Merge branch 'dev' into mcb-SOP-creation-SOP

GenomicDataInfrastructure · Aug 16, 2024 · 841aa92 · 841aa92
2 parents 6c60541 + 573a8ab
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diff --git a/docs/GDI-SOP_sop-template.md b/docs/GDI-SOP_sop-template.md
@@ -14,6 +14,7 @@ _< Title of the SOP prepended by "European GDI:". The title must remain the same
 |-------------------|---------------------|
 | Template SOP number  | _< ``GDI-SOP000...``. The number should be unique in the GDI SOP namespace. See [documentation](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/docs/GDI-SOP_sop-accessioning.md#identifier-format) for further details. >_ |
 | Template SOP version      | _< ``vY``. See [documentation](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/docs/GDI-SOP_sop-accessioning.md#identifier-format) >_ |
+| Topic      | _< One of the 4 topics in scope of the SOPs: Data protection & security; Data & metadata management; Technical infrastructure & software development; Helpdesk & operations >_ |
 | Template SOP Type      | _< Either "Node-specific SOP" or "European-Level SOP". See [documentation](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/docs/GDI-SOP_sop-accessioning.md#sop-life-cycle) >_ |
 | GDI Node   | _< Unique Alpha-3 code for the node (e.g. SWE for Sweden). Only needed if the node is instancing the template. >_ |
 | Instance version     | _< ``vZ``. See [documentation](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/docs/GDI-SOP_sop-accessioning.md#identifier-format). Only needed if a node is instancing the template. >_ |
@@ -25,8 +26,8 @@ _< Title of the SOP prepended by "European GDI:". The title must remain the same
 3. [Roles and Responsibilities](#3-roles-and-responsibilities)
 4. [Purpose](#4-purpose)
 5. [Scope](#5-scope)
-6. [Introduction and Background Information - as needed](#6-introduction-and-background-information)
-7. [Summary or Context Diagram - as needed](#7-summary-or-context-diagram)
+6. [Introduction and Background Information](#6-introduction-and-background-information)
+7. [Summary or Context Diagram](#7-summary-or-context-diagram)
 8. [Procedure](#8-procedure)
 9. [References](#9-references)
 
@@ -45,7 +46,7 @@ _< Manual or automated tracking of the history of changes for this SOP. Notice h
 ### 2. Glossary
 _< This section is required >_
 
-_< Include definitions of node and/or SOP-specific concepts used in this SOP. >_
+_< Include definitions of node and/or SOP-specific concepts used in this SOP. Order items alphabetically. >_
 
 Find GDI SOPs common Glossary at the [**charter document**](https://github.com/GenomicDataInfrastructure/standard-operating-procedures/blob/main/docs/GDI-SOP_charter.md).
 

diff --git a/scripts/sop_index.py b/scripts/sop_index.py
@@ -42,6 +42,7 @@ def parse_sop(self, file_path: str) -> Dict:
             "Name": name_with_link,
             "Identifier": metadata.get("template sop number", ""),
             "Template version": metadata.get("template sop version", ""),
+            "Topic": metadata.get("topic", ""),
             "Type": metadata.get("template sop type", ""),
             "GDI Node": metadata.get("gdi node", ""),
             "Instance version": metadata.get("instance version", ""),

diff --git a/scripts/sop_linter.py b/scripts/sop_linter.py
@@ -90,7 +90,8 @@ def lr_check_metadata_table(self, soup: BeautifulSoup, file_path: str):
         # Expected format of the "Value" column of each row
         expected_metadata = {
             "template sop number": r"GDI-SOP\d{4}", # e.g.: GDI-SOP0001
-            "template sop version": self.is_valid_version, # e.g.: v1
+            "template sop version": self.is_valid_version, # e.g.: v1,
+            "topic": ["Data protection & security", "Data & metadata management", "Technical infrastructure & software development", "Helpdesk & operations"],
             "template sop type": ["Node-specific SOP", "European-level SOP"],
             "gdi node": r"^[A-Z]{3}$", # e.g.: SWE (for Sweden)
             "instance version": self.is_valid_version, # e.g.: v1