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Pre-release merge into Main #43

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Oct 28, 2024
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e5a1b03
mcb-SOP-creation-SOP - Add GDI-SOP0007 materials and document
M-casado Jul 8, 2024
d2002f5
mcb-SOP-creation-SOP - Transform MP4 to GIF
M-casado Jul 8, 2024
c2ec77f
mcb-SOP-creation-SOP - Ammend filepath
M-casado Jul 8, 2024
7697bfd
cb-SOP-creation-SOP - Add gif file
M-casado Jul 8, 2024
badf245
mcb-SOP-creation-SOP - Reorganise SOP
M-casado Jul 8, 2024
8b04784
mcb-SOP-creation-SOP - Amend history text
M-casado Jul 18, 2024
9b127f7
mcb-SOP-creation-SOP - Added extra tip on google docs
M-casado Jul 24, 2024
a6370f1
mcb-SOP-creation-SOP - Add more details to ORR section
M-casado Jul 29, 2024
48a635f
mcb-SOP-creation-SOP - Amend Organisations
M-casado Jul 29, 2024
c9683b1
mcb-SOP-creation-SOP - Update diagram
M-casado Jul 31, 2024
c107d5e
mcb-SOP-creation-SOP - Review process with GDI-CO feedback
M-casado Aug 2, 2024
1ea80cd
mcb-SOP-creation-SOP - Add more context
M-casado Aug 2, 2024
f39d61d
mcb-SOP-creation-SOP - Replace image
M-casado Aug 2, 2024
f08b730
mcb-SOP-creation-SOP - Update main README diagram
M-casado Aug 2, 2024
2da4a27
mcb-SOP-creation-SOP - Add feedback from Elisavet Torstensson
M-casado Aug 9, 2024
5b3a22e
mcb-SOP-creation-SOP - Clarify authorization text
M-casado Aug 12, 2024
35dc9da
Merge branch 'main' into mcb-SOP-creation-SOP
M-casado Aug 12, 2024
5bf77d3
mcb-SOP-creation-SOP - Update SOP index and lint SOP
M-casado Aug 12, 2024
15de7a2
mcb-SOP-creation-SOP - Update roles
M-casado Aug 12, 2024
fe4b0b6
mcb-SOP-creation-SOP - Add Topic to SOP index table and SOP
M-casado Aug 14, 2024
6c60541
mcb-SOP-creation-SOP - Address https://github.com/GenomicDataInfrastr…
M-casado Aug 16, 2024
841aa92
Merge branch 'dev' into mcb-SOP-creation-SOP
M-casado Aug 16, 2024
7b4d314
Merge pull request #13 from GenomicDataInfrastructure/mcb-SOP-creatio…
M-casado Aug 16, 2024
481c68b
ZH-261 - Add base document and image
M-casado Sep 27, 2024
71c3dbb
ZH-261 - New modifications to SOP
M-casado Sep 27, 2024
96d28a5
ZH-261 - Update CHANGELOG
M-casado Sep 27, 2024
0b3f8dc
ZH-261 - Update SOP index table
M-casado Sep 27, 2024
1095ab5
ZH-261 - Fix strict constraint for node-specific SOP templates
M-casado Sep 27, 2024
935a067
Merge branch 'main' into dev
M-casado Sep 27, 2024
ff52b9c
Merge branch 'dev' into ZH-261
M-casado Sep 27, 2024
76b6336
dev - Quick-fix to diagram newlines
M-casado Sep 27, 2024
e5a8520
ZH-252 - Addition of base SOP transformed to markdown
M-casado Sep 27, 2024
08bdcef
ZH-261 - Small correction on NCP acronym
M-casado Sep 27, 2024
64fe8f3
ZH-252 - New modifications to SOP
M-casado Sep 30, 2024
31b58e1
ZZH-252 - Amend title
M-casado Sep 30, 2024
a75208b
ZH-252 - Update Changelog and SOP table
M-casado Sep 30, 2024
fef1c69
ZH-252 - Amend mermaid diagram
M-casado Sep 30, 2024
044e5e2
ZH-261 - Address https://github.com/GenomicDataInfrastructure/standar…
M-casado Oct 4, 2024
7406ceb
ZH-261 - Address https://github.com/GenomicDataInfrastructure/standar…
M-casado Oct 4, 2024
a03b9a2
Merge branch 'ZH-261' of github.com:GenomicDataInfrastructure/standar…
M-casado Oct 4, 2024
69e4b11
Merge pull request #32 from GenomicDataInfrastructure/ZH-261
M-casado Oct 4, 2024
3e11fe3
ZH-252 - Address https://github.com/GenomicDataInfrastructure/standar…
M-casado Oct 4, 2024
51487b8
Merge branch 'dev' into ZH-252
M-casado Oct 4, 2024
f67d031
ZH-252 - Update date of last edit
M-casado Oct 4, 2024
2f02645
Merge pull request #34 from GenomicDataInfrastructure/ZH-252
M-casado Oct 4, 2024
0e40bd1
sop3-feedback - https://docs.google.com/document/d/1uWERFwki2KJJ3H28M…
M-casado Oct 22, 2024
514058d
sop3-feedback - https://docs.google.com/document/d/1uWERFwki2KJJ3H28M…
M-casado Oct 22, 2024
976ade7
sop3-feedback - https://docs.google.com/document/d/1uWERFwki2KJJ3H28M…
M-casado Oct 22, 2024
fc74c8e
sop3-feedback - https://docs.google.com/document/d/1uWERFwki2KJJ3H28M…
M-casado Oct 22, 2024
78e5464
sop3-feedback - https://docs.google.com/document/d/1uWERFwki2KJJ3H28M…
M-casado Oct 22, 2024
69c6dd3
sop3-feedback - Added Gergo as reviewer
M-casado Oct 22, 2024
6889118
sop3-feedback - https://docs.google.com/document/d/1uWERFwki2KJJ3H28M…
M-casado Oct 22, 2024
0d72a87
sop3-feedback - https://docs.google.com/document/d/1uWERFwki2KJJ3H28M…
M-casado Oct 22, 2024
9045e25
sop3-feedback - https://docs.google.com/document/d/1uWERFwki2KJJ3H28M…
M-casado Oct 22, 2024
7730a25
sop3-feedback - https://docs.google.com/document/d/1uWERFwki2KJJ3H28M…
M-casado Oct 22, 2024
d488f0d
sop3-feedback - https://docs.google.com/document/d/1uWERFwki2KJJ3H28M…
M-casado Oct 22, 2024
c258b4f
sop3-feedback - https://docs.google.com/document/d/1uWERFwki2KJJ3H28M…
M-casado Oct 22, 2024
17c65fb
sop3-feedback - Amend last edit date
M-casado Oct 23, 2024
e927098
sop3-feedback - Update index table
M-casado Oct 23, 2024
f4df33d
sop3-feedback - Address nfeedback from live session
M-casado Oct 24, 2024
0b77e0d
Merge pull request #38 from GenomicDataInfrastructure/sop3-feedback
M-casado Oct 28, 2024
862a9b2
Merge branch 'main' into dev
M-casado Oct 28, 2024
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8 changes: 6 additions & 2 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,15 +7,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased]

### 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 preiodically (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_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
- [``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
Expand All @@ -30,5 +36,3 @@ 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
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9 changes: 8 additions & 1 deletion scripts/sop_linter.py
Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand Down
8 changes: 5 additions & 3 deletions sops/README.md
Original file line number Diff line number Diff line change
@@ -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 |
1 change: 0 additions & 1 deletion sops/european-level/.gitignore

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