Merge pull request #731 from hubmapconsortium/Derek-Furst/change-coll…

…ections-creators-to-contributors

Derek furst/change collections creators to contributors

bulk-registration/example-sample-registrations.tsv

@@ -4,7 +4,7 @@ f083597a5ebb0fae68c17b28bd5b3bc7	test_smpl_01	organ	HT	https://dx.doi.org/10.175
 HBM854.MBMF.586	test_sample_2	biopsy		https://dx.doi.org/10.17504/protocols.io.dkasfkkaadf	another random comment	
 a0572d23c12e18e963f5404292b3d153	test sample 3	blood		10.17504/protocols.io.adskfadfadf		
 ff5180d5994eef2526629a710017874f	test sample 4	FRESH_TISSUE		10.17504/protocols.io.mjeisdfasdf		
-2f9522d5462d7cc22a667417c6b80623	test sample 4a	fresh_frozen_oct_block		10.17504/protocols.io.zujdiskshjy		{"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084", "@type": "SpatialEntity", "label": "SpatialEntity for Male, Age 21, BMI 21.8", "creator": "Jeff Spraggins", "creator_first_name": "Jeff", "creator_last_name": "Spraggins", "creation_date": "2/12/2020 9:48:13 AM", "ccf_annotations": [], "x_dimension": 23, "y_dimension": 18, "z_dimension": 5, "dimension_units": "millimeter", "placement": {"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084_placement", "@type": "SpatialPlacement", "target": "http://purl.org/ccf/latest/ccf.owl#VHRightKidney", "placement_date": "2/12/2020 9:48:13 AM", "x_scaling": 1, "y_scaling": 1, "z_scaling": 1, "scaling_units": "ratio", "x_rotation": 0, "y_rotation": 0, "z_rotation": 247.9199981689453, "rotation_order": "XYZ", "rotation_units": "degree", "x_translation": -2.729999542236328, "y_translation": 33.220001220703125, "z_translation": -8.940000534057617, "translation_units": "millimeter"}}
+2f9522d5462d7cc22a667417c6b80623	test sample 4a	fresh_frozen_oct_block		10.17504/protocols.io.zujdiskshjy		{"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084", "@type": "SpatialEntity", "label": "SpatialEntity for Male, Age 21, BMI 21.8", "contributor": "Jeff Spraggins", "contributor_first_name": "Jeff", "contributor_last_name": "Spraggins", "creation_date": "2/12/2020 9:48:13 AM", "ccf_annotations": [], "x_dimension": 23, "y_dimension": 18, "z_dimension": 5, "dimension_units": "millimeter", "placement": {"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084_placement", "@type": "SpatialPlacement", "target": "http://purl.org/ccf/latest/ccf.owl#VHRightKidney", "placement_date": "2/12/2020 9:48:13 AM", "x_scaling": 1, "y_scaling": 1, "z_scaling": 1, "scaling_units": "ratio", "x_rotation": 0, "y_rotation": 0, "z_rotation": 247.9199981689453, "rotation_order": "XYZ", "rotation_units": "degree", "x_translation": -2.729999542236328, "y_translation": 33.220001220703125, "z_translation": -8.940000534057617, "translation_units": "millimeter"}}
 a22c4514e7e40a641d1ea5cdcdb63582	test sample 5 fail invalid organ type	fresh_frozen_oct_block	LV	10.17504/protocols.io.kkdjdiudi		
 HBM265.FCRT.233	test sample 6 fail bad organ code	organ	bad_code	10.17504/protocols.io.zsdfasdfadf		
 ba906793fcba084898ac24e850d5a964	test sample 7 fail bad protocol	fresh_frozen_oct_block		10.A7504/protocols.io.adskfadfadf	If this were a real description you'd be finding out some relevant information now	
@@ -17,5 +17,5 @@ ffd96a39274136284f5x66c7730a4d98	test-sample-13-misformatted id	gdna		10.17504/p
 6b955ebeafe9c351831bc36aa086575f	test-sample-14 fail incorrect source type	gdna		10.17504/protocols.io.siaskasfadsf		
 75f837c40c1248e9d53cecf049dc88a6	test-sample-15 fail incorrect source type2	organ	RK	10.17504/protocols.io.fiadsfiasdfadf		
 	fail test_sample_16 missing protocol	biopsy				
-1222af1638d9bc176f393710cc8b2ebf	fail test sample-16 invalid rui json	fresh_frozen_oct_block		10.17504/protocols.io.ifjoijrlksfsdf		{ "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084", "@type": "SpatialEntity", "label": "SpatialEntity for Male, Age 21, BMI 21.8", "creator": "Jeff Spraggins", "creator_first_name": "Jeff", "creator_last_name": "Spraggins", "creation_date": "2/12/2020 9:48:13 AM", "ccf_annotations": [], "x_dimension": 23, "y_dimension": 18, "z_dimension": 5, "dimension_units": "millimeter", "placement": {"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084_placement", "@type": "SpatialPlacement", "target": "http://purl.org/ccf/latest/ccf.owl#VHRightKidney", "placement_date": "2/12/2020 9:48:13 AM", "x_scaling": 1, "y_scaling": 1, "z_scaling": 1, "scaling_units": "ratio", "x_rotation": 0, "y_rotation": 0, "z_rotation": 247.9199981689453, "rotation_order": "XYZ", "rotation_units": "degree", "x_translation": -2.729999542236328, "y_translation": 33.220001220703125, "z_translation": -8.940000534057617, "translation_units": "millimeter"}}"
-0cf6c31efb7463eb036d474369dfec11	fail test sample-17 organ with RUI info	organ	LK	10.17504/protocols.io.yeuiwwerwe		{"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084", "@type": "SpatialEntity", "label": "SpatialEntity for Male, Age 21, BMI 21.8", "creator": "Jeff Spraggins", "creator_first_name": "Jeff", "creator_last_name": "Spraggins", "creation_date": "2/12/2020 9:48:13 AM", "ccf_annotations": [], "x_dimension": 23, "y_dimension": 18, "z_dimension": 5, "dimension_units": "millimeter", "placement": {"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084_placement", "@type": "SpatialPlacement", "target": "http://purl.org/ccf/latest/ccf.owl#VHRightKidney", "placement_date": "2/12/2020 9:48:13 AM", "x_scaling": 1, "y_scaling": 1, "z_scaling": 1, "scaling_units": "ratio", "x_rotation": 0, "y_rotation": 0, "z_rotation": 247.9199981689453, "rotation_order": "XYZ", "rotation_units": "degree", "x_translation": -2.729999542236328, "y_translation": 33.220001220703125, "z_translation": -8.940000534057617, "translation_units": "millimeter"}}
+1222af1638d9bc176f393710cc8b2ebf	fail test sample-16 invalid rui json	fresh_frozen_oct_block		10.17504/protocols.io.ifjoijrlksfsdf		{ "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084", "@type": "SpatialEntity", "label": "SpatialEntity for Male, Age 21, BMI 21.8", "contributor": "Jeff Spraggins", "contributor_first_name": "Jeff", "contributor_last_name": "Spraggins", "creation_date": "2/12/2020 9:48:13 AM", "ccf_annotations": [], "x_dimension": 23, "y_dimension": 18, "z_dimension": 5, "dimension_units": "millimeter", "placement": {"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084_placement", "@type": "SpatialPlacement", "target": "http://purl.org/ccf/latest/ccf.owl#VHRightKidney", "placement_date": "2/12/2020 9:48:13 AM", "x_scaling": 1, "y_scaling": 1, "z_scaling": 1, "scaling_units": "ratio", "x_rotation": 0, "y_rotation": 0, "z_rotation": 247.9199981689453, "rotation_order": "XYZ", "rotation_units": "degree", "x_translation": -2.729999542236328, "y_translation": 33.220001220703125, "z_translation": -8.940000534057617, "translation_units": "millimeter"}}"
+0cf6c31efb7463eb036d474369dfec11	fail test sample-17 organ with RUI info	organ	LK	10.17504/protocols.io.yeuiwwerwe		{"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084", "@type": "SpatialEntity", "label": "SpatialEntity for Male, Age 21, BMI 21.8", "contributor": "Jeff Spraggins", "contributor_first_name": "Jeff", "contributor_last_name": "Spraggins", "creation_date": "2/12/2020 9:48:13 AM", "ccf_annotations": [], "x_dimension": 23, "y_dimension": 18, "z_dimension": 5, "dimension_units": "millimeter", "placement": {"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084_placement", "@type": "SpatialPlacement", "target": "http://purl.org/ccf/latest/ccf.owl#VHRightKidney", "placement_date": "2/12/2020 9:48:13 AM", "x_scaling": 1, "y_scaling": 1, "z_scaling": 1, "scaling_units": "ratio", "x_rotation": 0, "y_rotation": 0, "z_rotation": 247.9199981689453, "rotation_order": "XYZ", "rotation_units": "degree", "x_translation": -2.729999542236328, "y_translation": 33.220001220703125, "z_translation": -8.940000534057617, "translation_units": "millimeter"}}

entity-api-spec.yaml

@@ -902,7 +902,7 @@ components:
           type: string
           readOnly: true
           description: "The url from the doi registry for this entity. e.g. https://doi.org/10.35079/hbm289.pcbm.487"
-        creators:
+        contributors:
           type: array
           items:
             $ref: '#/components/schemas/Person'

src/app.py

@@ -584,9 +584,9 @@ def _get_entity_visibility(normalized_entity_type, entity_dict):
         'registered_doi' in entity_dict and \
         'doi_url' in entity_dict and \
         'contacts' in entity_dict and \
-        'creators' in entity_dict and \
+        'contributors' in entity_dict and \
         len(entity_dict['contacts']) > 0 and \
-        len(entity_dict['creators']) > 0:
+        len(entity_dict['contributors']) > 0:
             # Get the data_access_level for each Dataset in the Collection from Neo4j
             collection_dataset_statuses = schema_neo4j_queries.get_collection_datasets_statuses(neo4j_driver_instance
                                                                                                 ,entity_dict['uuid'])

src/schema/provenance_schema.yaml

@@ -240,8 +240,8 @@ ENTITIES:
           - halt_update_if_DOI_exists
           - halt_DOI_if_collection_missing_elements
           - halt_if_DOI_for_unpublished_dataset
-      # Creators and contacts are required for a Collection to be public
-      creators:
+      # Contributors and contacts are required for a Collection to be public
+      contributors:
         type: list
         indexed: true
         description: "See description in doi_properties section above"

src/schema/schema_validators.py

@@ -157,9 +157,9 @@ def halt_DOI_if_collection_missing_elements(property_key, normalized_entity_type
     if 'contacts' not in existing_data_dict:
         raise ValueError(f"Unable to modify existing {existing_data_dict['entity_type']}"
                          f" {existing_data_dict['uuid']} for DOI because it has no contacts.")
-    if 'creators' not in existing_data_dict:
+    if 'contributors' not in existing_data_dict:
         raise ValueError(f"Unable to modify existing {existing_data_dict['entity_type']}"
-                         f" {existing_data_dict['uuid']} for DOI because it has no creators.")
+                         f" {existing_data_dict['uuid']} for DOI because it has no contributors.")
     # Count up other validations to check 'datasets', since a transient property
 
 """

src/schema_templating/example-yaml-templates/api-template-test/entity-Template.yaml

@@ -855,7 +855,7 @@ x-ref-components:
           type: string
           readOnly: true
           description: "The url from the doi registry for this entity. e.g. https://doi.org/10.35079/hbm289.pcbm.487"
-        creators:
+        contributors:
           type: array
           items:
             $ref: '#/components/schemas/Person'

src/schema_templating/example-yaml-templates/collections-schema.yaml

@@ -53,7 +53,7 @@ Collection:
       type: string
       readOnly: true
       description: "The url from the doi registry for this entity. e.g. https://doi.org/10.35079/hbm289.pcbm.487"
-    creators:
+    contributors:
       type: array
       items:
         $ref: '#/components/schemas/Person'

src/schema_templating/example-yaml-templates/entity-api-spec-TEMPLATE.yaml

@@ -793,7 +793,7 @@ components:
           type: string
           readOnly: true
           description: "The url from the doi registry for this entity. e.g. https://doi.org/10.35079/hbm289.pcbm.487"
-        creators:
+        contributors:
           type: array
           items:
             $ref: '#/components/schemas/Person'