Merge branch 'main' into ZH-349

CHANGELOG.md

@@ -8,15 +8,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 - [``GDI-SOP_github-introduction-for-maintainers.md``](docs/GDI-SOP_github-introduction-for-maintainers.md) - Introductory guide for GDI SOP Repository maintainers.
-- [``review_reminder.yml``](.github/workflows/review_reminder.yml) - GH Workflow to preiodically (monthly) and automatically (through [check_sop_reviews.py](scripts/check_sop_reviews.py)) create SOP review reminders (GH issues)
+
+### Modified
+### Fixed
+
+## [1.0.0](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/releases/tag/v1.0.0) - 2024-10-28
+
+### Added
+- [``GDI-SOP0003_SOP-1+MG-DAC-Recommendation-Approval.md``](sops/european-level/GDI-SOP0003_SOP-1+MG-DAC-Recommendation-Approval.md) - European-level SOP describing how the 1+MG DAC is to review data access requests and recommend their rejection or approval.
+- [``GDI-SOP0002_NCPs-veto-EDIC-decision.md``](sops/node-specific/GDI-SOP0002_NCPs-veto-EDIC-decision.md) - Node-specific SOP Template describing how NCPs may veto EDIC decisions on data requests.
+- [``GDI-SOP0007_SOP-template-creation.md``](sops/european-level/GDI-SOP0007_SOP-template-creation.md) - European-level SOP describing how to develop new SOP templates.
+- [``review_reminder.yml``](.github/workflows/review_reminder.yml) - GH Workflow to periodically (monthly) and automatically (through [check_sop_reviews.py](scripts/check_sop_reviews.py)) create SOP review reminders (GH issues)
 - [``check_sop_reviews.py``](scripts/check_sop_reviews.py) - Script to automatically check if SOPs are due for review and create GitHub issues if so
 - [``GDI-SOP_organisational-roles-and-responsibilities.md``](docs/GDI-SOP_organisational-roles-and-responsibilities.md) - Documentation containing Organisational Roles and Responsibilities for GDI SOPs.
+- [``GDI-SOP_information-service-management.md``](GDI-SOP_information-service-management.md) - Framework designed to systematically manage SOPs information flows across the GDI infrastructure
 - [``GDI-SOP_review-checklist.md``](docs/GDI-SOP_review-checklist.md) - Documentation guidelines in the form of checklists, for reviewers, approvers and authorizers of SOPs.
-- [``GDI-SOP_charter.md``](docs/GDI-SOP_charter.md) - Documentation Charter of the task 4.3
 - [``compare_index.py``](scripts/compare_index.py) - Script to automatically check if the SOP index table is up to date
 - [``sop_index.py``](scripts/sop_index.py) - Script to automatically create the SOP index table
 - [``utils.py``](scripts/utils.py) - General functions used by other scripts
 - [``sops/README.md``](sops/README.md) - Markdown containing the SOP index table
+- [``GDI-SOP_charter.md``](docs/GDI-SOP_charter.md) - Documentation Charter of the task 4.3
 - [``tests/``](tests/) - Directory containing tests to run GH repo's code
 - [``requirements.txt``](requirements.txt) - Needed modules to run GH repo's code
 - [``lint_sops.yml``](.github/workflows/lint_sops.yml) - GH Workflow to trigger linter on PRs
@@ -31,5 +42,3 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [``GDI-SOP_style-guide.md``](docs/GDI-SOP_style-guide.md) - Draft of styling guide
 - [``README.md``](README.md) - Main repository's readme
 - [``LICENSE``](LICENSE) - Repository license
-- [``CONTRIBUTING.md``](CONTRIBUTING.md) - Guidance for repository contributions
-- [``GDI-SOP_information-service-management.md``](GDI-SOP_information-service-management.md) - Framework designed to systematically manage SOPs information flows across the GDI infrastructure

scripts/sop_linter.py

@@ -110,13 +110,20 @@ def lr_check_metadata_table(self, soup: BeautifulSoup, file_path: str):
 
         for key, value in table_dict.items():
             # Linting rules for node-specific SOPs should not apply for european-level ones
-            if key in ["gdi node", "instance version"]:
+            node_specific_keys = ["gdi node", "instance version"]
+            if key in node_specific_keys:
                 try:
                     if table_dict["template sop type"].lower() == "European-level SOP".lower():
                         continue
                 except:
                     pass
 
+                # We only want to evaluate each key Node-specific key format if any is present.
+                #   Otherwise, it could be a Node-specific SOP template (correct without these keys)
+                if all(table_dict.get(key) in [None, "", []] for key in node_specific_keys):
+                    self.report_issue(f"At the metadata table, value column for '{key}' was empty. If the SOP is a Node-specific SOP Instance (not a template), it should have a value.", file_path, warning=True)
+                    continue
+
             if key in expected_metadata:
                 # Depending on the type of format rules for each row, we apply them differently
                 if isinstance(expected_metadata[key], str) and not re.match(expected_metadata[key], value):

sops/README.md

@@ -1,5 +1,7 @@
 # European GDI SOP Index
 Below you can find the full list of SOPs in this repository.
-| Name                                                                                                | Identifier   | Template version   | Topic                      | Type               | GDI Node   | Instance version   |   Nº steps | Last modified   |
-|:----------------------------------------------------------------------------------------------------|:-------------|:-------------------|:---------------------------|:-------------------|:-----------|:-------------------|-----------:|:----------------|
-| | | | | | | | | |
+| Name                                                                                                                        | Identifier   | Template version   | Topic                      | Type               | GDI Node   | Instance version   |   Nº steps | Last modified   |
+|:----------------------------------------------------------------------------------------------------------------------------|:-------------|:-------------------|:---------------------------|:-------------------|:-----------|:-------------------|-----------:|:----------------|
+| [GDI-SOP0002_NCPs-veto-EDIC-decision.md](./node-specific/GDI-SOP0002_NCPs-veto-EDIC-decision.md)                            | GDI-SOP0002  | v1                 | Helpdesk & operations      | Node-specific SOP  |            |                    |          7 | 2024.09.27      |
+| [GDI-SOP0003_SOP-1+MG-DAC-Recommendation-Approval.md](./european-level/GDI-SOP0003_SOP-1+MG-DAC-Recommendation-Approval.md) | GDI-SOP0003  | v1                 | Data & metadata management | European-Level SOP |            |                    |         10 | 2024.10.24      |
+| [GDI-SOP0007_SOP-template-creation.md](./european-level/GDI-SOP0007_SOP-template-creation.md)                               | GDI-SOP0007  | v1                 | Helpdesk & operations      | European-Level SOP |            |                    |          7 | 2024.07.08      |