diff --git a/.github/workflows/compare_index.yml b/.github/workflows/compare_index.yml index 361fd198..5fbab0ec 100644 --- a/.github/workflows/compare_index.yml +++ b/.github/workflows/compare_index.yml @@ -26,7 +26,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v4 with: - python-version: 3.x + python-version: "3.11" - name: Install dependencies run: | diff --git a/.github/workflows/lint_sops.yml b/.github/workflows/lint_sops.yml index e9de046e..0fddf485 100644 --- a/.github/workflows/lint_sops.yml +++ b/.github/workflows/lint_sops.yml @@ -26,7 +26,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v4 with: - python-version: 3.x + python-version: "3.11" - name: Install dependencies run: | diff --git a/.github/workflows/review_reminder.yml b/.github/workflows/review_reminder.yml index 3fc5246b..ac53c3e4 100644 --- a/.github/workflows/review_reminder.yml +++ b/.github/workflows/review_reminder.yml @@ -27,7 +27,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v4 with: - python-version: 3.x + python-version: "3.11" - name: Install dependencies run: | diff --git a/CHANGELOG.md b/CHANGELOG.md index eb38e383..8d7e4592 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [``GDI-SOP_github-introduction-for-maintainers.md``](docs/GDI-SOP_github-introduction-for-maintainers.md) - Introductory guide for GDI SOP Repository maintainers. ### Modified +- [``GDI-SOP_github-management.md``](docs/GDI-SOP_github-management.md) - Added reference to recorded session +- [``GDI-SOP0003_SOP-1+MG-DAC-Recommendation-Approval.md``](sops/european-level/GDI-SOP0003_SOP-1+MG-DAC-Recommendation-Approval.md) - Updated references to _[Data Governance for Research](https://docs.google.com/document/d/1P_nzGxMXG4CWzqkVbceY2fA3MQ7PEAwW/edit)_ document. - [``sop_linter.py``](scripts/sop_linter.py) - Added new Linting Rules (LR) modules: ``lr_check_procedure_step_numbering``, ``lr_check_step_consistency``, ``lr_check_glossary_in_charter``, ``lr_check_undefined_acronyms``, ``lr_check_resolvable_references``, ``lr_check_identifier_and_casing``, ``lr_check_title_match``, ``lr_check_image_paths`` - Improved code and added a new file location check to ``lr_check_metadata_table``. @@ -17,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [``tests/``](tests/) - Updated ``tests/GDI-SOP0000_sop-template-for-linting.md`` to fit testing standards of the linting script. - [``GDI-SOP_charter.md``](docs/GDI-SOP_charter.md) - Updated Glossary section with new acronyms and terms from other three SOPs. - [``GDI-SOP_style-guide.md``](docs/GDI-SOP_style-guide.md) - Added section regarding positioning of tables in MD files. + ### Fixed - [``GDI-SOP0002_ncps-veto-edic-decision.md``](sops/node-specific/GDI-SOP0002_ncps-veto-edic-decision.md): - ``v1.0.1``: Updated Glossary, fixed Procedure headers, and renamed file (previously in uppercase). diff --git a/docs/GDI-SOP_github-management.md b/docs/GDI-SOP_github-management.md index 6bf53b80..ec70d8e7 100644 --- a/docs/GDI-SOP_github-management.md +++ b/docs/GDI-SOP_github-management.md @@ -1,6 +1,8 @@ # Copying GDI SOP repository The GDI SOP repository ([**GenomicDataInfrastructure/standard-operating-procedures**](https://github.com/GenomicDataInfrastructure/standard-operating-procedures)) contains both European-level SOP _instances_ and Node-specific SOP _templates_. In order to adapt the Node-specific SOP templates, GDI nodes are expected to make a copy of this GitHub repository and modify them to suit them to their needs. +If you are a member of GDI, you are welcome to go through the [**recorded session**](https://drive.google.com/file/d/1DMbFP1xwu48aOPARTK2y_IVjFYt1bz10/view?usp=drive_link) where we covered this introduction. + Given that the base repository is public, forks of this repository cannot be private. Therefore, making a node's copy of the repository can be done in different ways, explained in this document, depending on the level of privacy that each node may require: - **Public node's repository**. If the node does not require a private repository, copying the source repository is straightforward. See section _[1. Public repository](#1-public-repository)_. - **Private node's repository**. On the contrary, if nodes need their SOP instances to be private (e.g. for security reasons), an alternative route is taken. See section _[2. Private repository](#2-private-repository)_. diff --git a/sops/README.md b/sops/README.md index 51c0c3b9..e06b3844 100644 --- a/sops/README.md +++ b/sops/README.md @@ -3,5 +3,5 @@ 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 | |:--------------------------------------------------------------------------------------------------------------------|:-------------|:-------------------|:---------------------------|:-------------------|:-----------|:-------------------|-----------:|:----------------| | [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 | 2024.10.29 | -| [GDI-SOP0003_1+mg-dac-recommendation-approval.md](./european-level/GDI-SOP0003_1+mg-dac-recommendation-approval.md) | GDI-SOP0003 | v1 | Data & metadata management | European-Level SOP | | | 10 | 2024.10.29 | +| [GDI-SOP0003_1+mg-dac-recommendation-approval.md](./european-level/GDI-SOP0003_1+mg-dac-recommendation-approval.md) | GDI-SOP0003 | v1 | Data & metadata management | European-Level SOP | | | 10 | 2024.11.11 | | [GDI-SOP0007_sop-template-creation.md](./european-level/GDI-SOP0007_sop-template-creation.md) | GDI-SOP0007 | v1 | Helpdesk & operations | European-Level SOP | | | 7 | 2024.10.29 | \ No newline at end of file diff --git a/sops/european-level/GDI-SOP0003_1+mg-dac-recommendation-approval.md b/sops/european-level/GDI-SOP0003_1+mg-dac-recommendation-approval.md index d6eab6cb..ed6b9fa3 100644 --- a/sops/european-level/GDI-SOP0003_1+mg-dac-recommendation-approval.md +++ b/sops/european-level/GDI-SOP0003_1+mg-dac-recommendation-approval.md @@ -25,6 +25,7 @@ | Template Version | Instance version | Author(s) | Description of changes | Date | |------------------|------------------|-------------------|----------------------------------|------------| +| ``v1.0.3`` | | Marcos Casado Barbero | Update references to Data Governance for Research document | ``2024.11.11`` | | ``v1.0.2`` | | Marcos Casado Barbero | Updated to linting rules - [PR46](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/pull/46) | ``2024.10.29`` | | ``v1.0.1`` | | Marcos Casado Barbero | Transform document to markdown and complete version | ``2024.10.24`` | | ``v1`` | | Marcos Casado Barbero | Transform document to markdown and complete version | ``2024.10.04`` | @@ -124,7 +125,7 @@ graph TB |-----------------|--------------------------------------------|--------------| | 1 | On receipt of notification of a new data access application | 1+MG DAC | -As the 1+MG DAC, **check the requester's application**, based on the criteria in the [**Data Access Review**](https://docs.google.com/document/d/19HVf7SP2R_fCI-KugVStZR4yEAkV6vhvSbVd6a2ZviU/edit?tab=t.0#bookmark=kix.9o5agsar78sq) section of the Data Governance document. The application form, which is used to help the data requester enter valid and complete information for the application, must be checked to ensure that: +As the 1+MG DAC, **check the requester's application**, based on the criteria in the _**Data Access Review**_ section of the [**Data Governance document**](https://docs.google.com/document/d/1P_nzGxMXG4CWzqkVbceY2fA3MQ7PEAwW/edit) (``v1.0``). The application form, which is used to help the data requester enter valid and complete information for the application, must be checked to ensure that: - The research has [institutional sign-off](https://docs.google.com/document/d/1LJa_vWhqUtpNnw8hW7cmPoihImqELv9dgK7Bd826EHg/edit#heading=h.94zixl2wbth), if applicable. - The **data analysis plan** is present and suitable for the proposed research. - The **data minimisation principle** is met. @@ -132,11 +133,11 @@ As the 1+MG DAC, **check the requester's application**, based on the criteria in - The **ethical approval** has been obtained for the proposed research, where applicable, and that the approval is applicable for the proposed research and conclusions of the ethics review are followed. - The **funding mechanisms** for the proposed research are in place (if required). - The **project description** corresponds with the data analysis plan, and the **ethical approval and legal requirements** exist with respect to the requested data. -- Any **peer review** of the scientific validity of the proposed research exists. In case it does not, follow [**section II.3**](https://docs.google.com/document/d/19HVf7SP2R_fCI-KugVStZR4yEAkV6vhvSbVd6a2ZviU/edit?tab=t.0#bookmark=id.utnaek5ua0aa) of the Data Governance document. +- Any **peer review** of the scientific validity of the proposed research exists. In case it does not, follow section _**II.3**_ of the [**Data Governance document**](https://docs.google.com/document/d/1P_nzGxMXG4CWzqkVbceY2fA3MQ7PEAwW/edit) (``v1.0``). -You must **finish this initial assessment within 5 working days** (review [**agreed timelines**](https://docs.google.com/document/d/19HVf7SP2R_fCI-KugVStZR4yEAkV6vhvSbVd6a2ZviU/edit?tab=t.0#bookmark=kix.9o5agsar78sq) if needed). After this period,you shall **transmit the outcome of the review and a decision recommendation** to the 1+MG NCPs who can channel it to relevant bodies on the national level. +You must **finish this initial assessment within 5 working days** (review **agreed timelines** at section _**III. DATA ACCESS REVIEW**_ of the [**Data Governance document**](https://docs.google.com/document/d/1P_nzGxMXG4CWzqkVbceY2fA3MQ7PEAwW/edit) (``v1.0``) if needed). After this period, you shall **transmit the outcome of the review and a decision recommendation** to the 1+MG NCPs who can channel it to relevant bodies on the national level. -Be mindful that **this timeline may be affected** where the planned research affects vulnerable subjects or groups, as specified in [**section III.2**](https://docs.google.com/document/d/19HVf7SP2R_fCI-KugVStZR4yEAkV6vhvSbVd6a2ZviU/edit?tab=t.0#bookmark=id.xez4tqfoy9hq) of the Data Governance document. +Be mindful that **this timeline may be affected** where the planned research affects vulnerable subjects or groups, as specified in section _**III.2**_ of the [**Data Governance document**](https://docs.google.com/document/d/1P_nzGxMXG4CWzqkVbceY2fA3MQ7PEAwW/edit) (``v1.0``). Depending on the outcome of this initial evaluation: - If all steps are correct, move to **[step 2](#82-recommend-application-for-approval)**. @@ -238,4 +239,5 @@ This concludes the process resulting in rejection of the data request. | [3](../node-specific/GDI-SOP0002_ncps-veto-edic-decision.md) | European GDI SOP - NCPs veto EDIC Decision | | [4](https://docs.google.com/document/d/19HVf7SP2R_fCI-KugVStZR4yEAkV6vhvSbVd6a2ZviU) | 1+MG Data Access Governance for Research | | [5](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/issues/33) | European GDI - NCP review process of disagreement with 1+MG DAC recommendation | -| [6](https://docs.google.com/document/d/1LJa_vWhqUtpNnw8hW7cmPoihImqELv9dgK7Bd826EHg/edit#heading=h.94zixl2wbth) | European GDI - Obtain Institutional Sign-off | \ No newline at end of file +| [6](https://docs.google.com/document/d/1LJa_vWhqUtpNnw8hW7cmPoihImqELv9dgK7Bd826EHg/edit#heading=h.94zixl2wbth) | European GDI - Obtain Institutional Sign-off | +| [7](https://docs.google.com/document/d/1P_nzGxMXG4CWzqkVbceY2fA3MQ7PEAwW/edit) | Data Governance document (``v1.0``) | \ No newline at end of file