Merge pull request #527 from unity-sds/develop

release/9.6.0
unity-sds · Feb 3, 2025 · f2fa8f2 · f2fa8f2
2 parents b210a79 + ffe4493
commit f2fa8f2
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diff --git a/.github/workflows/makefile.yml b/.github/workflows/makefile.yml
@@ -23,7 +23,7 @@ jobs:
     - run: |
         python3 "${GITHUB_WORKSPACE}/setup.py" install_lib
     - run: |
-        python3 -m pip uninstall botocore boto3 -y
+        python3 -m pip uninstall botocore boto3 s3transfer -y
     - run: |
         # make file runnable, might not be necessary
         chmod +x "${GITHUB_WORKSPACE}/ci.cd/create_aws_lambda_zip.sh"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,26 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [9.6.0] - 2025-02-03
+### Changed
+- [#517](https://github.com/unity-sds/unity-data-services/pull/517) feat: stac browser oidc cookie
+
+## [9.5.2] - 2025-01-31
+### Fixed
+- [#524](https://github.com/unity-sds/unity-data-services/pull/524) fix: default boto3 from aws already has s3transfer library
+
+## [9.5.1] - 2025-01-17
+### Fixed
+- [#502](https://github.com/unity-sds/unity-data-services/pull/502) fix: get granules pagination
+
+## [9.5.0] - 2025-01-17
+### Changed
+- [#499](https://github.com/unity-sds/unity-data-services/pull/499) feat: duplicate granules diff index
+
+## [9.4.2] - 2025-01-17
+### Fixed
+- [#498](https://github.com/unity-sds/unity-data-services/pull/498) fix: restructure bbox for geoshape
+
 ## [9.4.1] - 2024-12-18
 ### Fixed
 - [#489](https://github.com/unity-sds/unity-data-services/pull/489) fix: delete bug

diff --git a/cumulus_lambda_functions/lib/uds_db/granules_db_index.py b/cumulus_lambda_functions/lib/uds_db/granules_db_index.py
@@ -34,12 +34,25 @@ def __init__(self):
 
     @staticmethod
     def to_es_bbox(bbox_array):
+        # lon = x, lat = y
+        # lon, lat, lon, lat
+        # x can be 170 to -170
+        # 170, 0, -170, 10
+        minX, minY, maxX, maxY = bbox_array
+
+        # Ensure the values are properly sorted
+        # if minX > maxX:
+        #     minX, maxX = maxX, minX
+        if minY > maxY:
+            minY, maxY = maxY, minY
+
         return {
             "type": "envelope",
-            "coordinates": [
-                [bbox_array[0], bbox_array[3]],  # Top-left corner (minLon, maxLat)
-                [bbox_array[2], bbox_array[1]]   # Bottom-right corner (maxLon, minLat)
-            ]
+            "coordinates": [[minX, maxY], [maxX, minY]],
+            # "coordinates": [
+            #     [bbox_array[0], bbox_array[3]],  # Top-left corner (minLon, maxLat)
+            #     [bbox_array[2], bbox_array[1]]   # Bottom-right corner (maxLon, minLat)
+            # ]
         }
 
     @staticmethod
@@ -152,16 +165,20 @@ def create_new_index(self, tenant, tenant_venue, es_mapping: dict):
         self.__es.swap_index_for_alias(write_perc_alias_name, current_perc_index_name, new_perc_index_name)
         try:
             self.__es.migrate_index_data(current_perc_index_name, new_perc_index_name)
-        except Exception as e:
+        except:
             LOGGER.exception(f'failed to migrate index data: {(current_perc_index_name, new_perc_index_name)}')
         return
 
-    def get_latest_index(self, tenant, tenant_venue):
+    def get_latest_index_name(self, tenant, tenant_venue):
         write_alias_name = f'{DBConstants.granules_write_alias_prefix}_{tenant}_{tenant_venue}'.lower().strip()
         write_alias_name = self.__es.get_alias(write_alias_name)
         if len(write_alias_name) != 1:
             raise ValueError(f'missing index for {tenant}_{tenant_venue}. {write_alias_name}')
         latest_index_name = [k for k in write_alias_name.keys()][0]
+        return latest_index_name
+
+    def get_latest_index(self, tenant, tenant_venue):
+        latest_index_name = self.get_latest_index_name(tenant, tenant_venue)
         index_mapping = self.__es.get_index_mapping(latest_index_name)
         if index_mapping is None:
             raise ValueError(f'missing index: {latest_index_name}')
@@ -201,53 +218,106 @@ def get_entry(self, tenant: str, tenant_venue: str, doc_id: str, ):
             raise ValueError(f"no such granule: {doc_id}")
         return result
 
-    def delete_entry(self, tenant: str, tenant_venue: str, doc_id: str, ):
+    def __query_by_id_local(self, tenant: str, tenant_venue: str, doc_id: str, ):
         read_alias_name = f'{DBConstants.granules_read_alias_prefix}_{tenant}_{tenant_venue}'.lower().strip()
-        result = self.__es.query({
+        dsl = {
             'size': 9999,
-            'query': {'term': {'_id': doc_id}}
-        }, read_alias_name)
-        if result is None:
-            raise ValueError(f"no such granule: {doc_id}")
-        for each_granule in result['hits']['hits']:
+            'sort': [
+                {'properties.datetime': {'order': 'desc'}},
+                {'id': {'order': 'asc'}}
+            ],
+            'query': {
+                'term': {'_id': doc_id}
+            }
+        }
+        result = self.__es.query(dsl, read_alias_name)
+        if result is None or len(result['hits']['hits']) < 1:
+            return []
+        return result['hits']['hits']
+
+    def __delete_old_entries(self, dsl_result):
+        for each_granule in dsl_result:
             LOGGER.debug(f"deleting {each_granule['_id']} from {each_granule['_index']}")
             delete_result = self.__es.delete_by_query({
                 'query': {'term': {'id': each_granule['_id']}}
             }, each_granule['_index'])
             LOGGER.debug(f'delete_result: {delete_result}')
             if delete_result is None:
                 raise ValueError(f"error deleting {each_granule}")
+        return
+
+    def delete_entry(self, tenant: str, tenant_venue: str, doc_id: str, ):
+        result = self.__query_by_id_local(tenant, tenant_venue, doc_id)
+        if len(result) < 1:
+            raise ValueError(f"no such granule: {doc_id}")
+        self.__delete_old_entries(result)
         return result
 
     def update_entry(self, tenant: str, tenant_venue: str, json_body: dict, doc_id: str, ):
+        # find existing doc_id
+        # if not found, throw error. Cannot update
+        # if found, check index.
+        # if latest index, proceed with update
+        # if older index, proceed with get + delete
+        # tweak meta locally, and add it.
         write_alias_name = f'{DBConstants.granules_write_alias_prefix}_{tenant}_{tenant_venue}'.lower().strip()
         json_body['event_time'] = TimeUtils.get_current_unix_milli()
-        self.__es.update_one(json_body, doc_id, index=write_alias_name)  # TODO assuming granule_id is prefixed with collection id
-        LOGGER.debug(f'custom_metadata indexed')
+        existing_entries = self.__query_by_id_local(tenant, tenant_venue, doc_id)
+        if len(existing_entries) < 1:
+            raise ValueError(f'unable to update {doc_id} as it is not found. ')
+        latest_index_name = self.get_latest_index_name(tenant, tenant_venue)
+        existing_entry = existing_entries[0]
+        if existing_entry['_index'] == latest_index_name:
+            LOGGER.debug(f'{doc_id} in latest index: {latest_index_name}. continuing with update')
+            self.__es.update_one(json_body, doc_id, index=write_alias_name)  # TODO assuming granule_id is prefixed with collection id
+            self.__delete_old_entries(existing_entries[1:])
+            return
+        LOGGER.debug(f'{doc_id} in older index: {latest_index_name} v. {existing_entry["_index"]}')
+        new_doc = {**existing_entry['_source'], **json_body}
+        self.__es.index_one(new_doc, doc_id, index=write_alias_name)  # TODO assuming granule_id is prefixed with collection id
+        self.__delete_old_entries(existing_entries)
         return
 
     def add_entry(self, tenant: str, tenant_venue: str, json_body: dict, doc_id: str, ):
+        # find existing doc_id
+        # if not found, add it
+        # if found, and it is in latest index, add it.
+        # if found, and it is in older index, add current one, and delete the older one.
+
         write_alias_name = f'{DBConstants.granules_write_alias_prefix}_{tenant}_{tenant_venue}'.lower().strip()
         json_body['event_time'] = TimeUtils.get_current_unix_milli()
-        # TODO validate custom metadata vs the latest index to filter extra items
+        existing_entries = self.__query_by_id_local(tenant, tenant_venue, doc_id)
+        if len(existing_entries) < 1:
+            self.__es.index_one(json_body, doc_id, index=write_alias_name)  # TODO assuming granule_id is prefixed with collection id
+            return
+        latest_index_name = self.get_latest_index_name(tenant, tenant_venue)
+        existing_entry = existing_entries[0]
+        if existing_entry['_index'] == latest_index_name:
+            self.__es.index_one(json_body, doc_id, index=write_alias_name)  # TODO assuming granule_id is prefixed with collection id
+            self.__delete_old_entries(existing_entries[1:])
+            return
         self.__es.index_one(json_body, doc_id, index=write_alias_name)  # TODO assuming granule_id is prefixed with collection id
-        LOGGER.debug(f'custom_metadata indexed')
+        self.__delete_old_entries(existing_entries)
+        # TODO validate custom metadata vs the latest index to filter extra items
         return
 
     def dsl_search(self, tenant: str, tenant_venue: str, search_dsl: dict):
         read_alias_name = f'{DBConstants.granules_read_alias_prefix}_{tenant}_{tenant_venue}'.lower().strip()
-        if 'sort' not in search_dsl:
-            search_result = self.__es.query(search_dsl,
-                                            querying_index=read_alias_name) if 'sort' in search_dsl else self.__es.query(
-                search_dsl, querying_index=read_alias_name)
+        if 'sort' not in search_dsl:  # We cannot paginate w/o sort. So, max is 10k items:
+            # This also assumes "size" should be part of search_dsl
+            search_result = self.__es.query(search_dsl, querying_index=read_alias_name)
             LOGGER.debug(f'search_finished: {len(search_result["hits"]["hits"])}')
             return search_result
+        # we can run paginate search
         original_size = search_dsl['size'] if 'size' in search_dsl else 20
+        total_size = -999
         result = []
         duplicates = set([])
         while len(result) < original_size:
             search_dsl['size'] = (original_size - len(result)) * 2
-            search_result = self.__es.query_pages(search_dsl, querying_index=read_alias_name) if 'sort' in search_dsl else self.__es.query(search_dsl, querying_index=read_alias_name)
+            search_result = self.__es.query_pages(search_dsl, querying_index=read_alias_name)
+            if total_size == -999:
+                total_size = self.__es.get_result_size(search_result)
             if len(search_result['hits']['hits']) < 1:
                 break
             for each in search_result['hits']['hits']:
@@ -257,11 +327,16 @@ def dsl_search(self, tenant: str, tenant_venue: str, search_dsl: dict):
             search_dsl['search_after'] = search_result['hits']['hits'][-1]['sort']
 
         LOGGER.debug(f'search_finished: {len(result)}')
+        if len(result) > original_size:
+            result = result[:original_size]
         return {
             'hits': {
                 "total": {
-                    "value": len(result)
+                    "value": total_size,
                 },
                 'hits': result
             }
         }
+
+
+
diff --git a/cumulus_lambda_functions/uds_api/dapa/granules_dapa_query_es.py b/cumulus_lambda_functions/uds_api/dapa/granules_dapa_query_es.py
@@ -39,7 +39,7 @@ def __generate_es_dsl(self):
         if self.__filter_input is not None:
             query_terms.append(CqlParser('properties').transform(self.__filter_input))
         query_dsl = {
-            'track_total_hits': True,
+            'track_total_hits': self.__offset is None,
             'size': self.__limit,
             # "collapse": {"field": "id"},
             'sort': [
@@ -228,11 +228,11 @@ def start(self):
                 each_granules_query_result_stripped['links'].append(self_link)
                 self.__restructure_each_granule_result(each_granules_query_result_stripped)
 
-            pagination_link = '' if len(granules_query_result['hits']['hits']) < self.__limit else ','.join([k if isinstance(k, str) else str(k) for k in granules_query_result['hits']['hits'][-1]['sort']])
+            pagination_link = '' if len(granules_query_result['hits']['hits']) < 1 else ','.join([k if isinstance(k, str) else str(k) for k in granules_query_result['hits']['hits'][-1]['sort']])
             return {
                 'statusCode': 200,
                 'body': {
-                    'numberMatched': {'total_size': result_size},
+                    'numberMatched': {'total_size': -1 if self.__offset is not None else result_size},
                     'numberReturned': len(granules_query_result['hits']['hits']),
                     'stac_version': '1.0.0',
                     'type': 'FeatureCollection',  # TODO correct name?

diff --git a/cumulus_lambda_functions/uds_api/misc_api.py b/cumulus_lambda_functions/uds_api/misc_api.py
@@ -46,6 +46,13 @@ async def stac_entry(request: Request, response: Response):
 @router.get(f'/stac_entry')
 @router.get(f'/stac_entry/')
 async def stac_entry(request: Request, response: Response):
+    """
+    How to re-load UCS
+    https://github.com/unity-sds/unity-data-services/issues/381#issuecomment-2201165672
+    :param request:
+    :param response:
+    :return:
+    """
     request_headers = dict(request.headers)
     LOGGER.debug(f'stac_entry - request_headers: {request_headers}')
     print(request_headers)

diff --git a/cumulus_lambda_functions/uds_api/stac_browser/index.html b/cumulus_lambda_functions/uds_api/stac_browser/index.html
@@ -1 +1 @@
-<!doctype html><html lang="en"><head><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width,initial-scale=1"><meta id="meta-description" name="description" content=""><title>STAC Browser</title><script defer="defer" src="/to/be/replaced/stac_browser/js/chunk-vendors.eae96ced.js"></script><script defer="defer" src="/to/be/replaced/stac_browser/js/app.79583f94.js"></script><link href="/to/be/replaced/stac_browser/css/chunk-vendors.de510de6.css" rel="stylesheet"><link href="/to/be/replaced/stac_browser/css/app.b5efa536.css" rel="stylesheet"></head><body><noscript><strong>We're sorry but STAC Browser doesn't work properly without JavaScript enabled. Please enable it to continue.</strong></noscript><div id="stac-browser"></div></body></html>
+<!doctype html><html lang="en"><head><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width,initial-scale=1"><meta id="meta-description" name="description" content=""><title>STAC Browser</title><script defer="defer" src="/to/be/replaced/stac_browser/js/chunk-vendors.eae96ced.js"></script><script defer="defer" src="/to/be/replaced/stac_browser/js/app.ad7851bb.js"></script><link href="/to/be/replaced/stac_browser/css/chunk-vendors.de510de6.css" rel="stylesheet"><link href="/to/be/replaced/stac_browser/css/app.b5efa536.css" rel="stylesheet"></head><body><noscript><strong>We're sorry but STAC Browser doesn't work properly without JavaScript enabled. Please enable it to continue.</strong></noscript><div id="stac-browser"></div></body></html>
diff --git a/cumulus_lambda_functions/uds_api/stac_browser/js/app.79583f94.js.map b/cumulus_lambda_functions/uds_api/stac_browser/js/app.79583f94.js.map
diff --git a/...s/uds_api/stac_browser/js/app.79583f94.js → ...s/uds_api/stac_browser/js/app.ad7851bb.js b/...s/uds_api/stac_browser/js/app.79583f94.js → ...s/uds_api/stac_browser/js/app.ad7851bb.js
diff --git a/cumulus_lambda_functions/uds_api/stac_browser/js/app.ad7851bb.js.map b/cumulus_lambda_functions/uds_api/stac_browser/js/app.ad7851bb.js.map
diff --git a/cwl/stage-in-daac/README.md b/cwl/stage-in-daac/README.md
@@ -0,0 +1,7 @@
+# Test stage in data from DAAC
+
+Update `stac_json` value in stage-in-job-01.yml
+
+Run the following command with a CWL runner.
+
+`cwltool stage-in-workflow.cwl stage-in-job-01.yml`
diff --git a/cwl/stage-in-daac/stage-in-job-01.yml b/cwl/stage-in-daac/stage-in-job-01.yml
@@ -0,0 +1,2 @@
+download_dir: "granules"
+stac_json: "https://cmr.earthdata.nasa.gov/stac/LPCLOUD/collections/EMITL1BRAD_001/items?limit=2"
diff --git a/cwl/stage-in-daac/stage-in-workflow.cwl b/cwl/stage-in-daac/stage-in-workflow.cwl
@@ -0,0 +1,31 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+label: Workflow that executes the Sounder SIPS end-to-end chirp rebinngin workflow
+
+$namespaces:
+  cwltool: http://commonwl.org/cwltool#
+
+requirements:
+  SubworkflowFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
+  InlineJavascriptRequirement: {}
+  NetworkAccess:
+    networkAccess: true
+
+inputs:
+  download_dir: string
+  stac_json: string
+
+outputs:
+  data:
+    type: Directory
+    outputSource: stage-in/download_dir
+
+steps:
+    stage-in:
+      run: "stage-in.cwl"
+      in:
+        stac_json: stac_json
+        download_dir: download_dir
+      out: [download_dir]
diff --git a/cwl/stage-in-daac/stage-in.cwl b/cwl/stage-in-daac/stage-in.cwl
@@ -0,0 +1,39 @@
+cwlVersion: v1.2
+class: CommandLineTool
+
+baseCommand: ["DOWNLOAD"]
+
+requirements:
+  DockerRequirement:
+    dockerPull: ghcr.io/unity-sds/unity-data-services:9.4.0
+  NetworkAccess:
+    networkAccess: true
+  EnvVarRequirement:
+    envDef:
+      DOWNLOAD_DIR: $(runtime.outdir)/$(inputs.download_dir)
+      STAC_JSON: $(inputs.stac_json)
+      LOG_LEVEL: '10'
+      PARALLEL_COUNT: '-1'
+      DOWNLOAD_RETRY_WAIT_TIME: '30'
+      DOWNLOAD_RETRY_TIMES: '5'
+      DOWNLOADING_ROLES: 'data'
+
+      EDL_BASE_URL: 'https://urs.earthdata.nasa.gov/'
+      EDL_USERNAME: '/sps/processing/workflows/edl_username'
+      EDL_PASSWORD: '/sps/processing/workflows/edl_password'
+      EDL_PASSWORD_TYPE: 'PARAM_STORE'
+
+      VERIFY_SSL: 'TRUE'
+      STAC_AUTH_TYPE: 'NONE'
+
+inputs:
+  download_dir:
+    type: string
+  stac_json:
+    type: string
+
+outputs:
+  download_dir:
+    type: Directory
+    outputBinding:
+      glob: "$(inputs.download_dir)"
diff --git a/cwl/stage-in-json-str/README.md b/cwl/stage-in-json-str/README.md
@@ -0,0 +1,7 @@
+# Test stage in data from DAAC
+
+Update `stac_json` value in stage-in-job-01.yml
+
+Run the following command with a CWL runner.
+
+`cwltool stage-in-workflow.cwl stage-in-job-01.yml`
diff --git a/cwl/stage-in-json-str/stage-in-job-01.yml b/cwl/stage-in-json-str/stage-in-job-01.yml
@@ -0,0 +1,2 @@
+download_dir: "granules"
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		<!doctype html><html lang="en"><head><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width,initial-scale=1"><meta id="meta-description" name="description" content=""><title>STAC Browser</title><script defer="defer" src="/to/be/replaced/stac_browser/js/chunk-vendors.eae96ced.js"></script><script defer="defer" src="/to/be/replaced/stac_browser/js/app.ad7851bb.js"></script><link href="/to/be/replaced/stac_browser/css/chunk-vendors.de510de6.css" rel="stylesheet"><link href="/to/be/replaced/stac_browser/css/app.b5efa536.css" rel="stylesheet"></head><body><noscript><strong>We're sorry but STAC Browser doesn't work properly without JavaScript enabled. Please enable it to continue.</strong></noscript><div id="stac-browser"></div></body></html>
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		download_dir: "granules"
		stac_json: "https://cmr.earthdata.nasa.gov/stac/LPCLOUD/collections/EMITL1BRAD_001/items?limit=2"
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		download_dir: "granules"
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