IGVF-2381-genomic-elements

src/igvfd/schemas/changelogs/reference_file.md

@@ -1,5 +1,24 @@
 ## Changelog for *`reference_file.json`*
 
+### Schema version 16
+
+* Adjust `content_type` enum list to remove `regulatory_regions`.
+* Adjust `content_type` enum list to remove `regulatory_regions_genes`.
+* Adjust `content_type` enum list to remove `regulatory_regions_genes_biosamples`.
+* Adjust `content_type` enum list to remove `regulatory_regions_genes_biosamples_donors`.
+* Adjust `content_type` enum list to remove `regulatory_regions_genes_biosamples_treatments_chebi`.
+* Adjust `content_type` enum list to remove `regulatory_regions_genes_biosamples_treatments_proteins`.
+* Adjust `content_type` enum list to remove `regulatory_regions_regulatory_regions`.
+* Adjust `content_type` enum list to remove `variants_regulatory_regions`.
+* Extend `content_type` enum list to include `genomic_elements` for admins.
+* Extend `content_type` enum list to include `genomic_elements_genes` for admins.
+* Extend `content_type` enum list to include `genomic_elements_genes_biosamples` for admins.
+* Extend `content_type` enum list to include `genomic_elements_genes_biosamples_donors` for admins.
+* Extend `content_type` enum list to include `genomic_elements_genes_biosamples_treatments_chebi` for admins.
+* Extend `content_type` enum list to include `genomic_elements_genes_biosamples_treatments_proteins` for admins.
+* Extend `content_type` enum list to include `genomic_elements_genomic_elements` for admins.
+* Extend `content_type` enum list to include `variants_genomic_elements` for admins.
+
 ### Minor changes since schema version 15
 
 * Extend `transcriptome_annotation` enum list to include `GENCODE 22`.

src/igvfd/schemas/reference_file.json

@@ -127,7 +127,7 @@
     "type": "object",
     "properties": {
         "schema_version": {
-            "default": "15"
+            "default": "16"
         },
         "content_type": {
             "comment": "Content Type describes the content of the file.",
@@ -172,13 +172,13 @@
                         "pathways_pathways",
                         "proteins",
                         "proteins_proteins",
-                        "regulatory_regions",
-                        "regulatory_regions_genes",
-                        "regulatory_regions_genes_biosamples",
-                        "regulatory_regions_genes_biosamples_donors",
-                        "regulatory_regions_genes_biosamples_treatments_chebi",
-                        "regulatory_regions_genes_biosamples_treatments_proteins",
-                        "regulatory_regions_regulatory_regions",
+                        "genomic_elements",
+                        "genomic_elements_genes",
+                        "genomic_elements_genes_biosamples",
+                        "genomic_elements_genes_biosamples_donors",
+                        "genomic_elements_genes_biosamples_treatments_chebi",
+                        "genomic_elements_genes_biosamples_treatments_proteins",
+                        "genomic_elements_genomic_elements",
                         "sequence barcodes",
                         "studies",
                         "studies_variants",
@@ -199,7 +199,7 @@
                         "variants_proteins_terms",
                         "variants_proteins_biosamples",
                         "variants_proteins_phenotypes",
-                        "variants_regulatory_regions",
+                        "variants_genomic_elements",
                         "variants_variants",
                         "vector sequences"
                     ],

src/igvfd/tests/data/inserts/reference_file.json

@@ -211,13 +211,13 @@
         "uuid": "6d1a1811-2133-474d-b3b1-a07ad1f7e4e1",
         "accession": "IGVFFI6791GUEE",
         "aliases": [
-            "igvf:tsv_regulatory_regions_regulatory_regions"
+            "igvf:tsv_genomic_elements_genomic_elements"
         ],
         "lab": "j-michael-cherry",
         "award": "HG012012",
         "md5sum": "ee570198468d172dc018978a49b7db53",
         "file_format": "tsv",
-        "content_type": "regulatory_regions_regulatory_regions",
+        "content_type": "genomic_elements_genomic_elements",
         "file_format_specifications": [
             "igvf:file_format_specification_insert"
         ],

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

@@ -155,3 +155,83 @@ def reference_file_v14(reference_file_v6):
         'external_id': 'ENCFF743WOO'
     })
     return item
+
+
+@pytest.fixture
+def reference_file_v15_regulatory_regions(reference_file_v6):
+    item = reference_file_v6.copy()
+    item.update({
+        'schema_version': '15',
+        'content_type': 'regulatory_regions'
+    })
+    return item
+
+
+@pytest.fixture
+def reference_file_v15_regulatory_regions_genes(reference_file_v6):
+    item = reference_file_v6.copy()
+    item.update({
+        'schema_version': '15',
+        'content_type': 'regulatory_regions_genes'
+    })
+    return item
+
+
+@pytest.fixture
+def reference_file_v15_regulatory_regions_genes_biosamples(reference_file_v6):
+    item = reference_file_v6.copy()
+    item.update({
+        'schema_version': '15',
+        'content_type': 'regulatory_regions_genes_biosamples'
+    })
+    return item
+
+
+@pytest.fixture
+def reference_file_v15_regulatory_regions_genes_biosamples_donors(reference_file_v6):
+    item = reference_file_v6.copy()
+    item.update({
+        'schema_version': '15',
+        'content_type': 'regulatory_regions_genes_biosamples_donors'
+    })
+    return item
+
+
+@pytest.fixture
+def reference_file_v15_regulatory_regions_genes_biosamples_treatments_chebi(reference_file_v6):
+    item = reference_file_v6.copy()
+    item.update({
+        'schema_version': '15',
+        'content_type': 'regulatory_regions_genes_biosamples_treatments_chebi'
+    })
+    return item
+
+
+@pytest.fixture
+def reference_file_v15_regulatory_regions_genes_biosamples_treatments_proteins(reference_file_v6):
+    item = reference_file_v6.copy()
+    item.update({
+        'schema_version': '15',
+        'content_type': 'regulatory_regions_genes_biosamples_treatments_proteins'
+    })
+    return item
+
+
+@pytest.fixture
+def reference_file_v15_regulatory_regions_regulatory_regions(reference_file_v6):
+    item = reference_file_v6.copy()
+    item.update({
+        'schema_version': '15',
+        'content_type': 'regulatory_regions_regulatory_regions'
+    })
+    return item
+
+
+@pytest.fixture
+def reference_file_v15_variants_regulatory_regions(reference_file_v6):
+    item = reference_file_v6.copy()
+    item.update({
+        'schema_version': '15',
+        'content_type': 'variants_regulatory_regions'
+    })
+    return item

src/igvfd/tests/test_upgrade_reference_file.py

@@ -78,3 +78,59 @@ def test_reference_file_upgrade_14_15(upgrader, reference_file_v14):
     value = upgrader.upgrade('reference_file', reference_file_v14, current_version='14', target_version='15')
     assert 'external_id' not in value
     assert value['schema_version'] == '15'
+
+
+def test_reference_file_upgrade_15_16_regulatory_regions(upgrader, reference_file_v15_regulatory_regions):
+    value = upgrader.upgrade('reference_file', reference_file_v15_regulatory_regions,
+                             current_version='15', target_version='16')
+    assert value['content_type'] == 'genomic_elements'
+    assert value['schema_version'] == '16'
+
+
+def test_reference_file_upgrade_15_16_regulatory_regions_genes(upgrader, reference_file_v15_regulatory_regions_genes):
+    value = upgrader.upgrade('reference_file', reference_file_v15_regulatory_regions_genes,
+                             current_version='15', target_version='16')
+    assert value['content_type'] == 'genomic_elements_genes'
+    assert value['schema_version'] == '16'
+
+
+def test_reference_file_upgrade_15_16_regulatory_regions_genes_biosamples(upgrader, reference_file_v15_regulatory_regions_genes_biosamples):
+    value = upgrader.upgrade('reference_file', reference_file_v15_regulatory_regions_genes_biosamples,
+                             current_version='15', target_version='16')
+    assert value['content_type'] == 'genomic_elements_genes_biosamples'
+    assert value['schema_version'] == '16'
+
+
+def test_reference_file_upgrade_15_16_regulatory_regions_genes_biosamples_donors(upgrader, reference_file_v15_regulatory_regions_genes_biosamples_donors):
+    value = upgrader.upgrade('reference_file', reference_file_v15_regulatory_regions_genes_biosamples_donors,
+                             current_version='15', target_version='16')
+    assert value['content_type'] == 'genomic_elements_genes_biosamples_donors'
+    assert value['schema_version'] == '16'
+
+
+def test_reference_file_upgrade_15_16_regulatory_regions_genes_biosamples_treatments_chebi(upgrader, reference_file_v15_regulatory_regions_genes_biosamples_treatments_chebi):
+    value = upgrader.upgrade('reference_file', reference_file_v15_regulatory_regions_genes_biosamples_treatments_chebi,
+                             current_version='15', target_version='16')
+    assert value['content_type'] == 'genomic_elements_genes_biosamples_treatments_chebi'
+    assert value['schema_version'] == '16'
+
+
+def test_reference_file_upgrade_15_16_regulatory_regions_genes_biosamples_treatments_proteins(upgrader, reference_file_v15_regulatory_regions_genes_biosamples_treatments_proteins):
+    value = upgrader.upgrade('reference_file', reference_file_v15_regulatory_regions_genes_biosamples_treatments_proteins,
+                             current_version='15', target_version='16')
+    assert value['content_type'] == 'genomic_elements_genes_biosamples_treatments_proteins'
+    assert value['schema_version'] == '16'
+
+
+def test_reference_file_upgrade_15_16_regulatory_regions_regulatory_regions(upgrader, reference_file_v15_regulatory_regions_regulatory_regions):
+    value = upgrader.upgrade('reference_file', reference_file_v15_regulatory_regions_regulatory_regions,
+                             current_version='15', target_version='16')
+    assert value['content_type'] == 'genomic_elements_genomic_elements'
+    assert value['schema_version'] == '16'
+
+
+def test_reference_file_upgrade_15_16_variants_regulatory_regions(upgrader, reference_file_v15_variants_regulatory_regions):
+    value = upgrader.upgrade('reference_file', reference_file_v15_variants_regulatory_regions,
+                             current_version='15', target_version='16')
+    assert value['content_type'] == 'variants_genomic_elements'
+    assert value['schema_version'] == '16'

src/igvfd/upgrade/file.py

@@ -393,3 +393,49 @@ def sequence_file_14_15_alignment_file_12_13(value, system):
         # Coerce values like 28.0 to ints.
         if k in value:
             value[k] = int(value[k])
+
+
+@upgrade_step('reference_file', '15', '16')
+def reference_file_15_16(value, system):
+    # https://igvf.atlassian.net/browse/IGVF-2381
+    notes = value.get('notes', '')
+    if value['content_type'] == 'regulatory_regions':
+        value['content_type'] = 'genomic_elements'
+        notes += f' This file\'s content_type was regulatory_regions, but has been upgraded to genomic_elements.'
+    if notes.strip() != '':
+        value['notes'] = notes.strip()
+    if value['content_type'] == 'regulatory_regions_genes':
+        value['content_type'] = 'genomic_elements_genes'
+        notes += f' This file\'s content_type was regulatory_regions_genes, but has been upgraded to genomic_elements_genes.'
+    if notes.strip() != '':
+        value['notes'] = notes.strip()
+    if value['content_type'] == 'regulatory_regions_genes_biosamples':
+        value['content_type'] = 'genomic_elements_genes_biosamples'
+        notes += f' This file\'s content_type was regulatory_regions_genes_biosamples, but has been upgraded to genomic_elements_genes_biosamples.'
+    if notes.strip() != '':
+        value['notes'] = notes.strip()
+    if value['content_type'] == 'regulatory_regions_genes_biosamples_donors':
+        value['content_type'] = 'genomic_elements_genes_biosamples_donors'
+        notes += f' This file\'s content_type was regulatory_regions_genes_biosamples_donors, but has been upgraded to genomic_elements_genes_biosamples_donors.'
+    if notes.strip() != '':
+        value['notes'] = notes.strip()
+    if value['content_type'] == 'regulatory_regions_genes_biosamples_treatments_chebi':
+        value['content_type'] = 'genomic_elements_genes_biosamples_treatments_chebi'
+        notes += f' This file\'s content_type was regulatory_regions_genes_biosamples_treatments_chebi, but has been upgraded to genomic_elements_genes_biosamples_treatments_chebi.'
+    if notes.strip() != '':
+        value['notes'] = notes.strip()
+    if value['content_type'] == 'regulatory_regions_genes_biosamples_treatments_proteins':
+        value['content_type'] = 'genomic_elements_genes_biosamples_treatments_proteins'
+        notes += f' This file\'s content_type was regulatory_regions_genes_biosamples_treatments_proteins, but has been upgraded to genomic_elements_genes_biosamples_treatments_proteins.'
+    if notes.strip() != '':
+        value['notes'] = notes.strip()
+    if value['content_type'] == 'regulatory_regions_regulatory_regions':
+        value['content_type'] = 'genomic_elements_genomic_elements'
+        notes += f' This file\'s content_type was regulatory_regions_regulatory_regions, but has been upgraded to genomic_elements_genomic_elements.'
+    if notes.strip() != '':
+        value['notes'] = notes.strip()
+    if value['content_type'] == 'variants_regulatory_regions':
+        value['content_type'] = 'variants_genomic_elements'
+        notes += f' This file\'s content_type was variants_regulatory_regions, but has been upgraded to variants_genomic_elements.'
+    if notes.strip() != '':
+        value['notes'] = notes.strip()