IGVF-1686-software-version-req

src/igvfd/schemas/changelogs/software_version.md

@@ -1,5 +1,12 @@
 ## Changelog for *`software_version.json`*
 
+### Schema version 6
+
+* Require `award`.
+* Require `lab`.
+* Require `software`.
+* Require `version`.
+
 ### Schema version 5
 
 * Require `release_timestamp` for any objects with `released` or `archived` status.

src/igvfd/schemas/software_version.json

@@ -24,6 +24,12 @@
  ]
  }
  ],
+ "required": [
+ "award",
+ "lab",
+ "software",
+ "version"
+ ],
  "identifyingProperties": [
  "uuid",
  "aliases",
@@ -54,7 +60,7 @@
  },
  "properties": {
  "schema_version": {
- "default": "5"
+ "default": "6"
  },
  "software": {
  "title": "Software",

src/igvfd/tests/fixtures/schemas/software.py

@@ -15,6 +15,19 @@ def software(testapp, lab, award):
  return testapp.post_json('/software', item, status=201).json['@graph'][0]
 
 
+@pytest.fixture
+def software_graphreg(testapp, lab, award):
+ item = {
+ 'award': award['@id'],
+ 'lab': lab['@id'],
+ 'title': 'Graphreg',
+ 'name': 'graphreg',
+ 'description': 'GraphReg (Chromatin interaction aware gene regulatory modeling with graph attention networks) is a graph neural network based gene regulation model.',
+ 'source_url': 'https://genome.cshlp.org/content/32/5/930.full'
+ }
+ return testapp.post_json('/software', item, status=201).json['@graph'][0]
+
+
 @pytest.fixture
 def software_v1(software):
  item = software.copy()

src/igvfd/tests/fixtures/schemas/software_version.py

@@ -51,3 +51,9 @@ def software_version_v3(software_version_v2):
  'description': '',
  })
  return item
+
+
+@pytest.fixture
+def software_version_v5(testapp):
+ item = {}
+ return item

src/igvfd/tests/test_upgrade_software_version.py

@@ -30,3 +30,22 @@ def test_software_version_upgrade_3_4(upgrader, software_version_v3):
  current_version='3', target_version='4')
  assert value['schema_version'] == '4'
  assert 'description' not in value
+
+
+def test_software_version_upgrade_5_6(upgrader, software_version_v5):
+ value = upgrader.upgrade(
+ 'software_version', software_version_v5,
+ current_version='5', target_version='6')
+ assert value['schema_version'] == '6'
+ assert value['software'] == '/software/graphreg/'
+ assert value['version'] == 'v1.0.0'
+ assert value['notes'].endswith(
+ 'This software version lacked a link to a software '
+ 'and has been upgraded to link to /software/graphreg/ '
+ 'as a placeholder. This software version lacked a version '
+ 'and has been upgraded to v1.0.0 as a placeholder. This '
+ 'software version lacked a lab and has been upgraded to '
+ '/labs/j-michael-cherry/ as a placeholder. This software '
+ 'version lacked an award and has been upgraded to '
+ '/awards/HG012012/ as a placeholder.'
+ )

src/igvfd/upgrade/software_version.py

@@ -42,3 +42,29 @@ def software_version_4_5(value, system):
  notes = value.get('notes', '')
  notes += f'This object\'s release_timestamp has been set to 2024-03-06T12:34:56Z'
  value['notes'] = notes.strip()
+
+
+@upgrade_step('software_version', '5', '6')
+def software_version_5_6(value, system):
+ # https://igvf.atlassian.net/browse/IGVF-1686
+ software_note = ''
+ version_note = ''
+ lab_note = ''
+ award_note = ''
+ if 'software' not in value:
+ value['software'] = '/software/graphreg/'
+ software_note = 'This software version lacked a link to a software and has been upgraded to link to /software/graphreg/ as a placeholder.'
+ if 'version' not in value:
+ value['version'] = 'v1.0.0'
+ version_note = 'This software version lacked a version and has been upgraded to v1.0.0 as a placeholder.'
+ if 'lab' not in value:
+ value['lab'] = '/labs/j-michael-cherry/'
+ lab_note = 'This software version lacked a lab and has been upgraded to /labs/j-michael-cherry/ as a placeholder.'
+ if 'award' not in value:
+ value['award'] = '/awards/HG012012/'
+ award_note = 'This software version lacked an award and has been upgraded to /awards/HG012012/ as a placeholder.'
+ merged_note = ' '.join([x for x in [software_note, version_note, lab_note, award_note] if x != ''])
+ notes = value.get('notes', '')
+ notes += merged_note
+ if notes:
+ value['notes'] = notes.strip()