Merge pull request #121 from EOSC-synergy/release/2.0.0

Release/2.0.0
EOSC-synergy · Mar 8, 2024 · 255b279 · 255b279
2 parents fe4a854 + 79cdb76
commit 255b279
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diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
+    - uses: pre-commit/[email protected]
diff --git a/QC.FAIR/Dockerfile b/QC.FAIR/Dockerfile
@@ -1,16 +1,17 @@
 FROM python:3
 
-LABEL authors="Fernando Aguilar <[email protected]>, Pablo Orviz <[email protected]>"
-
-# FAIR-eva client
-COPY fair-eva.py /usr/bin/fair-eva.py
-RUN chmod +x /usr/bin/fair-eva.py
+LABEL authors="Pablo Orviz <[email protected]>, Fernando Aguilar <[email protected]>"
 
 # Deploy FAIR-eva API
 WORKDIR /FAIR_eva
-RUN git clone https://github.com/EOSC-synergy/FAIR_eva.git .
+RUN git clone https://github.com/EOSC-synergy/FAIR_eva.git -b release/2.0.0 .
 RUN pip3 install -r requirements.txt
 
+# FAIR-eva client
+RUN cp /FAIR_eva/scripts/fair-eva.py /usr/bin/fair-eva.py
+RUN chmod +x /usr/bin/fair-eva.py
+
+# Set config & run
 RUN cp config.ini.template config.ini
 EXPOSE 9090
 ENTRYPOINT ["/FAIR_eva/fair.py"]
diff --git a/QC.FAIR/fair-eva.py b/QC.FAIR/fair-eva.py
diff --git a/QC.Uni/pytest/Dockerfile b/QC.Uni/pytest/Dockerfile
@@ -0,0 +1,3 @@
+FROM python:3.9-alpine
+RUN python3 -m pip install pytest==7.1.3 \
+                           pytest-json-report==1.5.0
diff --git a/docs/tooling.md b/docs/tooling.md
@@ -56,7 +56,7 @@ The `args` property enables the definition of the arguments involved in the tool
 | `value` | *any type* | The value of the argument | |
 | `option` | string | The option name (*only applicable for optional arguments*). See [Special option values](#special-option-values) section for additional customization | :white_check_mark: (for optional arguments) |
 | `format` | string (enum) | (for API clients) the value's data type. Useful for graphical interfaces, provides the means to render the form elements (inputs, text areas, dropdowns, ..). Choose between [`string`, `array`] | :white_check_mark: (for API clients) |
-| `selectable` | boolean | (for API clients) Whether the argument's value shall be customized by the user, or otherwise it is a fixed (non-modifiable) value | :white_check_mark: (for API clients) |
+| `selectable` | boolean | (for API clients) Whether the argument's value shall be customized by the user, or otherwise it is a fixed (non-modifiable) value. Non-selectable arguments are always set | :white_check_mark: (for API clients) |
 | `repeatable` | boolean | (for API clients) Whether the same argument can be used several times | :white_check_mark: (for API clients) |
 | `explicit_paths` | boolean | (for API clients) Only applicable for the assessment, whether the `value` property shall be set with the explicit list of files detected in the repository  | :white_check_mark: (for API clients) |
 | `args` | object | Suitable when defining commands with more than one type of argument, it allows to define nested `args` properties | |

diff --git a/tooling.json b/tooling.json
@@ -239,6 +239,30 @@
             }
         },
         "Python": {
+	        "pytest": {
+                "version": "7.1.3",
+                "docs": "https://pytest.org/",
+                "docker": {
+                    "image": "eoscsynergy/sqaaas-pytest:7.1.3-alpha",
+                    "reviewed": "2023-08-09"
+                },
+                "args": [
+                    {
+                        "id": "test_path", "type": "positional", "description": "path to the folder containing the test cases", "value": "", "format": "string", "selectable": true, "repeatable": true
+                    },
+                    {
+                        "id": "json_report", "type": "optional", "description": "create JSON report", "option": "--json-report", "value": "", "format": "string", "selectable": false, "repeatable": false
+                    },
+                    {
+                        "id": "json_report_indent", "type": "optional", "description": "pretty-print JSON with specified indentation level", "option": "--json-report-indent", "value": "4", "format": "string", "selectable": false, "repeatable": false
+                    }
+                ],
+                "reporting": {
+                    "validator": "jenkins_exit_status",
+                    "requirement_level": "REQUIRED",
+                    "subcriterion": "QC.Uni01"
+                }
+            },
             "bandit": {
                 "version": "1.7.4",
                 "docs": "https://bandit.readthedocs.io/",
@@ -317,9 +341,15 @@
                         "type": "optional", "description": "Path to the tox.ini file", "option": "-c", "value": "tox.ini", "format": "string", "selectable": true
                     },
                     {
-                        "type": "optional", "description": "Test environment", "option": "-e", "value": "", "format": "string", "selectable": true, "repeatable": true
+                        "id": "tox_env", "type": "optional", "description": "Test environment", "option": "-e", "value": "", "format": "string", "selectable": true, "repeatable": true
                     }
-                ]
+                ],
+                "reporting": {
+                    "validator": "jenkins_exit_status",
+                    "subcriterion": ["QC.Uni01", "QC.Sec02", "QC.Sty01"],
+                    "lang_name": "Python",
+                    "tool_name": "tox"
+                }
 
             }
         },
@@ -329,22 +359,25 @@
                 "version": "latest",
                 "docs": "QC.FAIR/fair-eva.py",
                 "docker": {
-                    "image": "eoscsynergy/sqaaas-fair_eva:2.0.0-alpha1",
+                    "image": "eoscsynergy/sqaaas-fair_eva:epos-prototype-alpha6",
                     "oneshot": false,
                     "reviewed": "2022-04-05"
                 },
                 "args": [
                     {
-                        "type": "optional", "format": "string", "description": "Persistent Identifier", "id": "persistent_identifier", "option": "-ID", "value": "http://hdl.handle.net/10261/157765", "selectable": true
+                        "type": "optional", "format": "string", "description": "Identifier of the (meta)data", "id": "persistent_identifier", "option": "--id", "value": "http://hdl.handle.net/10261/157765", "selectable": true
+                    },
+                    {
+                        "type": "optional", "format": "string", "description": "FAIR EVA plugin name", "id": "metadata_protocol", "option": "--plugin", "value": "oai-pmh", "selectable": true
                     },
                     {
-                        "type": "optional", "format": "string", "description": "FAIR EVA plugin", "id": "metadata_protocol", "option": "-R", "value": "oai-pmh", "selectable": true
+                        "type": "optional", "format": "string", "description": "(meta)data repository endpoint", "id": "metadata_endpoint", "option": "--repository", "value": "http://digital.csic.es/dspace-oai/request", "selectable": true
                     },
                     {
-                        "type": "optional", "format": "string", "description": "OAI-PMH Endpoint", "id": "metadata_endpoint", "option": "-B", "value": "http://digital.csic.es/dspace-oai/request", "selectable": true
+                        "type": "optional", "format": "string", "description": "FAIR EVA endpoint", "id": "evaluator_endpoint", "option": "--api-endpoint", "value": "http://localhost:9090/v1.0/rda/rda_all", "selectable": false
                     },
                     {
-                        "type": "optional", "format": "string", "description": "FAIR EVA endpoint", "id": "evaluator_endpoint", "option": "--tool_endpoint", "value": "http://localhost:9090/v1.0/rda/rda_all", "selectable": false
+                        "type": "optional", "format": "string", "description": "Provides JSON output", "option": "--json", "value": "", "selectable": false
                     }
                 ],
             	"reporting": {
@@ -693,15 +726,21 @@
             "commands": {
                 "docs": "https://indigo-dc.github.io/jenkins-pipeline-library/2.0.0/user/config_file.html#commands",
                 "docker": {
-                    "image": "alpine:3.15.0",
+                    "image": "eoscsynergy/sqaaas-micromamba:1.5.3-1",
                     "reviewed": "1970-01-01"
                 },
                 "executable": "",
                 "args": [
                     {
-                        "type": "positional", "description": "Commands", "value": "", "format": "string", "selectable": true, "repeatable": true
+                        "id": "commands", "type": "positional", "description": "Commands", "value": "", "format": "string", "selectable": true, "repeatable": true
                     }
-                ]
+                ],
+                "reporting": {
+                    "validator": "jenkins_exit_status",
+                    "subcriterion": "QC.Uni01",
+                    "lang_name": "bash",
+                    "tool_name": "bash"
+                }
             }
         }
     },
@@ -804,7 +843,7 @@
                 "docs": "https://indigo-dc.github.io/sqa-baseline/#unit-testing-qc.uni"
             },
             "tools": {
-                "Python": ["tox"]
+                "Python": ["tox", "pytest"]
             }
         },
         "QC.Ver": {