tokenIndex": 390}, {"pageIndex": 0, "tokenIndex": 391}, {"pageIndex": 0, "tokenIndex": 392}, {"pageIndex": 0, "tokenIndex": 393}, {"pageIndex": 0, "tokenIndex": 394}, {"pageIndex": 0, "tokenIndex": 395}, {"pageIndex": 0, "tokenIndex": 396}, {"pageIndex": 0, "tokenIndex": 397}, {"pageIndex": 0, "tokenIndex": 398}, {"pageIndex": 0, "tokenIndex": 399}, {"pageIndex": 0, "tokenIndex": 400}, {"pageIndex": 0, "tokenIndex": 401}, {"pageIndex": 0, "tokenIndex": 402}, {"pageIndex": 0, "tokenIndex": 403}, {"pageIndex": 0, "tokenIndex": 404}, {"pageIndex": 0, "tokenIndex": 405}, {"pageIndex": 0, "tokenIndex": 406}, {"pageIndex": 0, "tokenIndex": 407}, {"pageIndex": 0, "tokenIndex": 408}, {"pageIndex": 0, "tokenIndex": 409}, {"pageIndex": 0, "tokenIndex": 410}, {"pageIndex": 0, "tokenIndex": 411}, {"pageIndex": 0, "tokenIndex": 412}, {"pageIndex": 0, "tokenIndex": 413}, {"pageIndex": 0, "tokenIndex": 414}, {"pageIndex": 0, "tokenIndex": 415}, {"pageIndex": 0, "tokenIndex": 416}, {"pageIndex": 0, "tokenIndex": 417}, {"pageIndex": 0, "tokenIndex": 418}, {"pageIndex": 0, "tokenIndex": 419}, {"pageIndex": 0, "tokenIndex": 420}, {"pageIndex": 0, "tokenIndex": 421}, {"pageIndex": 0, "tokenIndex": 422}, {"pageIndex": 0, "tokenIndex": 423}, {"pageIndex": 0, "tokenIndex": 424}, {"pageIndex": 0, "tokenIndex": 425}, {"pageIndex": 0, "tokenIndex": 426}, {"pageIndex": 0, "tokenIndex": 427}, {"pageIndex": 0, "tokenIndex": 428}, {"pageIndex": 0, "tokenIndex": 429}, {"pageIndex": 0, "tokenIndex": 430}, {"pageIndex": 0, "tokenIndex": 431}, {"pageIndex": 0, "tokenIndex": 432}, {"pageIndex": 0, "tokenIndex": 433}, {"pageIndex": 0, "tokenIndex": 434}, {"pageIndex": 0, "tokenIndex": 435}, {"pageIndex": 0, "tokenIndex": 436}, {"pageIndex": 0, "tokenIndex": 437}, {"pageIndex": 0, "tokenIndex": 438}, {"pageIndex": 0, "tokenIndex": 439}, {"pageIndex": 0, "tokenIndex": 440}, {"pageIndex": 0, "tokenIndex": 441}, {"pageIndex": 0, "tokenIndex": 442}, {"pageIndex": 0, "tokenIndex": 443}, {"pageIndex": 0, "tokenIndex": 444}, {"pageIndex": 0, "tokenIndex": 445}, {"pageIndex": 0, "tokenIndex": 446}]}], "relations": []}
\ No newline at end of file
diff --git a/cli/test/fixtures/pawls/name_mapping.json b/cli/test/fixtures/pawls/name_mapping.json
new file mode 100644
index 00000000..9c41e4fc
--- /dev/null
+++ b/cli/test/fixtures/pawls/name_mapping.json
@@ -0,0 +1 @@
+{"553c58a05e25f794d24e8db8c2b8fdb9603e6a29": "Systematic Review: Surveillance Systems for Early Detection of Bioterrorism-Related Diseases", "3febb2bed8865945e7fddc99efd791887bb7e14f": "Deep contextualized word representations", "34f25a8704614163c4095b3ee2fc969b60de4698": "Dropout: a simple way to prevent neural networks from overfitting"}
\ No newline at end of file
diff --git a/cli/test/fixtures/pawls/status/markn@example.com.json b/cli/test/fixtures/pawls/status/markn@example.com.json
new file mode 100644
index 00000000..c54025a9
--- /dev/null
+++ b/cli/test/fixtures/pawls/status/markn@example.com.json
@@ -0,0 +1,2 @@
+{"3febb2bed8865945e7fddc99efd791887bb7e14f": {"annotations": 0, "relations": 0, "finished": false, "junk": false, "comments": "", "completed_at": null},
+ "34f25a8704614163c4095b3ee2fc969b60de4698": {"annotations": 0, "relations": 0, "finished": true, "junk": false, "comments": "", "completed_at": null}}
\ No newline at end of file
diff --git a/cli/test/fixtures/pawls/status/shannons@example.com.json b/cli/test/fixtures/pawls/status/shannons@example.com.json
new file mode 100644
index 00000000..a1fa021e
--- /dev/null
+++ b/cli/test/fixtures/pawls/status/shannons@example.com.json
@@ -0,0 +1,2 @@
+{"34f25a8704614163c4095b3ee2fc969b60de4698": {"annotations": 0, "relations": 0, "finished": false, "junk": false, "comments": "", "completed_at": null},
+ "553c58a05e25f794d24e8db8c2b8fdb9603e6a29": {"annotations": 0, "relations": 0, "finished": false, "junk": false, "comments": "", "completed_at": null}}
\ No newline at end of file
diff --git a/cli/test/metric_test.py b/cli/test/metric_test.py
new file mode 100644
index 00000000..083d99cc
--- /dev/null
+++ b/cli/test/metric_test.py
@@ -0,0 +1,82 @@
+import os
+import unittest
+import tempfile
+import json
+
+import pandas as pd
+from click.testing import CliRunner
+
+from pawls.commands import metric
+
+"""
+Details of annotations in test/fixtures/pawls/
+
+There are three task:
+0. 3febb2bed8865945e7fddc99efd791887bb7e14f
+1. 34f25a8704614163c4095b3ee2fc969b60de4698
+2. 553c58a05e25f794d24e8db8c2b8fdb9603e6a29
+
+* Development user has annotations for all images
+* markn is assigned to task 0 and task 1
+* markn finishes task 1 but not task 0
+* shannons is assigned to task 1 and task 2
+* shannons finishes neither of the tasks
+* shannons does not have any annotations for task 1
+"""
+
+
+class TestMetric(unittest.TestCase):
+ def setUp(self):
+ super().setUp()
+ self.TEST_ANNO_DIR = "test/fixtures/pawls/"
+ self.TEST_CONFIG_FILE = "test/fixtures/configuration.json"
+ self.TEST_SELECTED_CATEGORY = "Figure Text"
+ self.PDF_SHAS = [
+ "3febb2bed8865945e7fddc99efd791887bb7e14f",
+ "34f25a8704614163c4095b3ee2fc969b60de4698",
+ "553c58a05e25f794d24e8db8c2b8fdb9603e6a29",
+ ]
+ self.USERS = ["markn@example.com", "shannons@example.com"]
+ self.DEFAULT_USER = "development_user@example.com"
+ self.TEXTUAL_CATEGORIES = (
+ "Figure Text,Section Header,Method,Task,Paragraph,Title"
+ )
+ self.NON_TEXTUAL_CATEGORIES = "Figure,Table,ListItem"
+
+ def test_export_annotation_from_all_annotators(self):
+ runner = CliRunner()
+ result = runner.invoke(
+ metric,
+ [
+ self.TEST_ANNO_DIR,
+ self.TEST_CONFIG_FILE,
+ "--textual-categories",
+ self.TEXTUAL_CATEGORIES,
+ "--non-textual-categories",
+ self.NON_TEXTUAL_CATEGORIES,
+ ],
+ )
+ assert result.exit_code == 0
+
+ def test_export_annotation_from_specific_annotators(self):
+ runner = CliRunner()
+ result = runner.invoke(
+ metric,
+ [
+ self.TEST_ANNO_DIR,
+ self.TEST_CONFIG_FILE,
+ "-u",
+ self.USERS[0],
+ "-u",
+ self.USERS[1],
+ "--textual-categories",
+ self.TEXTUAL_CATEGORIES,
+ "--non-textual-categories",
+ self.NON_TEXTUAL_CATEGORIES,
+ ],
+ )
+ assert result.exit_code == 0
+
+
+if __name__ == "__main__":
+ unittest.main()
\ No newline at end of file
diff --git a/cli/test/preannotate_test.py b/cli/test/preannotate_test.py
new file mode 100644
index 00000000..984512c4
--- /dev/null
+++ b/cli/test/preannotate_test.py
@@ -0,0 +1,103 @@
+import os
+import shutil
+import unittest
+import tempfile
+import json
+from glob import glob
+
+from click.testing import CliRunner
+
+from pawls.commands import preannotate
+from pawls.commands import preprocess
+
+
+def _load_json(filename: str):
+ with open(filename, "r") as fp:
+ return json.load(fp)
+
+
+class TestPreannotate(unittest.TestCase):
+ def setUp(self):
+ super().setUp()
+
+ self.TEST_ANNO_DIR = "test/fixtures/pawls/"
+ self.TEST_CONFIG_FILE = "test/fixtures/configuration.json"
+ self.TEST_ANNO_FILE = "test/fixtures/anno.json"
+
+ self.PDF_SHAS = [
+ "3febb2bed8865945e7fddc99efd791887bb7e14f",
+ "34f25a8704614163c4095b3ee2fc969b60de4698",
+ "553c58a05e25f794d24e8db8c2b8fdb9603e6a29",
+ ]
+ self.USERS = ["markn@example.com", "shannons@example.com"]
+ self.DEFAULT_USER = "development_user@example.com"
+
+ def copy_and_remove_existing_annotations(self, sub_temp_dir):
+
+ shutil.copytree(self.TEST_ANNO_DIR, sub_temp_dir)
+ for anno_file in glob(f"{sub_temp_dir}/*/*_annotations.json"):
+ os.remove(anno_file)
+
+ def test_add_annotation(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+
+ sub_temp_dir = os.path.join(tempdir, "pawls")
+ self.copy_and_remove_existing_annotations(sub_temp_dir)
+
+ result = runner.invoke(
+ preannotate,
+ [sub_temp_dir, self.TEST_CONFIG_FILE, self.TEST_ANNO_FILE]
+ + sum([["-u", user] for user in self.USERS], []),
+ )
+
+ assert result.exit_code == 0
+
+ for pdf_sha in self.PDF_SHAS:
+ for user in self.USERS:
+ assert os.path.exists(
+ os.path.join(sub_temp_dir, pdf_sha, f"{user}_annotations.json")
+ )
+
+ def test_add_annotation_without_preprocess(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+
+ sub_temp_dir = os.path.join(tempdir, "pawls")
+ self.copy_and_remove_existing_annotations(sub_temp_dir)
+
+ for pdf_sha in self.PDF_SHAS:
+ os.remove(f"{sub_temp_dir}/{pdf_sha}/pdf_structure.json")
+
+ result = runner.invoke(
+ preannotate,
+ [
+ sub_temp_dir,
+ self.TEST_CONFIG_FILE,
+ self.TEST_ANNO_FILE,
+ "-u",
+ self.USERS[0],
+ ],
+ )
+
+ assert result.exit_code == 1 # It should raise an exception
+
+ def test_add_annotation_all(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+
+ sub_temp_dir = os.path.join(tempdir, "pawls")
+ self.copy_and_remove_existing_annotations(sub_temp_dir)
+
+ result = runner.invoke(
+ preannotate,
+ [sub_temp_dir, self.TEST_CONFIG_FILE, self.TEST_ANNO_FILE, "-a"],
+ )
+
+ assert result.exit_code == 0 # It should raise an exception
+
+ for pdf_sha in self.PDF_SHAS:
+ for user in self.USERS:
+ assert os.path.exists(
+ os.path.join(sub_temp_dir, pdf_sha, f"{user}_annotations.json")
+ )
\ No newline at end of file
diff --git a/cli/test/status_test.py b/cli/test/status_test.py
new file mode 100644
index 00000000..f0b358a5
--- /dev/null
+++ b/cli/test/status_test.py
@@ -0,0 +1,61 @@
+import os
+import unittest
+import tempfile
+import json
+
+from click.testing import CliRunner
+
+from pawls.commands import status
+
+"""
+Details of annotations in test/fixtures/pawls/
+
+There are three task:
+0. 3febb2bed8865945e7fddc99efd791887bb7e14f
+1. 34f25a8704614163c4095b3ee2fc969b60de4698
+2. 553c58a05e25f794d24e8db8c2b8fdb9603e6a29
+
+* Development user has annotations for all images
+* markn is assigned to task 0 and task 1
+* markn finishes task 1 but not task 0
+* shannons is assigned to task 1 and task 2
+* shannons finishes neither of the tasks
+* shannons does not have any annotations for task 1
+"""
+
+
+def _load_json(filename: str):
+ with open(filename, "r") as fp:
+ return json.load(fp)
+
+
+class TestStatus(unittest.TestCase):
+ def setUp(self):
+ super().setUp()
+ self.TEST_ANNO_DIR = "test/fixtures/pawls/"
+ self.TEST_CONFIG_FILE = "test/fixtures/configuration.json"
+ self.PDF_SHAS = [
+ "3febb2bed8865945e7fddc99efd791887bb7e14f",
+ "34f25a8704614163c4095b3ee2fc969b60de4698",
+ "553c58a05e25f794d24e8db8c2b8fdb9603e6a29",
+ ]
+ self.USERS = ["markn", "shannons"]
+ self.DEFAULT_USER = "development_user"
+
+ def test_status(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+ result = runner.invoke(status, [self.TEST_ANNO_DIR])
+ assert result.exit_code == 0
+
+ def test_save(self):
+ runner = CliRunner()
+ with tempfile.TemporaryDirectory() as tempdir:
+ result = runner.invoke(
+ status, [self.TEST_ANNO_DIR, "--output", f"{tempdir}/test.csv"]
+ )
+ assert result.exit_code == 0
+
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/docker-compose.yaml b/docker-compose.yaml
new file mode 100644
index 00000000..9bea5853
--- /dev/null
+++ b/docker-compose.yaml
@@ -0,0 +1,48 @@
+version: '3'
+services:
+ sonar:
+ build: ./sonar
+ depends_on:
+ - api
+ - ui
+ - proxy
+ api:
+ build:
+ context: ./api
+ volumes:
+ - ./api:/usr/local/src/skiff/app/api
+ - ./skiff_files/apps/pawls:/skiff_files/apps/pawls
+ - ./api/config/allowed_users_local_development.txt:/users/allowed.txt
+ environment:
+ # This ensures that errors are printed as they occur, which
+ # makes debugging easier.
+ - PYTHONUNBUFFERED=1
+ - LOG_LEVEL=DEBUG
+ command: ["main:app", "--host", "0.0.0.0", "--reload"]
+ ui:
+ build: ./ui
+ # We can't mount the entire UI directory, since JavaScript dependencies
+ # (`node_modules`) live at that location.
+ volumes:
+ - ./ui/src:/usr/local/src/skiff/app/ui/src
+ - ./ui/public:/usr/local/src/skiff/app/ui/public
+ - ./ui/package.json:/usr/local/src/skiff/app/ui/package.json
+ - ./ui/tsconfig.json:/usr/local/src/skiff/app/ui/tsconfig.json
+ - ./ui/yarn.lock:/usr/local/src/skiff/app/ui/yarn.lock
+ proxy:
+ build: ./proxy
+ ports:
+ - 8080:80
+ depends_on:
+ - api
+ - ui
+
+ # This service is optional!
+ # It is not used during deployment, but simply runs a grobid service
+ # which the CLI can use for pre-processing PDFs, using grobid to provide
+ # the detailed token information.
+ grobid:
+ image: 'allenai/grobid:0.5.6-pdf-structure'
+ ports:
+ - '8070:8070'
+ - '8071:8071'
diff --git a/proxy/Dockerfile b/proxy/Dockerfile
new file mode 100644
index 00000000..503139ac
--- /dev/null
+++ b/proxy/Dockerfile
@@ -0,0 +1,8 @@
+FROM nginx:1.17.0-alpine
+
+COPY nginx.conf /etc/nginx/nginx.conf
+
+ARG CONF_FILE=local.conf
+COPY $CONF_FILE /etc/nginx/conf.d/default.conf
+
+COPY dist /var/www/skiff/ui/
diff --git a/proxy/dist/.gitignore b/proxy/dist/.gitignore
new file mode 100644
index 00000000..7a7ff6d2
--- /dev/null
+++ b/proxy/dist/.gitignore
@@ -0,0 +1,6 @@
+# Ignore everything in this directory
+*
+# Except this file.
+!.gitignore
+# This allows us to commit an empty directory into the repository,
+# which we need to ensure the build doesn't fail
diff --git a/proxy/local.conf b/proxy/local.conf
new file mode 100644
index 00000000..f02d77f2
--- /dev/null
+++ b/proxy/local.conf
@@ -0,0 +1,36 @@
+server {
+ listen [::]:80;
+ listen 80;
+
+ charset utf-8;
+
+ expires -1;
+
+ # For local development, it will appear that this is the logged-in user.
+ proxy_set_header X-Auth-Request-User 12345;
+ proxy_set_header X-Auth-Request-Email development_user@example.com;
+
+ location / {
+ proxy_pass http://ui:3000;
+ }
+
+ location /openapi.json {
+ proxy_pass http://api:8000;
+ }
+
+ location /docs {
+ proxy_pass http://api:8000;
+ }
+
+ # This allows a websocket connection between the client and the webpack development server,
+ # so that webpack can reload the developer's browser after they make changes.
+ location /sockjs-node {
+ proxy_pass http://ui:3000;
+ proxy_set_header Upgrade $http_upgrade;
+ proxy_set_header Connection "Upgrade";
+ }
+
+ location /api {
+ proxy_pass http://api:8000;
+ }
+}
diff --git a/proxy/nginx.conf b/proxy/nginx.conf
new file mode 100644
index 00000000..e1f75ab8
--- /dev/null
+++ b/proxy/nginx.conf
@@ -0,0 +1,45 @@
+user nginx;
+worker_processes auto;
+
+error_log stderr warn;
+pid /var/run/nginx.pid;
+
+events {
+ worker_connections 1024;
+}
+
+http {
+ # Accept the X-Forwarded-For header from all clients. By default NGINX discards the
+ # header.
+ set_real_ip_from 0.0.0.0/0;
+ real_ip_header X-Forwarded-For;
+
+ include /etc/nginx/mime.types;
+ default_type application/octet-stream;
+
+ sendfile on;
+ keepalive_timeout 65;
+
+ gzip on;
+
+ server_tokens off;
+
+ log_format json escape=json '{'
+ '"time": "$time_iso8601",'
+ '"request_method": "$request_method",'
+ '"request_uri": "$scheme://$host$request_uri",'
+ '"status": $status,'
+ '"request_length": $request_length,'
+ '"body_bytes_sent": $body_bytes_sent,'
+ '"user_agent": "$http_user_agent",'
+ '"ip": "$remote_addr",'
+ '"realip": "$realip_remote_addr",'
+ '"referer": "$http_referer",'
+ '"host": "$host",'
+ '"scheme": "$scheme",'
+ '"forwarded-for": "$http_x_forwarded_for"'
+ '}';
+ access_log /dev/stdout json;
+
+ include /etc/nginx/conf.d/*;
+}
diff --git a/proxy/prod.conf b/proxy/prod.conf
new file mode 100644
index 00000000..cb50ea68
--- /dev/null
+++ b/proxy/prod.conf
@@ -0,0 +1,19 @@
+server {
+ listen [::]:80;
+ listen 80;
+
+ charset utf-8;
+
+ expires -1;
+
+ root /var/www/skiff/ui/build;
+ index index.html;
+
+ location / {
+ try_files $uri /index.html;
+ }
+
+ location /api {
+ proxy_pass http://localhost:8000;
+ }
+}
diff --git a/scripts/ai2-internal/README.md b/scripts/ai2-internal/README.md
new file mode 100644
index 00000000..5c5e4693
--- /dev/null
+++ b/scripts/ai2-internal/README.md
@@ -0,0 +1,10 @@
+
+#### Fetching PDFs (AI2 Internal)
+
+The `fetch_pdfs.py` script fetches S2 pdfs for use by PAWLS using paper shas.
+This requires access to private S2 pdf buckets, so is for internal use only. However,
+you can use PAWLS without using this script if you already have pdfs locally! This is simply
+a utility for S2 Researchers.
+
+The `fetch_pdfs.py` script requires a AWS key with read access to the S2 Pdf buckets. Your `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY` which you use for day-to-day AI2 work will
+be suitable - just make sure they are set as environment variables when running the PAWLS CLI.
diff --git a/scripts/ai2-internal/fetch_pdfs.py b/scripts/ai2-internal/fetch_pdfs.py
new file mode 100644
index 00000000..5ecedbbb
--- /dev/null
+++ b/scripts/ai2-internal/fetch_pdfs.py
@@ -0,0 +1,184 @@
+import os
+import sys
+from typing import List, Callable, Set, Dict, Tuple, Optional
+
+import click
+import boto3
+import botocore
+import json
+import requests
+
+
+@click.command(context_settings={"help_option_names": ["--help", "-h"]})
+@click.argument("path", type=str, default="./")
+@click.argument("shas", type=str, nargs=-1, required=True)
+@click.option(
+ "--sha-file",
+ "-f",
+ type=click.Path(exists=True, file_okay=True, dir_okay=False),
+ help="A path to a file containing pdf shas.",
+)
+def fetch(path: click.Path, shas: Tuple[str], sha_file: click.Path = None):
+ """
+ Download pdfs from Semantic Scholar with metadata
+ to a particular location.
+ Pdfs can be specified by passing a list of pdf shas, or
+ by passing a file containing pdf shas, one per id.
+
+ Download a pdf and associated metadata to the current directory:
+
+ `pawls fetch ./ 34f25a8704614163c4095b3ee2fc969b60de4698`
+
+ """
+ shas = list(shas)
+ if sha_file is not None:
+ extra_ids = [x.strip("\n") for x in open(sha_file, "r")]
+ shas.extend(extra_ids)
+
+ result = bulk_fetch_pdfs_for_s2_ids(
+ shas, path, pdf_path_func=_per_dir_pdf_download,
+ )
+
+ metadata_failed = []
+ name_mapping = {}
+ for sha in result["success"]:
+ title = get_paper_title(sha)
+ if title is None:
+ metadata_failed.append(sha)
+ else:
+ name_mapping[sha] = title
+
+ with open(os.path.join(path, "pdf_metadata.json"), "w+") as f:
+ json.dump(name_mapping, f)
+
+ okay = True
+ if metadata_failed:
+ print(
+ f"Successfully saved {len(metadata_failed)} pdfs, but failed to find metadata for:"
+ )
+ for sha in metadata_failed:
+ print(sha)
+ print()
+ okay = False
+
+ not_found = result["not_found"]
+ if not_found:
+ print(f"Failed to find pdfs for the following ({len(not_found)}) shas:")
+ for sha in not_found:
+ print(sha)
+ print()
+ okay = False
+
+ error = result["error"]
+ if error:
+ print(f"Error fetching pdfs for the following ({len(error)}) shas:")
+ for sha in error:
+ print(sha)
+ print()
+ okay = False
+
+ if not okay:
+ sys.exit(1)
+
+ print(
+ f"Successfully saved {len(result['success']) - len(metadata_failed)} pdfs and metadata to {str(path)}"
+ )
+
+
+# settings for S3 buckets
+S3_BUCKET_PDFS = {"default": "ai2-s2-pdfs", "private": "ai2-s2-pdfs-private"}
+
+
+def _per_dir_pdf_download(target_dir: str, sha: str):
+ os.makedirs(os.path.join(target_dir, sha), exist_ok=True)
+ return os.path.join(target_dir, sha, f"{sha}.pdf")
+
+
+def _default_pdf_path(target_dir: str, sha: str):
+ return os.path.join(target_dir, f"{sha}.pdf")
+
+
+def bulk_fetch_pdfs_for_s2_ids(
+ s2_ids: List[str],
+ target_dir: str,
+ pdf_path_func: Callable[[str, str], str] = _default_pdf_path,
+) -> Dict[str, Set[str]]:
+ """
+ s2_ids: List[str]
+ A list of s2 pdf shas to download.
+
+ target_dir: str,
+ The directory to download them to.
+ pdf_path_func: str, optional (default = None)
+ A callable function taking 2 parameters: target_dir and sha,
+ which returns a string used as the path to download an individual pdf.
+
+ Note:
+ User is responsible for figuring out whether the PDF already exists before
+ calling this function. By default, will perform overwriting.
+
+ Returns
+ A dict containing "error", "not_found" and "success" keys,
+ listing pdf shas that were either not found or errored when fetching.
+ """
+
+ os.makedirs(target_dir, exist_ok=True)
+ s3 = boto3.resource("s3")
+ default_bucket = s3.Bucket(S3_BUCKET_PDFS["default"])
+ private_bucket = s3.Bucket(S3_BUCKET_PDFS["private"])
+
+ not_found = set()
+ error = set()
+ success = set()
+ for s2_id in s2_ids:
+ try:
+ default_bucket.download_file(
+ os.path.join(s2_id[:4], f"{s2_id[4:]}.pdf"),
+ pdf_path_func(target_dir, s2_id),
+ )
+ success.add(s2_id)
+
+ except botocore.exceptions.ClientError as e:
+ if e.response["Error"]["Code"] == "404":
+ try:
+ private_bucket.download_file(
+ os.path.join(s2_id[:4], f"{s2_id[4:]}.pdf"),
+ pdf_path_func(target_dir, s2_id),
+ )
+ success.add(s2_id)
+
+ except botocore.exceptions.ClientError as e:
+ if e.response["Error"]["Code"] == "404":
+ not_found.add(s2_id)
+ else:
+ error.add(s2_id)
+ else:
+ error.add(s2_id)
+
+ return {"error": error, "not_found": not_found, "success": success}
+
+
+S2_API = "https://www.semanticscholar.org/api/1/paper/"
+
+
+def get_paper_title(paper_sha: str) -> Optional[str]:
+ """
+ Fetch a small metadata blob from S2.
+
+ paper_sha: str, required
+ The paper id to search for.
+
+ returns:
+ str if the paper is found, otherwise None.
+ """
+
+ response = requests.get(S2_API + paper_sha)
+ if response.ok:
+ data = response.json()
+ return data["paper"]["title"]["text"]
+ else:
+ return None
+
+if __name__ == "__main__":
+
+ fetch()
diff --git a/scripts/generate_pdf_layouts.py b/scripts/generate_pdf_layouts.py
new file mode 100644
index 00000000..82e950b3
--- /dev/null
+++ b/scripts/generate_pdf_layouts.py
@@ -0,0 +1,90 @@
+"""This script uses a Mask RCNN model for generating block layouts
+for PDF files in the `annotation_folder`.
+
+Usage:
+ python generate_pdf_layouts.py --annotation_folder ../skiff_files/apps/pawls/papers --save_path anno.json
+
+The generated `anno.json` file could be used for `pawls preannotate`.
+
+You might need to install the layout-parser library for running the Mask RCNN
+layout detection model. See https://github.com/layout-Parser/layout-parser#installation
+"""
+
+import os
+import json
+from glob import glob
+from typing import List, Union, Dict, Dict, Any
+
+from tqdm import tqdm
+import layoutparser as lp
+from pdf2image import convert_from_path
+
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--annotation_folder", type=str)
+parser.add_argument("--save_path", type=str)
+
+
+def run_prediction(pdf_filename: str) -> List:
+ """It returns a list of block predictions.
+ Each item corresponds to a page in the pdf file:
+ [
+ {
+ "page": {"height": xx, "width": xx, "index": 0},
+ "blocks": [
+ [x, y, w, h, "category"]
+ ]
+ },
+ ....
+ ]
+ """
+ pdf_data = []
+ paper_images = convert_from_path(pdf_filename)
+
+ for idx, image in enumerate(paper_images):
+ width, height = image.size
+
+ layout = model.detect(image)
+
+ block_data = [
+ block.coordinates[:2]
+ + (
+ block.width,
+ block.height,
+ block.type,
+ )
+ for block in layout
+ ]
+
+ pdf_data.append(
+ {
+ "page": {"height": height, "width": width, "index": idx},
+ "blocks": block_data,
+ }
+ )
+
+ return pdf_data
+
+
+if __name__ == "__main__":
+ args = parser.parse_args()
+
+ model = lp.Detectron2LayoutModel(
+ "lp://PubLayNet/mask_rcnn_X_101_32x8d_FPN_3x/config",
+ extra_config=[
+ "MODEL.ROI_HEADS.SCORE_THRESH_TEST",
+ 0.55,
+ "MODEL.ROI_HEADS.NMS_THRESH_TEST",
+ 0.4,
+ ],
+ label_map={0: "Paragraph", 1: "Title", 2: "ListItem", 3: "Table", 4: "Figure"},
+ )
+
+ all_pdf_data = {}
+ for pdf_filename in tqdm(sorted(glob(f"{args.annotation_folder}/*/*.pdf"))):
+ pdf_data = run_prediction(pdf_filename)
+ all_pdf_data[os.path.basename(pdf_filename)] = pdf_data
+
+ with open(args.save_path, "w") as fp:
+ json.dump(all_pdf_data, fp)
\ No newline at end of file
diff --git a/skiff.json b/skiff.json
new file mode 100644
index 00000000..91e121c8
--- /dev/null
+++ b/skiff.json
@@ -0,0 +1,5 @@
+{
+ "appName": "pawls",
+ "contact": "s2-research",
+ "team": "s2"
+}
diff --git a/skiff_files/.git_keep b/skiff_files/.git_keep
new file mode 100644
index 00000000..e69de29b
diff --git a/sonar/Dockerfile b/sonar/Dockerfile
new file mode 100644
index 00000000..378e0487
--- /dev/null
+++ b/sonar/Dockerfile
@@ -0,0 +1,14 @@
+FROM python:3.7.2-alpine3.9
+
+WORKDIR /usr/src/local/skiff/sonar
+
+COPY requirements.txt .
+
+RUN pip install -r requirements.txt
+
+COPY ping.py .
+
+ENV PYTHONUNBUFFERED=1
+
+ENTRYPOINT [ "python" ]
+CMD [ "ping.py" ]
diff --git a/sonar/ping.py b/sonar/ping.py
new file mode 100644
index 00000000..3ac27759
--- /dev/null
+++ b/sonar/ping.py
@@ -0,0 +1,72 @@
+# -*- coding: utf-8 -*-
+
+import requests
+import time
+import math
+import signal
+
+def is_ok(url: str) -> bool:
+ """
+ Returns True if the provided URL responds with a 2XX when fetched via
+ a HTTP GET request.
+ """
+ try:
+ resp = requests.get(url)
+ except:
+ return False
+ return True if math.floor(resp.status_code / 100) == 2 else False
+
+def scan():
+ """
+ Broadcasts the availability of the proxy's HTTP server once both the
+ API and UI are ready for traffic.
+
+ This script exists solely to ease confusion locally, as both Flask and
+ the HTTP server bundled with `create-react-app` output logs telling the
+ user about the ports they're bound to (even though they're inaccessible).
+ """
+
+ print("")
+ print("⚓️ Ahoy!")
+ print("")
+ print(
+ "Your application is starting and will be available at " +
+ "http://localhost:8080 when it's ready."
+ )
+ print("")
+
+ # If someone tries to cancel the `docker-compose up` invocation, docker
+ # will send a SIGTERM to the program. We need to handle this and set a
+ # value that allows the loop to be broken.
+ term = False
+ def handle_interrupt(signal_number, stack_frame):
+ global term
+ term = True
+ signal.signal(signal.SIGTERM, handle_interrupt)
+
+ last_check = time.perf_counter()
+ is_api_live = False
+ is_ui_live = False
+ while (is_api_live != True or is_ui_live != True):
+ if term is True:
+ break
+ # We don't use `time.sleep()`, as that'd prevent us from being able
+ # to break the loop quickly in the event of a SIGTERM.
+ now = time.perf_counter()
+ if (now - last_check >= 5):
+ last_check = now
+ if not is_api_live:
+ is_api_live = is_ok("http://api:8000")
+ if not is_ui_live:
+ is_ui_live = is_ok("http://ui:3000")
+ if is_api_live and is_ui_live:
+ print("")
+ print("✨ Your local environment is ready:")
+ print("")
+ print(" http://localhost:8080")
+ print("")
+ print("⛵️ Smooth sailing!")
+ print("")
+
+if __name__ == "__main__":
+ scan()
diff --git a/sonar/requirements.txt b/sonar/requirements.txt
new file mode 100644
index 00000000..ef724edd
--- /dev/null
+++ b/sonar/requirements.txt
@@ -0,0 +1,5 @@
+certifi==2019.6.16
+chardet==3.0.4
+idna==2.8
+requests==2.22.0
+urllib3==1.25.3
diff --git a/ui/.dockerignore b/ui/.dockerignore
new file mode 100644
index 00000000..62638b5a
--- /dev/null
+++ b/ui/.dockerignore
@@ -0,0 +1,15 @@
+# git artifacts
+.gitignore
+.git/
+
+# Docker artifacts
+Dockerfile
+
+# UI dependencies
+node_modules/
+
+# UI build output
+build/
+
+# UI package manager debug output
+*.log
diff --git a/ui/.env b/ui/.env
new file mode 100644
index 00000000..b903d310
--- /dev/null
+++ b/ui/.env
@@ -0,0 +1,7 @@
+# To fix https://github.com/advisories/GHSA-h9rv-jmmf-4pgx we have to
+# update `webpack` to a version `react-scripts` doesn't explicitly support.
+# This disables a mechanism in `react-scripts` that breaks the build when
+# a version mismatch like this occurs. When `react-scripts` version `3.3.1`
+# is released we can remove this (and the associated "resolution" in
+# `package.json`.
+SKIP_PREFLIGHT_CHECK=true
diff --git a/ui/Dockerfile b/ui/Dockerfile
new file mode 100644
index 00000000..cfccc2ba
--- /dev/null
+++ b/ui/Dockerfile
@@ -0,0 +1,32 @@
+# NOTE: This Dockerfile is only used in development. It provides a runtime
+# environment where the JavaScript build process can run. In production the
+# files built by this process are served from disk, while in development a HTTP
+# server that's distributed with the UI build tools is used.
+FROM node:10.15.2
+
+# Setup a spot for our code
+WORKDIR /usr/local/src/skiff/app/ui
+
+# Install dependencies
+COPY package.json yarn.lock ./
+RUN yarn install
+
+# Copy in the source code
+COPY . .
+
+# This tells build scripts and libraries that we're in development, so they
+# can include stuff that's helpful for debugging even if it's a tad slower.
+ARG NODE_ENV=development
+ENV NODE_ENV $NODE_ENV
+ARG BABEL_ENV=development
+ENV BABEL_ENV $BABEL_ENV
+
+# Build the UI
+RUN yarn build
+
+# Tell `react-scripts` that it's not supposed to open a browser for us, since
+# it's not running on the host machine.
+ENV BROWSER none
+
+ENTRYPOINT [ "yarn" ]
+CMD [ "start" ]
diff --git a/ui/package.json b/ui/package.json
new file mode 100644
index 00000000..bf491243
--- /dev/null
+++ b/ui/package.json
@@ -0,0 +1,120 @@
+{
+ "name": "ui",
+ "version": "0.1.1",
+ "author": "reviz@allenai.org",
+ "license": "UNLICENSED",
+ "private": true,
+ "scripts": {
+ "lint": "eslint '**/*.{js,ts,tsx,json}' && echo 'Lint complete.'",
+ "lint:fix": "eslint '**/*.{js,ts,tsx,json}' --fix && echo 'Lint --fix complete.'",
+ "start": "react-scripts start",
+ "build": "react-scripts build",
+ "test": "react-scripts test"
+ },
+ "eslintConfig": {
+ "env": {
+ "browser": true,
+ "es6": true
+ },
+ "extends": [
+ "standard",
+ "plugin:prettier/recommended"
+ ],
+ "globals": {
+ "Atomics": "readonly",
+ "SharedArrayBuffer": "readonly"
+ },
+ "parser": "@typescript-eslint/parser",
+ "parserOptions": {
+ "ecmaFeatures": {
+ "jsx": true
+ },
+ "ecmaVersion": 2018,
+ "sourceType": "module"
+ },
+ "plugins": [
+ "react",
+ "@typescript-eslint",
+ "prettier"
+ ],
+ "rules": {
+ "prettier/prettier": [
+ "error",
+ {
+ "printWidth": 100,
+ "tabWidth": 4,
+ "singleQuote": true,
+ "jsxBracketSameLine": true,
+ "jsxSingleQuote": false
+ }
+ ],
+ "react/jsx-uses-react": 1,
+ "react/jsx-uses-vars": 1,
+ "no-unused-vars": "off",
+ "@typescript-eslint/no-unused-vars": [
+ "error",
+ {
+ "vars": "all",
+ "args": "after-used",
+ "ignoreRestSiblings": false,
+ "argsIgnorePattern": "^_"
+ }
+ ],
+ "no-useless-constructor": "off",
+ "@typescript-eslint/no-useless-constructor": "error"
+ }
+ },
+ "eslintIgnore": [
+ "build/",
+ "*.log",
+ "package.json",
+ "tsconfig.json"
+ ],
+ "browserslist": [
+ ">0.2%",
+ "not dead",
+ "not ie <= 11",
+ "not op_mini all"
+ ],
+ "dependencies": {
+ "@allenai/varnish": "^1.0.0",
+ "@allenai/varnish-react-router": "^1.0.4",
+ "@ant-design/icons": "^4.2.1",
+ "@types/jest": "^24.0.9",
+ "@types/node": "11.9.5",
+ "@types/pdfjs-dist": "^2.1.5",
+ "@types/react": "^16.9.0",
+ "@types/react-dom": "^16.9.0",
+ "@types/react-router-dom": "^5.0.1",
+ "@types/styled-components": "^5.1.2",
+ "@types/uuid": "^8.3.0",
+ "@typescript-eslint/eslint-plugin": "^2.3.1",
+ "@typescript-eslint/parser": "^2.3.1",
+ "axios": "^0.18.0",
+ "eslint": "^6.7.2",
+ "eslint-config-prettier": "^6.3.0",
+ "eslint-config-standard": "^14.1.0",
+ "eslint-plugin-import": "^2.18.2",
+ "eslint-plugin-node": "^10.0.0",
+ "eslint-plugin-prettier": "^3.1.1",
+ "eslint-plugin-promise": "^4.2.1",
+ "eslint-plugin-react": "^7.14.3",
+ "eslint-plugin-standard": "^4.0.1",
+ "pdfjs-dist": "^2.4.456",
+ "prettier": "^1.18.2",
+ "react": "^16.9.0",
+ "react-dom": "^16.9.0",
+ "react-is": "^16.13.1",
+ "react-router-dom": "^5.0.1",
+ "react-scripts": "3.4.0",
+ "react-test-renderer": "^16.8.3",
+ "styled-components": "^5.1.1",
+ "typescript": "3.6.3",
+ "uuid": "^8.3.0",
+ "webpack": "^4.41.3"
+ },
+ "resolutions": {
+ "react-scripts/webpack": "^4.41.3"
+ },
+ "devDependencies": {}
+}
diff --git a/ui/public/favicon.ico b/ui/public/favicon.ico
new file mode 100644
index 00000000..bdebc298
Binary files /dev/null and b/ui/public/favicon.ico differ
diff --git a/ui/public/index.html b/ui/public/index.html
new file mode 100644
index 00000000..4467b195
--- /dev/null
+++ b/ui/public/index.html
@@ -0,0 +1,13 @@
+
+
+
+
+
+ PAWLS
+
+
+ You need to enable JavaScript to run this app.
+
+
+
+
diff --git a/ui/public/robots.txt b/ui/public/robots.txt
new file mode 100644
index 00000000..848da249
--- /dev/null
+++ b/ui/public/robots.txt
@@ -0,0 +1,12 @@
+# If you would like to obtain the data behind this application, please contact
+# The Allen Institute for AI: http://www.allenai.org
+#
+# Our models can require a significant amount of computation, and crawling the
+# API comes at our expense and can even cause applications to fail.
+# We will block unauthorized crawling of the API.
+#
+# Privacy Policy: https://allenai.org/privacy-policy.html
+# Terms and Conditions of use: https://allenai.org/terms.html
+
+User-agent: *
+Disallow: /api
diff --git a/ui/src/App.tsx b/ui/src/App.tsx
new file mode 100644
index 00000000..f727582e
--- /dev/null
+++ b/ui/src/App.tsx
@@ -0,0 +1,59 @@
+/**
+ * This is the top-level component that defines your UI application.
+ *
+ * This is an appropriate spot for application wide components and configuration,
+ * stuff like application chrome (headers, footers, navigation, etc), routing
+ * (what urls go where), etc.
+ *
+ * @see https://github.com/reactjs/react-router-tutorial/tree/master/lessons
+ */
+
+import React, { useEffect, useState } from 'react';
+import { createGlobalStyle } from 'styled-components';
+import { Spin } from "@allenai/varnish";
+import { BrowserRouter, Route, Redirect} from 'react-router-dom';
+
+import { PDFPage } from './pages';
+import { CenterOnPage } from "./components"
+import { getAllocatedPaperStatus } from "./api"
+
+
+const RedirectToFirstPaper = () => {
+ const [sha, setSha] = useState();
+ useEffect(() => {
+ getAllocatedPaperStatus().then((allocation) => {
+ const first = allocation.papers[0]
+ setSha(first.sha)
+ })
+ },[])
+
+ return sha ? : (
+
+
+
+ )
+}
+
+
+const App = () => {
+ return (
+ <>
+
+
+
+
+
+ >
+ )
+ };
+
+
+// Setup the viewport so it takes up all available real-estate.
+const GlobalStyles = createGlobalStyle`
+ html, body, #root {
+ display: flex;
+ flex-grow: 1;
+ }
+`;
+
+export default App;
diff --git a/ui/src/api/index.ts b/ui/src/api/index.ts
new file mode 100644
index 00000000..9aae8ced
--- /dev/null
+++ b/ui/src/api/index.ts
@@ -0,0 +1,111 @@
+import axios from 'axios';
+import { Annotation, RelationGroup, PdfAnnotations } from '../context';
+
+export interface Token {
+ x: number;
+ y: number;
+ height: number;
+ width: number;
+ text: string;
+}
+
+interface Page {
+ index: number;
+ width: number;
+ height: number;
+}
+
+export interface PageTokens {
+ page: Page;
+ tokens: Token[];
+}
+
+function docURL(sha: string): string {
+ return `/api/doc/${sha}`;
+}
+
+export function pdfURL(sha: string): string {
+ return `${docURL(sha)}/pdf`;
+}
+
+export async function getTokens(sha: string): Promise {
+ return axios.get(`${docURL(sha)}/tokens`)
+ .then(r => r.data);
+}
+
+export interface Label {
+ text: string,
+ color: string
+}
+
+export async function getLabels(): Promise {
+ return axios.get("/api/annotation/labels")
+ .then(r => r.data)
+}
+
+export async function getRelations(): Promise {
+ return axios.get("/api/annotation/relations")
+ .then(r => r.data)
+}
+
+
+export interface PaperStatus {
+ sha: string,
+ name: string,
+ annotations: number,
+ relations: number,
+ finished: boolean,
+ junk: boolean,
+ comments: string,
+ completedAt?: Date
+}
+
+export interface Allocation {
+ papers: PaperStatus[]
+ hasAllocatedPapers: boolean
+}
+
+export async function setPdfComment(sha: string, comments: string) {
+ return axios.post(`/api/doc/${sha}/comments`, comments)
+}
+
+export async function setPdfFinished(sha: string, finished: boolean) {
+ return axios.post(`/api/doc/${sha}/finished`, finished)
+}
+
+export async function setPdfJunk(sha: string, junk: boolean) {
+ return axios.post(`/api/doc/${sha}/junk`, junk)
+}
+
+export async function getAllocatedPaperStatus(): Promise {
+ return axios.get("/api/annotation/allocation/info")
+ .then(r => r.data)
+}
+
+export function saveAnnotations(
+ sha: string,
+ pdfAnnotations: PdfAnnotations
+): Promise {
+ return axios.post(
+ `/api/doc/${sha}/annotations`,
+ {
+ annotations: pdfAnnotations.annotations,
+ relations: pdfAnnotations.relations
+ }
+ )
+}
+
+export async function getAnnotations(sha: string): Promise {
+ return axios.get(`/api/doc/${sha}/annotations`)
+ .then(response => {
+ const ann: PdfAnnotations = response.data
+ const annotations = ann.annotations.map(a => Annotation.fromObject(a))
+ const relations = ann.relations.map(r => RelationGroup.fromObject(r))
+
+ return new PdfAnnotations(
+ annotations,
+ relations
+ )
+ }
+ )
+ }
diff --git a/ui/src/components/AnnotationSummary.tsx b/ui/src/components/AnnotationSummary.tsx
new file mode 100644
index 00000000..2557a13f
--- /dev/null
+++ b/ui/src/components/AnnotationSummary.tsx
@@ -0,0 +1,73 @@
+import React, {useContext} from 'react';
+import { Annotation } from '../context';
+import { Tag } from "@allenai/varnish";
+import styled from 'styled-components';
+import { DeleteFilled } from "@ant-design/icons"
+import { PDFStore, AnnotationStore } from "../context"
+
+interface AnnotationSummaryProps {
+ annotation: Annotation
+}
+
+export const AnnotationSummary = ({annotation}: AnnotationSummaryProps) => {
+
+ const pdfStore = useContext(PDFStore)
+ const annotationStore = useContext(AnnotationStore)
+
+ const onDelete = () => {
+ annotationStore.setPdfAnnotations(
+ annotationStore.pdfAnnotations.deleteAnnotation(annotation)
+ )
+ }
+
+ if (!pdfStore.pages) {
+ return null
+ }
+
+ const pageInfo = pdfStore.pages[annotation.page]
+
+ const text = annotation.tokens === null ? "Freeform" :
+ annotation.tokens
+ .map(t => pageInfo.tokens[t.tokenIndex].text)
+ .join(" ")
+
+ return (
+
+
+ {text}
+
+
+ {annotation.label.text}
+
+
+ Page {pageInfo.page.pageNumber}
+
+
+
+ );
+
+}
+
+const PaddedRow = styled.div(({ theme }) => `
+ padding: 4px 0;
+ border-radius: 2px;
+ display: grid;
+ grid-template-columns: minmax(0, 1fr) min-content min-content min-content;
+
+`);
+
+
+const SmallTag = styled(Tag)`
+ font-size: 0.65rem;
+ padding: 2px 2px;
+ border-radius: 4px;
+ color: black;
+ line-height: 1;
+`
+const Overflow = styled.span`
+ line-height: 1;
+ font-size: 0.8rem;
+ white-space: nowrap;
+ text-overflow: ellipsis;
+ overflow: hidden;
+`
\ No newline at end of file
diff --git a/ui/src/components/CenterOnPage.tsx b/ui/src/components/CenterOnPage.tsx
new file mode 100644
index 00000000..f17d8215
--- /dev/null
+++ b/ui/src/components/CenterOnPage.tsx
@@ -0,0 +1,8 @@
+import styled from 'styled-components';
+
+export const CenterOnPage = styled.div`
+ display: flex;
+ flex-grow: 1;
+ align-items: center;
+ justify-content: center;
+`;
diff --git a/ui/src/components/PDF.tsx b/ui/src/components/PDF.tsx
new file mode 100644
index 00000000..5b453425
--- /dev/null
+++ b/ui/src/components/PDF.tsx
@@ -0,0 +1,274 @@
+import React, { useContext, useRef, useEffect, useState } from 'react';
+import styled from 'styled-components';
+import { PDFPageProxy, PDFRenderTask } from 'pdfjs-dist';
+
+import { PDFPageInfo, AnnotationStore, PDFStore, Bounds, normalizeBounds, getNewAnnotation } from '../context';
+import { Selection} from '../components'
+import { SelectionBoundary, SelectionTokens } from './Selection';
+
+class PDFPageRenderer {
+ private currentRenderTask?: PDFRenderTask;
+ constructor(
+ readonly page: PDFPageProxy,
+ readonly canvas: HTMLCanvasElement,
+ readonly onError: (e: Error) => void
+ ) {}
+ cancelCurrentRender() {
+ if (this.currentRenderTask === undefined) {
+ return;
+ }
+ this.currentRenderTask.promise.then(
+ () => {},
+ (err: any) => {
+ if (
+ err instanceof Error
+ && err.message.indexOf('Rendering cancelled') !== -1
+ ) {
+ // Swallow the error that's thrown when the render is canceled.
+ return;
+ }
+ const e = err instanceof Error ? err : new Error(err);
+ this.onError(e);
+ }
+ );
+ this.currentRenderTask.cancel();
+ }
+ render(scale: number) {
+ const viewport = this.page.getViewport({ scale });
+
+ this.canvas.height = viewport.height;
+ this.canvas.width = viewport.width;
+
+ const canvasContext = this.canvas.getContext('2d');
+ if (canvasContext === null) {
+ throw new Error('No canvas context');
+ }
+ this.currentRenderTask = this.page.render({ canvasContext, viewport });
+ return this.currentRenderTask;
+ }
+ rescaleAndRender(scale: number) {
+ this.cancelCurrentRender();
+ return this.render(scale);
+ }
+}
+
+function getPageBoundsFromCanvas(canvas: HTMLCanvasElement): Bounds {
+ if (canvas.parentElement === null) {
+ throw new Error('No canvas parent');
+ }
+ const parent = canvas.parentElement;
+ const parentStyles = getComputedStyle(canvas.parentElement);
+
+ const leftPadding = parseFloat(parentStyles.paddingLeft || "0");
+ const left = parent.offsetLeft + leftPadding;
+
+ const topPadding = parseFloat(parentStyles.paddingTop || "0");
+ const top = parent.offsetTop + topPadding;
+
+ const parentWidth =
+ parent.clientWidth - leftPadding - parseFloat(parentStyles.paddingRight || "0");
+ const parentHeight =
+ parent.clientHeight - topPadding - parseFloat(parentStyles.paddingBottom || "0");
+ return {
+ left,
+ top,
+ right: left + parentWidth,
+ bottom: top + parentHeight
+ };
+}
+
+interface PageProps {
+ pageInfo: PDFPageInfo;
+ onError: (e: Error) => void;
+}
+
+const Page = ({ pageInfo, onError }: PageProps) => {
+ const canvasRef = useRef(null);
+ const [ isVisible, setIsVisible ] = useState(false);
+ const [ scale, setScale ] = useState(1);
+
+ const annotationStore = useContext(AnnotationStore);
+
+ const containerRef = useRef(null);
+ const [ selection, setSelection ] = useState();
+
+ const annotations = annotationStore.pdfAnnotations.annotations
+ .filter(a => a.page === pageInfo.page.pageNumber - 1)
+
+ useEffect(() => {
+ try {
+ const determinePageVisiblity = () => {
+ if (canvasRef.current !== null) {
+ const windowTop = 0;
+ const windowBottom = window.innerHeight;
+ const rect = canvasRef.current.getBoundingClientRect();
+ setIsVisible(
+ // Top is in within window
+ (windowTop < rect.top && rect.top < windowBottom) ||
+ // Bottom is in within window
+ (windowTop < rect.bottom && rect.bottom < windowBottom) ||
+ // top is negative and bottom is +ve
+ (rect.top < windowTop && rect.bottom > windowTop)
+ );
+ }
+ };
+
+ if (canvasRef.current === null) {
+ onError(new Error('No canvas element'));
+ return;
+ }
+
+ pageInfo.bounds = getPageBoundsFromCanvas(canvasRef.current);
+ const renderer = new PDFPageRenderer(pageInfo.page, canvasRef.current, onError);
+ renderer.render(pageInfo.scale);
+
+ determinePageVisiblity();
+
+ const handleResize = () => {
+ if (canvasRef.current === null) {
+ onError(new Error('No canvas element'));
+ return;
+ }
+ pageInfo.bounds = getPageBoundsFromCanvas(canvasRef.current)
+ renderer.rescaleAndRender(pageInfo.scale);
+ setScale(pageInfo.scale)
+ determinePageVisiblity();
+ };
+ window.addEventListener('resize', handleResize);
+ window.addEventListener('scroll', determinePageVisiblity);
+ return () => {
+ window.removeEventListener('resize', handleResize)
+ window.removeEventListener('scroll', determinePageVisiblity);
+ };
+ } catch (e) {
+ onError(e);
+ }
+ }, [ pageInfo, onError ]); // We deliberately only run this once.
+
+ return (
+ {
+ if (containerRef.current === null) {
+ throw new Error('No Container');
+ }
+ if (!selection) {
+ const left = event.pageX - containerRef.current.offsetLeft;
+ const top = event.pageY - containerRef.current.offsetTop;
+ setSelection({
+ left,
+ top,
+ right: left,
+ bottom: top
+ });
+ }
+ }}
+ onMouseMove={selection ? (
+ (event) => {
+ if (containerRef.current === null) {
+ throw new Error('No Container');
+ }
+ setSelection({
+ ...selection,
+ right: event.pageX - containerRef.current.offsetLeft,
+ bottom: event.pageY - containerRef.current.offsetTop
+ });
+ }
+ ) : undefined}
+ onMouseUp={selection ? (
+ () => {
+ if (annotationStore.activeLabel) {
+ const newAnnotation = getNewAnnotation(
+ //TODO(Mark): Change
+ pageInfo,
+ selection,
+ annotationStore.activeLabel,
+ annotationStore.freeFormAnnotations
+ )
+ if (newAnnotation) {
+
+ annotationStore.setPdfAnnotations(
+ annotationStore.pdfAnnotations.withNewAnnotation(newAnnotation)
+ )
+ }
+ }
+ setSelection(undefined);
+
+ }
+ ) : undefined}
+
+ >
+
+ {// We only render the tokens if the page is visible, as rendering them all makes the
+ // page slow and/or crash.
+ scale && isVisible && annotations.map((annotation) => (
+
+ )
+ )
+ }
+ {selection && annotationStore.activeLabel ? (() => {
+ if (selection && annotationStore.activeLabel){
+ const annotation = pageInfo.getAnnotationForBounds(normalizeBounds(selection), annotationStore.activeLabel)
+ const tokens = annotation && annotation.tokens && !annotationStore.freeFormAnnotations ? annotation.tokens : null
+
+ return(
+ <>
+
+
+ >
+ )
+ }
+ })() : null}
+
+
+ );
+};
+
+export const PDF = () => {
+
+ const pdfStore = useContext(PDFStore);
+
+ // TODO (@codeviking): Use error boundaries to capture these.
+ if (!pdfStore.doc) {
+ throw new Error('No Document');
+ }
+ if (!pdfStore.pages) {
+ throw new Error('Document without Pages');
+ }
+
+ return (
+ <>
+ {pdfStore.pages.map((p) => {
+ return (
+
+ );
+ })}
+ >
+ );
+};
+
+const PageAnnotationsContainer = styled.div(({ theme }) =>`
+ position: relative;
+ box-shadow: 2px 2px 4px 0 rgba(0, 0, 0, 0.2);
+ margin: 0 0 ${theme.spacing.xs};
+
+ &:last-child {
+ margin-bottom: 0;
+ }
+`);
+
+const PageCanvas = styled.canvas`
+ display: block;
+`;
diff --git a/ui/src/components/RelationModal.tsx b/ui/src/components/RelationModal.tsx
new file mode 100644
index 00000000..70c9b02e
--- /dev/null
+++ b/ui/src/components/RelationModal.tsx
@@ -0,0 +1,69 @@
+import React, { useState, useContext} from 'react';
+import { Modal, Tag, Transfer } from '@allenai/varnish';
+import { Annotation, RelationGroup, AnnotationStore } from '../context';
+import { Label } from '../api';
+import { AnnotationSummary } from "./AnnotationSummary";
+
+const { CheckableTag } = Tag;
+
+interface RelationModalProps {
+ visible: boolean
+ onClick: (group: RelationGroup) => void
+ onCancel: () => void
+ source: Annotation[]
+ label: Label,
+}
+
+
+export const RelationModal = ({visible, onClick, onCancel, source, label}: RelationModalProps) => {
+
+ const annotationStore = useContext(AnnotationStore)
+ const [targetKeys, setTargetKeys] = useState([])
+ const transferSource = source.map((a) => ({key: a.id, annotation: a}))
+
+ return (
+
+ {
+ setTargetKeys([])
+ onCancel()
+ }}
+ onOk={() => {
+
+ const sourceIds = source
+ .filter(s => !targetKeys.some((k) => k === s.id))
+ .map(s => s.id)
+ onClick(new RelationGroup(sourceIds, targetKeys, label));
+ setTargetKeys([])
+ }}
+ >
+ Choose a Relation
+ {annotationStore.relationLabels.map(relation => (
+ {annotationStore.setActiveRelationLabel(relation)}}
+ checked={relation === annotationStore.activeRelationLabel}
+ >
+ {relation.text}
+
+ ))}
+
+ (
+
+ )}
+ />
+
+ )
+}
diff --git a/ui/src/components/Selection.tsx b/ui/src/components/Selection.tsx
new file mode 100644
index 00000000..296cb619
--- /dev/null
+++ b/ui/src/components/Selection.tsx
@@ -0,0 +1,232 @@
+import React, { useContext } from 'react';
+import styled, { ThemeContext } from 'styled-components';
+
+import { Bounds, TokenId, PDFPageInfo, Annotation, AnnotationStore } from '../context';
+import { CloseCircleFilled } from '@ant-design/icons';
+
+ function hexToRgb(hex: string) {
+ var result = /^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(hex);
+ if (!result) {
+ throw new Error("Unable to parse color.")
+ }
+ return {
+ r: parseInt(result[1], 16),
+ g: parseInt(result[2], 16),
+ b: parseInt(result[3], 16)
+ }
+ }
+
+function getBorderWidthFromBounds(bounds: Bounds): number {
+ //
+ const width = bounds.right - bounds.left;
+ const height = bounds.bottom - bounds.top;
+ if (width < 100 || height < 100) {
+ return 1;
+ }
+ else {
+ return 3;
+ }
+}
+
+interface SelectionBoundaryProps {
+ color: string
+ bounds: Bounds
+ selected: boolean
+ children?: React.ReactNode
+ annotationId?: string
+ onClick?: () => void
+}
+
+
+export const SelectionBoundary = ({color, bounds, children, onClick, selected}: SelectionBoundaryProps) => {
+
+ const width = bounds.right - bounds.left;
+ const height = bounds.bottom - bounds.top;
+ const rotateY = width < 0 ? -180 : 0;
+ const rotateX = height < 0 ? -180 : 0;
+ const rgbColor = hexToRgb(color)
+ const border = getBorderWidthFromBounds(bounds)
+
+ return (
+ {
+ // Here we are preventing the default PdfAnnotationsContainer
+ // behaviour of drawing a new bounding box if the shift key
+ // is pressed in order to allow users to select multiple
+ // annotations and associate them together with a relation.
+ if (e.shiftKey && onClick) {
+ e.stopPropagation();
+ onClick()
+
+ }
+ }}
+ onMouseDown={(e) => {
+ if (e.shiftKey && onClick) {
+ e.stopPropagation()
+ }
+ }}
+ style={{
+ position: "absolute",
+ left: `${bounds.left}px`,
+ top: `${bounds.top}px`,
+ width: `${Math.abs(width)}px`,
+ height: `${Math.abs(height)}px`,
+ transform: `rotateY(${rotateY}deg) rotateX(${rotateX}deg)`,
+ transformOrigin: 'top left',
+ border: `${border}px solid ${color}`,
+ background: `rgba(${rgbColor.r}, ${rgbColor.g}, ${rgbColor.b}, ${selected ? 0.3: 0.1})`,
+ }}
+ >
+ {children ? children: null}
+
+ )
+}
+
+
+interface TokenSpanProps {
+ isSelected?: boolean;
+}
+
+const TokenSpan = styled.span(({ theme, isSelected }) =>`
+ position: absolute;
+ background: ${isSelected ? theme.color.B3 : 'none'};
+ opacity: 0.2;
+ border-radius: 3px;
+`);
+
+interface SelectionTokenProps {
+ pageInfo: PDFPageInfo
+ tokens: TokenId[] | null
+}
+export const SelectionTokens = ({pageInfo, tokens}: SelectionTokenProps) => {
+
+ return (
+ <>
+ {tokens && tokens.map((t, i) => {
+ const b = pageInfo.getScaledTokenBounds(pageInfo.tokens[t.tokenIndex]);
+ return (
+
+ )
+ })}
+ >
+ )
+}
+
+interface SelectionProps {
+ pageInfo: PDFPageInfo
+ annotation: Annotation
+ showInfo?: boolean
+ }
+
+export const Selection = ({
+ pageInfo,
+ annotation,
+ showInfo = true,
+}: SelectionProps) => {
+
+ const label = annotation.label
+ const theme = useContext(ThemeContext)
+ const annotationStore = useContext(AnnotationStore)
+ let color;
+ if (!label) {
+ color = theme.color.N4.hex // grey as the default.
+ } else {
+ color = label.color
+ }
+
+ const bounds = pageInfo.getScaledBounds(annotation.bounds)
+ const border = getBorderWidthFromBounds(bounds)
+
+ const removeAnnotation = () => {
+ annotationStore.setPdfAnnotations(
+ annotationStore.pdfAnnotations.deleteAnnotation(annotation)
+ )
+ }
+
+ const onShiftClick = () => {
+ const current = annotationStore.selectedAnnotations.slice(0)
+
+ // Current contains this annotation, so we remove it.
+ if (current.some((other) => other.id === annotation.id)) {
+ const next = current.filter((other) => other.id !== annotation.id)
+ annotationStore.setSelectedAnnotations(next)
+ // Otherwise we add it.
+ } else {
+ current.push(annotation)
+ annotationStore.setSelectedAnnotations(current)
+ }
+ }
+
+ const selected = annotationStore.selectedAnnotations.includes(annotation)
+
+ return (
+ <>
+
+ {showInfo && !annotationStore.hideLabels ? (
+
+
+ {label.text}
+
+ {
+ e.stopPropagation();
+ removeAnnotation()
+ }}
+ // We have to prevent the default behaviour for
+ // the pdf canvas here, in order to be able to capture
+ // the click event.
+ onMouseDown={(e) => {e.stopPropagation()}}
+ />
+
+ ): null}
+
+ {
+ // NOTE: It's important that the parent element of the tokens
+ // is the PDF canvas, because we need their absolute position
+ // to be relative to that and not another absolute/relatively
+ // positioned element. This is why SelectionTokens are not inside
+ // SelectionBoundary.
+ annotation.tokens ? : null
+ }
+ >
+ );
+ }
+
+// We use transform here because we need to translate the label upward
+// to sit on top of the bounds as a function of *its own* height,
+// not the height of it's parent.
+interface SelectionInfoProps {
+ border: number
+ color: string
+}
+const SelectionInfo = styled.div(({ border, color }) => `
+ position: absolute;
+ right: -${border}px;
+ transform:translateY(-100%);
+ border: ${border} solid ${color};
+ background: ${color};
+ font-weight: bold;
+ font-size: 12px;
+ user-select: none;
+ * {
+ margin: 2px;
+ vertical-align: middle;
+ }
+`);
diff --git a/ui/src/components/index.ts b/ui/src/components/index.ts
new file mode 100644
index 00000000..f6a4bbd0
--- /dev/null
+++ b/ui/src/components/index.ts
@@ -0,0 +1,5 @@
+export * from './PDF';
+export * from './CenterOnPage';
+export * from './sidebar/Labels';
+export * from './Selection';
+export * from './RelationModal';
diff --git a/ui/src/components/sidebar/Annotations.tsx b/ui/src/components/sidebar/Annotations.tsx
new file mode 100644
index 00000000..2543fb65
--- /dev/null
+++ b/ui/src/components/sidebar/Annotations.tsx
@@ -0,0 +1,113 @@
+
+import React from 'react';
+import styled from "styled-components"
+import { SidebarItem, SidebarItemTitle } from "./common";
+import { Switch, notification } from '@allenai/varnish';
+import { Annotation } from "../../context";
+
+import { CheckOutlined, CloseOutlined, InfoCircleOutlined } from '@ant-design/icons';
+import { AnnotationSummary } from "../AnnotationSummary";
+import { setPdfJunk, setPdfFinished } from '../../api';
+
+interface AnnotationsProps {
+ sha: string
+ annotations: Annotation[]
+}
+
+
+export const Annotations = ({sha, annotations}: AnnotationsProps) => {
+
+ const onFinishToggle = (isFinished: boolean) => {
+
+ setPdfFinished(sha, isFinished).then(() => {
+ if (isFinished) {
+ notification.success({message: "Marked paper as Finished!"})
+ } else {
+ notification.info({message: "Marked paper as In Progress."})
+ }
+
+ })
+ }
+
+ const onJunkToggle = (isJunk: boolean) => {
+
+ setPdfJunk(sha, isJunk).then(() => {
+ if (isJunk) {
+ notification.warning({message: "Marked paper as Junk!"})
+ } else {
+ notification.info({message: "Marked paper as In Progress."})
+ }
+
+ })
+ }
+
+
+ return (
+
+
+ Annotations
+
+
+
+ Use CMD + z to undo the last annotation.
+
+
+
+ Press CTRL to show/hide annotation labels for small annotations.
+
+
+
+ Finished?
+
+ onFinishToggle(e)}
+ checkedChildren={ }
+ unCheckedChildren={ }
+ />
+
+
+
+ Junk
+
+ onJunkToggle(e)}
+ checkedChildren={ }
+ unCheckedChildren={ }
+ />
+
+
+ {annotations.length === 0 ? (
+ <>No Annotations Yet :(>
+ ) : (
+
+ {annotations.map((annotation, i) => (
+
+ ))}
+
+ )}
+
+
+ );
+}
+
+const ExplainerText = styled.div`
+ font-size: ${({ theme }) => theme.spacing.sm};
+
+ &, & * {
+ color: ${({ theme }) => theme.color.N6};
+ }
+`
+
+
+const Toggle = styled(Switch)`
+ margin: 8px 8px;
+`
+const ToggleDescription = styled.span`
+ font-size: 0.85rem;
+ color: ${({ theme }) => theme.color.N6};
+`
\ No newline at end of file
diff --git a/ui/src/components/sidebar/AssignedPaperList.tsx b/ui/src/components/sidebar/AssignedPaperList.tsx
new file mode 100644
index 00000000..85eb602a
--- /dev/null
+++ b/ui/src/components/sidebar/AssignedPaperList.tsx
@@ -0,0 +1,118 @@
+import React, { useState } from 'react';
+import styled from "styled-components";
+import { SidebarItem, SidebarItemTitle, Contrast } from "./common";
+import { PaperStatus } from "../../api";
+import { Switch, Tag, Statistic } from "@allenai/varnish";
+
+import { FileDoneOutlined, CloseOutlined, CommentOutlined, EditFilled, DeleteFilled } from "@ant-design/icons";
+
+
+const AssignedPaperRow = ({status}: {status: PaperStatus}) => {
+
+ const getIcon = (status: PaperStatus) => {
+ if (status.junk) {
+ return
+ }
+ else if (status.comments) {
+ return
+ } else {
+ return null
+ }
+ }
+
+ const getStatusColour = (status: PaperStatus) => {
+ if (status.junk) {
+ return "#d5a03a"
+ }
+ if (status.finished) {
+ return "#1EC28E"
+ }
+
+ return "#AEB7C4"
+ }
+
+ return (
+
+
+
+
+ {status.name}
+
+
+
+ {status.annotations}
+
+
+ {getIcon(status)}
+
+
+ )
+}
+
+export const AssignedPaperList = ({papers}: {papers: PaperStatus[]}) => {
+
+ const [showFinished, setShowFinished] = useState(false)
+
+ const unfinished = papers.filter(p => !p.finished)
+ const finished = papers.filter(p => p.finished)
+ const ordered = unfinished.concat(finished)
+ const papersToShow = showFinished ? ordered: unfinished
+
+ return (
+
+
+ Papers
+
+
+ Show Finished Papers:
+
+ setShowFinished(!showFinished)}
+ checkedChildren={ }
+ unCheckedChildren={ }
+ />
+ {papers.length !== 0 ? (
+ <>
+ {papersToShow.map((info) => (
+
+ ))}
+ >
+ ) : (
+ <>No Pdfs Allocated!>
+ )}
+
+ )
+}
+
+const Toggle = styled(Switch)`
+ margin: 4px;
+`
+const ToggleDescription = styled.span`
+ font-size: 0.85rem;
+ color: ${({ theme }) => theme.color.N6};
+
+`
+
+// TODO(Mark): ask for help figuring out how to style this icon.
+const DarkEditIcon = styled(EditFilled)`
+ margin-left: 4px;
+ &, & * {
+ color: ${({ theme }) => theme.color.N9};
+ }
+`
+
+const PaddedRow = styled.div(({ theme }) => `
+ padding: 4px 0;
+ display: grid;
+ grid-template-columns: minmax(0, 1fr) min-content minmax(20px, min-content);
+`);
+
+const SmallTag = styled(Tag)`
+ font-size: 0.70rem;
+ padding: 2px 2px;
+ margin-left: 4px;
+ border-radius: 4px;
+ color: ${({ theme }) => theme.color.N9};
+ line-height: 1;
+`
\ No newline at end of file
diff --git a/ui/src/components/sidebar/Comment.tsx b/ui/src/components/sidebar/Comment.tsx
new file mode 100644
index 00000000..ce620374
--- /dev/null
+++ b/ui/src/components/sidebar/Comment.tsx
@@ -0,0 +1,37 @@
+import React, {useState} from 'react';
+import styled from "styled-components";
+import { Input} from "@allenai/varnish";
+
+import { SidebarItem, SidebarItemTitle } from "./common";
+import { PaperStatus, setPdfComment } from "../../api";
+
+interface CommentProps {
+ sha: string
+ paperStatus: PaperStatus
+}
+
+export const Comment = ({ sha, paperStatus}: CommentProps) => {
+
+ const [comment, setComment] = useState(paperStatus.comments)
+
+ return (
+
+
+ Comments
+
+ setComment(e.target.value)}
+ onBlur={() => setPdfComment(sha, comment)}
+ autoSize={{minRows: 6}}
+ />
+
+ );
+};
+
+const DarkTextArea = styled(Input.TextArea)`
+ color: black;
+ padding: 2px 2px;
+ background: lightgrey;
+ font-size: 0.8rem;
+`
diff --git a/ui/src/components/sidebar/Header.tsx b/ui/src/components/sidebar/Header.tsx
new file mode 100644
index 00000000..f0faed56
--- /dev/null
+++ b/ui/src/components/sidebar/Header.tsx
@@ -0,0 +1,24 @@
+import React from 'react';
+import { Logos } from '@allenai/varnish';
+
+import pawlsLogo from "./pawlsLogo.png";
+import styled from 'styled-components';
+
+const { AI2Logo } = Logos;
+
+export const Header = () => {
+
+ return (
+ <>
+
+
+ >
+ );
+
+};
+
+const Logo = styled.img`
+ margin: 20px 4px 10px 0px;
+ padding: 4px;
+ max-width:100%;
+`
\ No newline at end of file
diff --git a/ui/src/components/sidebar/Labels.tsx b/ui/src/components/sidebar/Labels.tsx
new file mode 100644
index 00000000..24539a87
--- /dev/null
+++ b/ui/src/components/sidebar/Labels.tsx
@@ -0,0 +1,138 @@
+import React, { useContext, useEffect } from 'react';
+import styled from "styled-components";
+import { Tag, Switch} from "@allenai/varnish";
+
+import { AnnotationStore } from "../../context";
+import { CheckOutlined, CloseOutlined, InfoCircleOutlined } from '@ant-design/icons';
+
+import { SidebarItem, SidebarItemTitle } from "./common";
+
+const { CheckableTag } = Tag;
+
+export const Labels = () => {
+
+ const annotationStore = useContext(AnnotationStore)
+
+ const onToggle = () => {
+ annotationStore.toggleFreeFormAnnotations(
+ !annotationStore.freeFormAnnotations
+ )
+ }
+
+ useEffect(() => {
+
+ const onKeyPress = (e: KeyboardEvent) => {
+ // Numeric keys 1-9
+ if (49 <= e.keyCode && e.keyCode <= 57) {
+
+ const index = Number.parseInt(e.key) - 1
+ if (index < annotationStore.labels.length) {
+ annotationStore.setActiveLabel(annotationStore.labels[index])
+ }
+ }
+ // Left/Right Arrow keys
+ if (e.keyCode === 37 || e.keyCode === 39) {
+ if (!annotationStore.activeLabel) {
+ annotationStore.setActiveLabel(annotationStore.labels[0])
+ return;
+ }
+ const currentIndex = annotationStore.labels.indexOf(annotationStore.activeLabel)
+ // Right goes forward
+ let next = currentIndex === annotationStore.labels.length - 1 ? 0 : currentIndex + 1
+ // Left goes backward
+ if (e.keyCode === 37) {
+ next = currentIndex === 0 ? annotationStore.labels.length - 1 : currentIndex - 1
+ }
+ annotationStore.setActiveLabel(annotationStore.labels[next])
+ }
+ }
+ window.addEventListener("keydown", onKeyPress)
+ return (() => {
+ window.removeEventListener("keydown", onKeyPress)
+ })
+ }, [annotationStore])
+
+ // TODO(Mark): Style the tags so it's clear you can select them with the numeric keys.
+ return (
+
+
+ Labels
+
+
+
+ Use arrow keys to select labels to annotate.
+
+
+
+ {annotationStore.labels.map(label => (
+ {annotationStore.setActiveLabel(label)}}
+ checked={label === annotationStore.activeLabel}
+ style={{color: label.color}}
+ >
+ {label.text}
+
+ ))}
+
+ {annotationStore.relationLabels.length !== 0 ? (
+ <>
+
+ Relations
+
+
+ {annotationStore.relationLabels.map(relation => (
+ {annotationStore.setActiveRelationLabel(relation)}}
+ checked={relation === annotationStore.activeRelationLabel}
+ style={{color: relation.color}}
+ >
+ {relation.text}
+
+ ))}
+
+ >
+ ) : null }
+
+
+ Free Form Annotations
+ }
+ unCheckedChildren={ }
+ />
+
+
+
+ )
+}
+
+
+const ExplainerText = styled.div`
+ font-size: ${({ theme }) => theme.spacing.sm};
+
+ &, & * {
+ color: ${({ theme }) => theme.color.N6};
+ }
+`
+
+const LabelTag = styled(CheckableTag)`
+
+ &.ant-tag-checkable-checked {
+ background-color: #303030;
+}
+`
+
+const Toggle = styled(Switch)`
+ margin: 4px;
+`
+
+const Container = styled.div(({ theme }) => `
+ margin-top: ${theme.spacing.sm};
+ div + div {
+ margin-top: ${theme.spacing.md};
+ }
+
+`);
diff --git a/ui/src/components/sidebar/Relations.tsx b/ui/src/components/sidebar/Relations.tsx
new file mode 100644
index 00000000..ab8c5380
--- /dev/null
+++ b/ui/src/components/sidebar/Relations.tsx
@@ -0,0 +1,31 @@
+
+import React from 'react';
+import { SidebarItem, SidebarItemTitle } from "./common";
+import { RelationGroup } from "../../context";
+
+interface RelationProps {
+ relations: RelationGroup[]
+}
+
+// TODO(Mark): Improve the UX of this component.
+export const Relations = ({ relations }: RelationProps) => {
+
+ return (
+
+
+ Relations
+
+ {relations.length === 0 ? (
+ <>None>
+ ) : (
+
+ {relations.map((relation, i) => (
+
+ Relation #{i + 1}
+
+ ))}
+
+ )}
+
+ );
+}
\ No newline at end of file
diff --git a/ui/src/components/sidebar/common.tsx b/ui/src/components/sidebar/common.tsx
new file mode 100644
index 00000000..518cc9d3
--- /dev/null
+++ b/ui/src/components/sidebar/common.tsx
@@ -0,0 +1,60 @@
+
+import styled from "styled-components"
+import { Link, Button } from '@allenai/varnish';
+
+interface HasWidth {
+ width: string;
+}
+
+export const SidebarContainer = styled.div(({ theme, width }) => `
+ width: ${width};
+ position: fixed;
+ left: 0;
+ overflow-y: scroll;
+ background: ${theme.color.N10};
+ color: ${theme.color.N2};
+ padding: ${theme.spacing.md} ${theme.spacing.md};
+ height: 100vh;
+ * {
+ color: ${theme.color.N2};
+ }
+`);
+
+
+export const SidebarItem = styled.div(({ theme }) => `
+ min-height: 200px;
+ max-height: 400px;
+ overflow-y: scroll;
+ background: ${theme.color.N9};
+ margin-bottom: ${theme.spacing.md};
+ padding: ${theme.spacing.xxs} ${theme.spacing.sm};
+ border-radius: 5px;
+
+`);
+
+
+// text-transform is necessary because h5 is all caps in antd/varnish.
+export const SidebarItemTitle = styled.h5(({ theme }) => `
+ margin: ${theme.spacing.xs} 0;
+ text-transform: capitalize;
+ padding-bottom: ${theme.spacing.xs};
+ border-bottom: 2px solid ${theme.color.N8};
+`);
+
+export const Contrast = styled.div`
+ a[href] {
+ ${Link.contrastLinkColorStyles()};
+ }
+ line-height: 1;
+ font-size: 0.85rem;
+ white-space: nowrap;
+ text-overflow: ellipsis;
+ overflow: hidden;
+`;
+
+export const SmallButton = styled(Button)`
+ padding: 2px 4px;
+ height: auto;
+ font-size: 0.85rem;
+ margin-left: 10px;
+`
\ No newline at end of file
diff --git a/ui/src/components/sidebar/index.ts b/ui/src/components/sidebar/index.ts
new file mode 100644
index 00000000..a5fae0b8
--- /dev/null
+++ b/ui/src/components/sidebar/index.ts
@@ -0,0 +1,7 @@
+export * from "./common";
+export * from "./Annotations";
+export * from "./AssignedPaperList";
+export * from "./Labels";
+export * from "./Header";
+export * from "./Relations";
+export * from "./Comment";
\ No newline at end of file
diff --git a/ui/src/components/sidebar/pawlsLogo.png b/ui/src/components/sidebar/pawlsLogo.png
new file mode 100644
index 00000000..ed317007
Binary files /dev/null and b/ui/src/components/sidebar/pawlsLogo.png differ
diff --git a/ui/src/context/AnnotationStore.ts b/ui/src/context/AnnotationStore.ts
new file mode 100644
index 00000000..aaadb53e
--- /dev/null
+++ b/ui/src/context/AnnotationStore.ts
@@ -0,0 +1,200 @@
+import { createContext } from 'react';
+import { v4 as uuidv4 } from 'uuid';
+
+import { Bounds } from "./PDFStore";
+import { Label } from "../api";
+
+export class TokenId {
+ constructor(
+ public readonly pageIndex: number,
+ public readonly tokenIndex: number ) {}
+ toString() {
+ return [this.pageIndex.toString(), this.tokenIndex.toString()].join('-'); }
+ }
+
+
+export class RelationGroup {
+
+ constructor(
+ public sourceIds: string[],
+ public targetIds: string[],
+ public label: Label
+ ){}
+
+ updateForAnnotationDeletion(a: Annotation): RelationGroup | undefined {
+ const sourceEmpty = this.sourceIds.length === 0
+ const targetEmpty = this.targetIds.length === 0
+
+ const newSourceIds = this.sourceIds.filter((id) => id !== a.id)
+ const newTargetIds = this.targetIds.filter((id) => id !== a.id)
+
+ const nowSourceEmpty = this.sourceIds.length === 0
+ const nowTargetEmpty = this.targetIds.length === 0
+
+ // Only target had any annotations, now it has none,
+ // so delete.
+ if (sourceEmpty && nowTargetEmpty) {
+ return undefined
+ }
+ // Only source had any annotations, now it has none,
+ // so delete.
+ if (targetEmpty && nowSourceEmpty) {
+ return undefined
+ }
+ // Source was not empty, but now it is, so delete.
+ if (!sourceEmpty && nowSourceEmpty) {
+ return undefined
+ }
+ // Target was not empty, but now it is, so delete.
+ if (!targetEmpty && nowTargetEmpty) {
+ return undefined
+ }
+
+ return new RelationGroup(newSourceIds, newTargetIds, this.label)
+ }
+
+ static fromObject(obj: RelationGroup) {
+ return new RelationGroup(obj.sourceIds, obj.targetIds, obj.label)
+ }
+}
+
+
+export class Annotation {
+ public readonly id: string
+
+ constructor(
+ public bounds: Bounds,
+ public readonly page: number,
+ public readonly label: Label,
+ public readonly tokens: TokenId[] | null = null,
+ id: string | undefined = undefined
+ ) {
+ this.id = id ? id: uuidv4()
+ }
+
+ toString() {
+ return this.id
+ }
+
+ static fromObject(obj: Annotation) {
+ return new Annotation(obj.bounds, obj.page, obj.label, obj.tokens, obj.id)
+ }
+};
+
+export class PdfAnnotations {
+
+ constructor(
+ public readonly annotations: Annotation[],
+ public readonly relations: RelationGroup[],
+ public readonly unsavedChanges: boolean = false
+ ) {
+ }
+
+ saved(): PdfAnnotations {
+ return new PdfAnnotations(
+ this.annotations,
+ this.relations,
+ false
+ )
+ }
+
+ withNewAnnotation(a: Annotation): PdfAnnotations {
+
+ return new PdfAnnotations(
+ this.annotations.concat([a]),
+ this.relations,
+ true
+ )
+ }
+ withNewRelation(r: RelationGroup): PdfAnnotations {
+
+ return new PdfAnnotations(
+ this.annotations,
+ this.relations.concat([r]),
+ true
+ )
+ }
+
+ deleteAnnotation(a: Annotation): PdfAnnotations {
+
+ const newAnnotations = this.annotations.filter((ann) => ann.id !== a.id)
+ const newRelations = this.relations
+ .map((r) => r.updateForAnnotationDeletion(a))
+ .filter(r => r !== undefined)
+ return new PdfAnnotations(
+ newAnnotations,
+ newRelations as RelationGroup[],
+ true
+ )
+ }
+
+ undoAnnotation(): PdfAnnotations {
+
+ const popped = this.annotations.pop()
+ if (!popped) {
+ // No annotations, nothing to update
+ return this
+ }
+ const newRelations = this.relations
+ .map((r) => r.updateForAnnotationDeletion(popped))
+ .filter(r => r !== undefined)
+
+ return new PdfAnnotations(
+ this.annotations,
+ newRelations as RelationGroup[],
+ true
+ )
+ }
+}
+
+
+interface _AnnotationStore {
+ labels: Label[]
+ activeLabel?: Label
+ setActiveLabel: (label: Label) => void;
+
+ relationLabels: Label[]
+ activeRelationLabel?: Label
+ setActiveRelationLabel: (label: Label) => void;
+
+ pdfAnnotations: PdfAnnotations;
+ setPdfAnnotations: (t: PdfAnnotations) => void;
+
+ selectedAnnotations: Annotation[]
+ setSelectedAnnotations: (t: Annotation[]) => void;
+
+ freeFormAnnotations: boolean;
+ toggleFreeFormAnnotations: (state: boolean) => void;
+
+ hideLabels: boolean;
+ setHideLabels: (state: boolean) => void;
+}
+
+export const AnnotationStore = createContext<_AnnotationStore>({
+ pdfAnnotations: new PdfAnnotations([],[]),
+ labels: [],
+ activeLabel: undefined,
+ setActiveLabel:(_?: Label) => {
+ throw new Error("Unimplemented")
+ },
+ relationLabels: [],
+ activeRelationLabel: undefined,
+ setActiveRelationLabel:(_?: Label) => {
+ throw new Error("Unimplemented")
+ },
+ selectedAnnotations: [],
+ setSelectedAnnotations: (_?: Annotation[]) => {
+ throw new Error('Unimplemented');
+ },
+ setPdfAnnotations: (_: PdfAnnotations) => {
+ throw new Error('Unimplemented');
+ },
+ freeFormAnnotations: false,
+ toggleFreeFormAnnotations: (_: boolean) => {
+ throw new Error('Unimplemented');
+ },
+ hideLabels: false,
+ setHideLabels: (_: boolean) => {
+ throw new Error('Unimplemented');
+ },
+});
diff --git a/ui/src/context/PDFStore.ts b/ui/src/context/PDFStore.ts
new file mode 100644
index 00000000..e9fb348a
--- /dev/null
+++ b/ui/src/context/PDFStore.ts
@@ -0,0 +1,223 @@
+import { createContext } from 'react';
+import pdfjs from 'pdfjs-dist';
+
+import { Token, Label } from '../api';
+import { TokenId, Annotation } from './AnnotationStore';
+
+
+export type Optional = T | undefined;
+
+export interface Bounds {
+ left: number;
+ top: number;
+ right: number;
+ bottom: number;
+}
+
+/**
+ * Returns the provided bounds scaled by the provided factor.
+ */
+function scaled(bounds: Bounds, scale: number): Bounds {
+ return {
+ left: bounds.left * scale,
+ top: bounds.top * scale,
+ right: bounds.right * scale,
+ bottom: bounds.bottom * scale
+ };
+}
+
+/**
+ * Computes a bound which contains all of the bounds passed as arguments.
+ */
+function spanningBound(bounds: Bounds[], padding: number = 3): Bounds{
+
+ // Start with a bounding box for which any bound would be
+ // contained within, meaning we immediately update maxBound.
+ const maxBound: Bounds = {
+ left: Number.MAX_VALUE,
+ top: Number.MAX_VALUE,
+ right: 0,
+ bottom: 0
+ }
+
+ bounds.forEach(bound => {
+ maxBound.bottom = Math.max(bound.bottom, maxBound.bottom)
+ maxBound.top = Math.min(bound.top, maxBound.top)
+ maxBound.left = Math.min(bound.left, maxBound.left)
+ maxBound.right = Math.max(bound.right, maxBound.right)
+ })
+
+ maxBound.top = maxBound.top - padding
+ maxBound.left = maxBound.left - padding
+ maxBound.right = maxBound.right + padding
+ maxBound.bottom = maxBound.bottom + padding
+
+ return maxBound
+}
+
+/**
+ * Returns the provided bounds in their normalized form. Normalized means that the left
+ * coordinate is always less than the right coordinate, and that the top coordinate is always
+ * left than the bottom coordinate.
+ *
+ * This is required because objects in the DOM are positioned and sized by setting their top-left
+ * corner, width and height. This means that when a user composes a selection and moves to the left,
+ * or up, from where they started might result in a negative width and/or height. We don't normalize
+ * these values as we're tracking the mouse as it'd result in the wrong visual effect. Instead we
+ * rotate the bounds we render on the appropriate axis. This means we need to account for this
+ * later when calculating what tokens the bounds intersect with.
+ */
+export function normalizeBounds(b: Bounds): Bounds {
+ const normalized = Object.assign({}, b);
+ if (b.right < b.left) {
+ const l = b.left;
+ normalized.left = b.right;
+ normalized.right = l;
+ }
+ if (b.bottom < b.top) {
+ const t = b.top;
+ normalized.top = b.bottom;
+ normalized.bottom = t;
+ }
+ return normalized;
+}
+
+/**
+ * Returns true if the provided bounds overlap.
+ */
+function doOverlap(a: Bounds, b: Bounds): boolean {
+ if (a.left >= b.right || a.right <= b.left) {
+ return false;
+ } else if (a.bottom <= b.top || a.top >= b.bottom) {
+ return false;
+ }
+ return true;
+}
+
+export function getNewAnnotation(
+ page: PDFPageInfo,
+ selection: Bounds,
+ activeLabel: Label,
+ freeform: boolean,
+ ): Optional {
+
+ let annotation: Optional = undefined
+
+ const normalized = normalizeBounds(selection)
+ if (freeform){
+ annotation = page.getFreeFormAnnotationForBounds(normalized, activeLabel)
+ } else {
+ annotation = page.getAnnotationForBounds(normalized, activeLabel)
+ }
+ return annotation
+}
+
+
+
+export class PDFPageInfo {
+ constructor(
+ public readonly page: pdfjs.PDFPageProxy,
+ public readonly tokens: Token[] = [],
+ public bounds?: Bounds
+ ) {}
+
+ getFreeFormAnnotationForBounds(selection: Bounds, label: Label): Annotation {
+
+ if (this.bounds === undefined) {
+ throw new Error('Unknown Page Bounds');
+ }
+
+ // Here we invert the scale, because the user has drawn this bounding
+ // box, so it is *already* scaled with respect to the client's view. For
+ // the annotation, we want to remove this, because storing it with respect
+ // to the PDF page's original scale means we can render it everywhere.
+ const bounds = scaled(selection, 1 / this.scale)
+
+ return new Annotation(bounds, this.page.pageNumber - 1, label)
+
+ }
+
+ getAnnotationForBounds(selection: Bounds, label: Label): Optional {
+
+ /* This function is quite complicated. Our objective here is to
+ compute overlaps between a bounding box provided by a user and
+ grobid token spans associated with a pdf. The complexity here is
+ that grobid spans are relative to an absolute scale of the pdf,
+ but our user's bounding box is relative to the pdf rendered in their
+ client.
+
+ The critical key here is that anything we *store* must be relative
+ to the underlying pdf. So for example, inside the for loop, we are
+ computing:
+
+ whether a grobid token (tokenBound), scaled to the current scale of the
+ pdf in the client (scaled(tokenBound, this.scale)), is overlapping with
+ the bounding box drawn by the user (selection).
+
+ But! Once we have computed this, we store the grobid tokens and the bound
+ that contains all of them relative to the *original grobid tokens*.
+
+ This means that the stored data is not tied to a particular scale, and we
+ can re-scale it when we need to (mainly when the user resizes the browser window).
+ */
+
+ if (this.bounds === undefined) {
+ throw new Error('Unknown Page Bounds');
+ }
+ const ids: TokenId[] = [];
+ const tokenBounds: Bounds[] = [];
+ for(let i = 0; i < this.tokens.length; i++) {
+ const tokenBound = this.getTokenBounds(this.tokens[i])
+ if (doOverlap(scaled(tokenBound, this.scale), selection)) {
+ ids.push(new TokenId(this.page.pageNumber - 1, i));
+ tokenBounds.push(tokenBound);
+ }
+ }
+ if (ids.length === 0) {
+ return undefined
+ }
+ const bounds = spanningBound(tokenBounds)
+ return new Annotation(bounds, this.page.pageNumber - 1, label, ids)
+ }
+
+
+ getScaledTokenBounds(t: Token): Bounds {
+ return this.getScaledBounds(this.getTokenBounds(t));
+ }
+
+ getTokenBounds(t: Token): Bounds {
+ const b = {
+ left: t.x,
+ top: t.y,
+ right: t.x + t.width,
+ bottom: t.y + t.height
+ };
+ return b;
+ }
+
+ getScaledBounds(b: Bounds): Bounds {
+ return scaled(b, this.scale)
+ }
+
+ get scale(): number {
+ if (this.bounds === undefined) {
+ throw new Error('Unknown Page Bounds');
+ }
+ const pdfPageWidth = this.page.view[2] - this.page.view[1];
+ const domPageWidth = this.bounds.right - this.bounds.left;
+ return domPageWidth / pdfPageWidth;
+ }
+}
+
+interface _PDFStore {
+ pages?: PDFPageInfo[];
+ doc?: pdfjs.PDFDocumentProxy;
+ onError: (err: Error) => void;
+}
+
+export const PDFStore = createContext<_PDFStore>({
+ onError: (_: Error) => {
+ throw new Error('Unimplemented');
+ }
+});
+
diff --git a/ui/src/context/index.ts b/ui/src/context/index.ts
new file mode 100644
index 00000000..c7e74b6a
--- /dev/null
+++ b/ui/src/context/index.ts
@@ -0,0 +1,2 @@
+export * from './AnnotationStore';
+export * from './PDFStore';
diff --git a/ui/src/index.tsx b/ui/src/index.tsx
new file mode 100644
index 00000000..9bef1b17
--- /dev/null
+++ b/ui/src/index.tsx
@@ -0,0 +1,23 @@
+/**
+ * This is the main entry point for the UI. You should not need to make any
+ * changes here unless you want to update the theme.
+ *
+ * @see https://github.com/allenai/varnish
+ */
+
+import React from 'react';
+import ReactDOM from 'react-dom';
+import { BrowserRouter, Route } from 'react-router-dom';
+import { ThemeProvider } from '@allenai/varnish';
+import '@allenai/varnish/dist/varnish.css';
+
+import App from './App';
+
+ReactDOM.render(
+
+
+
+
+ ,
+ document.getElementById('root')
+);
diff --git a/ui/src/listeners/index.tsx b/ui/src/listeners/index.tsx
new file mode 100644
index 00000000..a4bdfc96
--- /dev/null
+++ b/ui/src/listeners/index.tsx
@@ -0,0 +1,164 @@
+import {useEffect, useContext} from "react";
+import { AnnotationStore } from "../context";
+import { saveAnnotations } from "../api";
+import { notification } from "@allenai/varnish";
+
+
+export const UndoAnnotation = () => {
+
+ const annotationStore = useContext(AnnotationStore)
+ const {pdfAnnotations, setPdfAnnotations } = annotationStore
+ useEffect(() => {
+ const handleUndo = (e: KeyboardEvent) => {
+
+ if (e.metaKey && e.keyCode === 90) {
+ setPdfAnnotations(pdfAnnotations.undoAnnotation())
+ }
+ }
+
+ window.addEventListener('keydown', handleUndo);
+ return () => {
+ window.removeEventListener('keydown', handleUndo)
+ };
+ }, [pdfAnnotations, setPdfAnnotations])
+
+ return null
+
+}
+
+
+export const HideAnnotationLabels = () => {
+ // Shows or hides the labels of annotations on pressing ctrl.
+ // This makes it easier to do detailed annotations.
+
+ const annotationStore = useContext(AnnotationStore)
+ const {hideLabels, setHideLabels } = annotationStore
+
+ // Toggle state on key down.
+ useEffect(() => {
+ const hideLabelsOnKeyDown = (e: KeyboardEvent) => {
+
+ if (e.ctrlKey) {
+ setHideLabels(!hideLabels)
+ }
+ }
+ window.addEventListener('keydown', hideLabelsOnKeyDown);
+ return () => {
+ window.removeEventListener('keydown', hideLabelsOnKeyDown)
+ };
+ }, [hideLabels, setHideLabels])
+
+ return null
+
+}
+
+
+
+interface HandleAnnotationSelectionProps {
+ setModalVisible: (v: boolean) => void
+}
+export const HandleAnnotationSelection = ({setModalVisible}: HandleAnnotationSelectionProps) => {
+
+ const annotationStore = useContext(AnnotationStore)
+ const {selectedAnnotations, setSelectedAnnotations, activeRelationLabel} = annotationStore
+ useEffect(() => {
+
+ const onShiftUp = (e: KeyboardEvent) => {
+
+ const shift = e.keyCode === 16
+ const somethingSelected = selectedAnnotations.length !== 0
+ const hasRelations = activeRelationLabel !== undefined
+ // Shift key up, the user has selected something,
+ // and this annotation project has relation labels.
+ if (shift && somethingSelected && hasRelations) {
+ setModalVisible(true)
+ }
+ // Otherwise we just clear the selection,
+ // if there is something selected, because
+ // there are no relations to annotate.
+ else if (shift && somethingSelected) {
+ setSelectedAnnotations([])
+ }
+ }
+
+ window.addEventListener("keyup", onShiftUp)
+ return (() => {
+ window.removeEventListener("keyup", onShiftUp)
+ })
+ }, [activeRelationLabel, selectedAnnotations, setModalVisible])
+
+ return null
+}
+
+
+
+interface WithSha {
+ sha: string,
+}
+
+export const SaveWithTimeout = ({sha}: WithSha) => {
+
+ const annotationStore = useContext(AnnotationStore)
+ const {pdfAnnotations, setPdfAnnotations } = annotationStore
+
+ useEffect(() => {
+ // We only save annotations once the annotations have
+ // been fetched, because otherwise we save when the
+ // annotations and relations are empty.
+ if (pdfAnnotations.unsavedChanges) {
+
+ const currentTimeout = setTimeout(() => {
+ saveAnnotations(sha, pdfAnnotations).then(() => {
+ setPdfAnnotations(
+ pdfAnnotations.saved()
+ )
+ }).catch((err) => {
+
+ notification.error({
+ message: "Sorry, something went wrong!",
+ description: "Try re-doing your previous annotation, or contact someone on the Semantic Scholar team."
+ })
+ console.log("Failed to save annotations: ", err)
+ })
+ }, 2000)
+ return () => clearTimeout(currentTimeout)
+ }
+ }, [sha, pdfAnnotations])
+
+ return null
+}
+
+// TODO(Mark): There is a lot of duplication between these two listeners,
+// deduplicate if I need to save at another time as well.
+
+export const SaveBeforeUnload = ({sha}: WithSha) => {
+
+ const annotationStore = useContext(AnnotationStore)
+ const {pdfAnnotations, setPdfAnnotations } = annotationStore
+ useEffect(() => {
+
+ const beforeUnload = (e: BeforeUnloadEvent) => {
+
+ e.preventDefault()
+ saveAnnotations(sha, pdfAnnotations).then(() => {
+ setPdfAnnotations(
+ pdfAnnotations.saved()
+ )
+ }).catch((err) => {
+
+ notification.error({
+ message: "Sorry, something went wrong!",
+ description: "Try re-doing your previous annotation, or contact someone on the Semantic Scholar team."
+ })
+ console.log("Failed to save annotations: ", err)
+ }).then(() => window.close())
+ }
+
+ window.addEventListener("beforeunload", beforeUnload)
+ return (() => {
+ window.removeEventListener("beforeunload", beforeUnload)
+ })
+ }, [sha, pdfAnnotations])
+
+ return null
+}
\ No newline at end of file
diff --git a/ui/src/pages/PDFPage.tsx b/ui/src/pages/PDFPage.tsx
new file mode 100644
index 00000000..ec5c1ad5
--- /dev/null
+++ b/ui/src/pages/PDFPage.tsx
@@ -0,0 +1,313 @@
+import React, { useContext, useCallback, useState, useEffect } from 'react';
+import styled, { ThemeContext } from 'styled-components';
+import { useParams } from 'react-router-dom';
+import pdfjs from 'pdfjs-dist';
+import { Result, Progress, notification } from '@allenai/varnish';
+
+import { QuestionCircleOutlined } from '@ant-design/icons';
+
+import { PDF, CenterOnPage, RelationModal } from '../components';
+import {SidebarContainer, Labels, Annotations, Relations, AssignedPaperList, Header, Comment} from "../components/sidebar";
+import { pdfURL, getTokens, PageTokens, PaperStatus, getAllocatedPaperStatus, getLabels, Label, getAnnotations, getRelations } from '../api';
+import { PDFPageInfo, Annotation, AnnotationStore, PDFStore, RelationGroup, PdfAnnotations } from '../context';
+
+import * as listeners from "../listeners";
+
+// This tells PDF.js the URL the code to load for it's webworker, which handles heavy-handed
+// tasks in a background thread. Ideally we'd load this from the application itself rather
+// than from the CDN to keep things local.
+// TODO (@codeviking): Figure out how to get webpack to package up the PDF.js webworker code.
+pdfjs.GlobalWorkerOptions.workerSrc =
+ `//cdnjs.cloudflare.com/ajax/libs/pdf.js/${pdfjs.version}/pdf.worker.js`;
+
+// This callback exists in the source code, but not in the TypeScript types. So we mix it in
+// to make TypeScript happy.
+// See: https://github.com/mozilla/pdf.js/blob/master/src/display/api.js#L510
+interface PDFLoadingTask extends pdfjs.PDFLoadingTask {
+ onProgress?: (p: pdfjs.PDFProgressData) => void;
+}
+
+enum ViewState {
+ LOADING, LOADED, NOT_FOUND, ERROR
+}
+
+export const PDFPage = () => {
+
+ const { sha } = useParams<{ sha: string }>();
+ const [ viewState, setViewState ] = useState(ViewState.LOADING);
+
+ const [ doc, setDocument ] = useState();
+ const [ progress, setProgress ] = useState(0);
+ const [ pages, setPages ] = useState();
+ const [ pdfAnnotations, setPdfAnnotations ] = useState(
+ new PdfAnnotations([], [])
+ );
+
+ const [ selectedAnnotations, setSelectedAnnotations ] = useState([])
+
+ const [ assignedPaperStatuses, setAssignedPaperStatuses] = useState([])
+ const [ activePaperStatus, setActivePaperStatus] = useState()
+ const [ activeLabel, setActiveLabel] = useState();
+ const [ labels, setLabels] = useState([]);
+ const [ relationLabels, setRelationLabels] = useState([]);
+ const [ activeRelationLabel, setActiveRelationLabel] = useState();
+ const [ freeFormAnnotations, toggleFreeFormAnnotations] = useState(false);
+ const [ hideLabels, setHideLabels] = useState(false);
+
+ const [ relationModalVisible, setRelationModalVisible] = useState(false);
+
+ // React's Error Boundaries don't work for us because a lot of work is done by pdfjs in
+ // a background task (a web worker). We instead setup a top level error handler that's
+ // passed around as needed so we can display a nice error to the user when something
+ // goes wrong.
+ //
+ // We have to use the `useCallback` hook here so that equality checks in child components
+ // don't trigger unintentional rerenders.
+ const onError = useCallback((err: Error) => {
+ console.error('Unexpected Error rendering PDF', err);
+ setViewState(ViewState.ERROR);
+ }, [ setViewState ]);
+
+ const theme = useContext(ThemeContext);
+
+ const onRelationModalOk = (group: RelationGroup) => {
+ setPdfAnnotations(pdfAnnotations.withNewRelation(group))
+ setRelationModalVisible(false)
+ setSelectedAnnotations([])
+ }
+
+ const onRelationModalCancel = () => {
+
+ setRelationModalVisible(false)
+ setSelectedAnnotations([])
+ }
+
+ useEffect(() => {
+ getLabels().then(labels => {
+ setLabels(labels)
+ setActiveLabel(labels[0])
+ })
+ }, [])
+
+ useEffect(() => {
+ getRelations().then(relations => {
+ setRelationLabels(relations)
+ setActiveRelationLabel(relations[0])
+ })
+ }, [sha])
+
+ useEffect( () => {
+ getAllocatedPaperStatus().then((allocation) => {
+ setAssignedPaperStatuses(allocation.papers)
+ setActivePaperStatus(
+ allocation.papers.filter(p => p.sha === sha)[0]
+ )
+ if (!allocation.hasAllocatedPapers) {
+ notification.warn({
+ message: "Read Only Mode!",
+ description: "This annotation project has no assigned papers for your email address. You can make annotations but they won't be saved."
+ })
+ }
+
+ }).catch((err: any) => {
+ setViewState(ViewState.ERROR);
+ console.log(err)
+ })
+ }, [sha])
+
+ useEffect(() => {
+ setDocument(undefined);
+ setViewState(ViewState.LOADING)
+ const loadingTask: PDFLoadingTask = pdfjs.getDocument(pdfURL(sha))
+ loadingTask.onProgress = (p: pdfjs.PDFProgressData) => {
+ setProgress(Math.round(p.loaded / p.total * 100));
+ };
+ Promise.all([
+ // PDF.js uses their own `Promise` type, which according to TypeScript doesn't overlap
+ // with the base `Promise` interface. To resolve this we (unsafely) cast the PDF.js
+ // specific `Promise` back to a generic one. This works, but might have unexpected
+ // side-effects, so we should remain wary of this code.
+ loadingTask.promise as unknown as Promise,
+ getTokens(sha)
+ ]).then(([ doc, resp ]: [ pdfjs.PDFDocumentProxy, PageTokens[] ]) => {
+ setDocument(doc);
+
+ // Load all the pages too. In theory this makes things a little slower to startup,
+ // as fetching and rendering them asynchronously would make it faster to render the
+ // first, visible page. That said it makes the code simpler, so we're ok with it for
+ // now.
+ const loadPages: Promise[] = [];
+ for (let i = 1; i <= doc.numPages; i++) {
+ // See line 50 for an explanation of the cast here.
+ loadPages.push(
+ doc.getPage(i).then(p => {
+ const pageIndex = p.pageNumber - 1;
+ const pageTokens = resp[pageIndex].tokens
+ return new PDFPageInfo(p, pageTokens);
+ }) as unknown as Promise
+ );
+ }
+ return Promise.all(loadPages);
+ }).then(pages => {
+ setPages(pages);
+ // Get any existing annotations for this pdf.
+ getAnnotations(sha).then(paperAnnotations => {
+ setPdfAnnotations(paperAnnotations)
+
+ setViewState(ViewState.LOADED);
+ }).catch((err: any) => {
+ console.error(`Error Fetching Existing Annotations: `, err);
+ setViewState(ViewState.ERROR);
+ })
+
+ }).catch((err: any) => {
+ if (err instanceof Error) {
+ // We have to use the message because minification in production obfuscates
+ // the error name.
+ if (err.message === 'Request failed with status code 404') {
+ setViewState(ViewState.NOT_FOUND);
+ return;
+ }
+ }
+ console.error(`Error Loading PDF: `, err);
+ setViewState(ViewState.ERROR);
+ });
+ }, [ sha ]);
+
+ const sidebarWidth = "300px";
+ switch (viewState) {
+ case ViewState.LOADING:
+ return (
+
+
+
+
+
+
+
+
+
+ );
+ case ViewState.NOT_FOUND:
+ return (
+
+
+
+
+
+
+ }
+ title="PDF Not Found" />
+
+
+ );
+ case ViewState.LOADED:
+ if (doc && pages && pdfAnnotations) {
+ return (
+
+
+
+
+
+
+
+
+
+
+
+
+ {activePaperStatus ?
+ : null}
+ {activeRelationLabel ?
+
+ : null
+ }
+ {activePaperStatus ?
+
+ : null
+ }
+
+
+ {activeRelationLabel ?
+
+ : null}
+
+
+
+
+
+ );
+ } else {
+ return (null);
+ }
+ // eslint-disable-line: no-fallthrough
+ case ViewState.ERROR:
+ return (
+
+
+
+
+
+
+
+
+
+ );
+ }
+};
+
+interface HasWidth {
+ width: string;
+}
+
+const WithSidebar = styled.div(({ width }) =>`
+ display: grid;
+ flex-grow: 1;
+ grid-template-columns: minmax(0, 1fr);
+ padding-left: ${width};
+`);
+
+
+const PDFContainer = styled.div(({ theme }) => `
+ background: ${theme.color.N4};
+ padding: ${theme.spacing.sm};
+`);
diff --git a/ui/src/pages/index.ts b/ui/src/pages/index.ts
new file mode 100644
index 00000000..8feeb76b
--- /dev/null
+++ b/ui/src/pages/index.ts
@@ -0,0 +1 @@
+export * from './PDFPage';
diff --git a/ui/src/react-app-env.d.ts b/ui/src/react-app-env.d.ts
new file mode 100644
index 00000000..6431bc5f
--- /dev/null
+++ b/ui/src/react-app-env.d.ts
@@ -0,0 +1 @@
+///
diff --git a/ui/src/utils.ts b/ui/src/utils.ts
new file mode 100644
index 00000000..f081b9b9
--- /dev/null
+++ b/ui/src/utils.ts
@@ -0,0 +1,29 @@
+/**
+ * Use this file as a spot for small utility methods used throughout your
+ * application.
+ */
+
+/**
+ * Query string values can be strings or an array of strings. This utility
+ * retrieves the value if it's a string, or takes the first string if it's an
+ * array of strings.
+ *
+ * If no value is provided, the provided default value is returned.
+ *
+ * @param {string} value
+ * @param {string} defaultValue
+ *
+ * @returns {string}
+ */
+export function unwrap(
+ value: string | string[] | undefined | null,
+ defaultValue: string = ''
+): string {
+ if (value === undefined || value === null) {
+ return defaultValue;
+ } else if (Array.isArray(value)) {
+ return value[0];
+ } else {
+ return value;
+ }
+}
diff --git a/ui/tsconfig.json b/ui/tsconfig.json
new file mode 100644
index 00000000..21a5a7ce
--- /dev/null
+++ b/ui/tsconfig.json
@@ -0,0 +1,30 @@
+{
+ "compilerOptions": {
+ "target": "es6",
+ "lib": [
+ "dom",
+ "dom.iterable",
+ "esnext"
+ ],
+ "allowJs": true,
+ "skipLibCheck": true,
+ "esModuleInterop": true,
+ "allowSyntheticDefaultImports": true,
+ "strict": true,
+ "forceConsistentCasingInFileNames": true,
+ "module": "esnext",
+ "moduleResolution": "node",
+ "resolveJsonModule": true,
+ "isolatedModules": true,
+ "noEmit": true,
+ "jsx": "preserve",
+ "sourceMap": true
+ },
+ "include": [
+ "./src/**/*"
+ ],
+ "exclude": [
+ "node_modules",
+ "**/*.test.ts*"
+ ]
+}
diff --git a/ui/yarn.lock b/ui/yarn.lock
new file mode 100644
index 00000000..a4668e61
--- /dev/null
+++ b/ui/yarn.lock
@@ -0,0 +1,11996 @@
+# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
+# yarn lockfile v1
+
+
+"@allenai/varnish-react-router@^1.0.4":
+ version "1.0.4"
+ resolved "https://registry.yarnpkg.com/@allenai/varnish-react-router/-/varnish-react-router-1.0.4.tgz#38c76f6614186d3e0d9965c68ea20ea0b1ef7615"
+ integrity sha512-kujhabmmHReT2hORnQzpuF3Phpa9hcncdFHxVHLklZx0jd6/JguW0FN/vhdURbc5oh9fkKXAJXLMHUEU+TEacw==
+
+"@allenai/varnish@^1.0.0":
+ version "1.0.0"
+ resolved "https://registry.yarnpkg.com/@allenai/varnish/-/varnish-1.0.0.tgz#a127468df06efc99b00c999a6860e673a2a2e9bb"
+ integrity sha512-Q/JiL1ryzvo6QS+NXHSzu2qyGahxuS5Ot13EuB0USTM5bkhvaCExjsINAQPukSrdr1PSDvPHrX4zsw6WIgxGfg==
+ dependencies:
+ "@ant-design/css-animation" "^1.7.2"
+ "@ant-design/icons" "^4.2.1"
+ "@ant-design/react-slick" "~0.27.0"
+ "@babel/runtime" "^7.10.4"
+ array-tree-filter "^2.1.0"
+ classnames "^2.2.6"
+ copy-to-clipboard "^3.2.0"
+ cssnano "^4.1.10"
+ file-loader "~3.0.1"
+ lodash "^4.17.13"
+ moment "^2.25.3"
+ omit.js "^2.0.2"
+ raf "^3.4.1"
+ rc-animate "~3.1.0"
+ rc-cascader "~1.3.0"
+ rc-checkbox "~2.3.0"
+ rc-collapse "~2.0.0"
+ rc-dialog "~8.1.0"
+ rc-drawer "~4.1.0"
+ rc-dropdown "~3.1.2"
+ rc-field-form "~1.8.0"
+ rc-input-number "~6.0.0"
+ rc-mentions "~1.4.0"
+ rc-menu "~8.5.0"
+ rc-notification "~4.4.0"
+ rc-pagination "~2.4.5"
+ rc-picker "~1.15.1"
+ rc-progress "~3.0.0"
+ rc-rate "~2.8.2"
+ rc-resize-observer "^0.2.3"
+ rc-select "~11.0.10"
+ rc-slider "~9.3.0"
+ rc-steps "~4.1.0"
+ rc-switch "~3.2.0"
+ rc-table "~7.8.0"
+ rc-tabs "~11.5.0"
+ rc-textarea "~0.3.0"
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