From 086ac1052948ba03f98bc898e9028b05648edd7d Mon Sep 17 00:00:00 2001 From: Noa Aviel Dove Date: Wed, 7 Aug 2024 18:01:25 -0700 Subject: [PATCH] fixup! [r] Use DCP2 schema name for HCA replica_type (#6453) --- .../data/verbatim/hca/pfb_entities.json | 14 +- .../service/data/verbatim/hca/pfb_schema.json | 222 +++++++++--------- 2 files changed, 118 insertions(+), 118 deletions(-) diff --git a/test/service/data/verbatim/hca/pfb_entities.json b/test/service/data/verbatim/hca/pfb_entities.json index dd65d389f..cdb1266ad 100644 --- a/test/service/data/verbatim/hca/pfb_entities.json +++ b/test/service/data/verbatim/hca/pfb_entities.json @@ -14,28 +14,28 @@ }, { "links": [], - "name": "file", + "name": "links", "ontology_reference": "", "properties": [], "values": {} }, { "links": [], - "name": "links", + "name": "project", "ontology_reference": "", "properties": [], "values": {} }, { "links": [], - "name": "project", + "name": "sequence_file", "ontology_reference": "", "properties": [], "values": {} }, { "links": [], - "name": "sample", + "name": "specimen_from_organism", "ontology_reference": "", "properties": [], "values": {} @@ -46,7 +46,7 @@ }, { "id": "70d1af4a-82c8-478a-8960-e9028b3616ca", - "name": "file", + "name": "sequence_file", "object": { "describedBy": "https://schema.humancellatlas.org/type/file/6.5.2/sequence_file", "file_core": { @@ -69,7 +69,7 @@ }, { "id": "0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb", - "name": "file", + "name": "sequence_file", "object": { "describedBy": "https://schema.humancellatlas.org/type/file/6.5.2/sequence_file", "file_core": { @@ -122,7 +122,7 @@ }, { "id": "a21dc760-a500-4236-bcff-da34a0e873d2", - "name": "sample", + "name": "specimen_from_organism", "object": { "biomaterial_core": { "biomaterial_id": "DID_scRSq06_pancreas", diff --git a/test/service/data/verbatim/hca/pfb_schema.json b/test/service/data/verbatim/hca/pfb_schema.json index 07228a90f..af50aa32f 100644 --- a/test/service/data/verbatim/hca/pfb_schema.json +++ b/test/service/data/verbatim/hca/pfb_schema.json @@ -222,85 +222,6 @@ "name": "cell_suspension", "type": "record" }, - { - "fields": [ - { - "name": "describedBy", - "namespace": "file", - "type": "string" - }, - { - "name": "file_core", - "namespace": "file", - "type": { - "fields": [ - { - "name": "file_format", - "namespace": "file.file_core", - "type": "string" - }, - { - "name": "file_name", - "namespace": "file.file_core", - "type": "string" - } - ], - "name": "file.file_core", - "type": "record" - } - }, - { - "name": "insdc_run", - "namespace": "file", - "type": { - "items": "string", - "type": "array" - } - }, - { - "name": "provenance", - "namespace": "file", - "type": { - "fields": [ - { - "name": "document_id", - "namespace": "file.provenance", - "type": "string" - }, - { - "name": "submission_date", - "namespace": "file.provenance", - "type": "string" - }, - { - "name": "update_date", - "namespace": "file.provenance", - "type": "string" - } - ], - "name": "file.provenance", - "type": "record" - } - }, - { - "name": "read_index", - "namespace": "file", - "type": "string" - }, - { - "name": "read_length", - "namespace": "file", - "type": "long" - }, - { - "name": "schema_type", - "namespace": "file", - "type": "string" - } - ], - "name": "file", - "type": "record" - }, { "fields": [ { @@ -592,59 +513,138 @@ "name": "project", "type": "record" }, + { + "fields": [ + { + "name": "describedBy", + "namespace": "sequence_file", + "type": "string" + }, + { + "name": "file_core", + "namespace": "sequence_file", + "type": { + "fields": [ + { + "name": "file_format", + "namespace": "sequence_file.file_core", + "type": "string" + }, + { + "name": "file_name", + "namespace": "sequence_file.file_core", + "type": "string" + } + ], + "name": "sequence_file.file_core", + "type": "record" + } + }, + { + "name": "insdc_run", + "namespace": "sequence_file", + "type": { + "items": "string", + "type": "array" + } + }, + { + "name": "provenance", + "namespace": "sequence_file", + "type": { + "fields": [ + { + "name": "document_id", + "namespace": "sequence_file.provenance", + "type": "string" + }, + { + "name": "submission_date", + "namespace": "sequence_file.provenance", + "type": "string" + }, + { + "name": "update_date", + "namespace": "sequence_file.provenance", + "type": "string" + } + ], + "name": "sequence_file.provenance", + "type": "record" + } + }, + { + "name": "read_index", + "namespace": "sequence_file", + "type": "string" + }, + { + "name": "read_length", + "namespace": "sequence_file", + "type": "long" + }, + { + "name": "schema_type", + "namespace": "sequence_file", + "type": "string" + } + ], + "name": "sequence_file", + "type": "record" + }, { "fields": [ { "name": "biomaterial_core", - "namespace": "sample", + "namespace": "specimen_from_organism", "type": { "fields": [ { "name": "biomaterial_id", - "namespace": "sample.biomaterial_core", + "namespace": "specimen_from_organism.biomaterial_core", "type": "string" }, { "name": "ncbi_taxon_id", - "namespace": "sample.biomaterial_core", + "namespace": "specimen_from_organism.biomaterial_core", "type": { "items": "long", "type": "array" } } ], - "name": "sample.biomaterial_core", + "name": "specimen_from_organism.biomaterial_core", "type": "record" } }, { "name": "describedBy", - "namespace": "sample", + "namespace": "specimen_from_organism", "type": "string" }, { "name": "diseases", - "namespace": "sample", + "namespace": "specimen_from_organism", "type": { "items": { "fields": [ { "name": "ontology", - "namespace": "sample.diseases", + "namespace": "specimen_from_organism.diseases", "type": "string" }, { "name": "ontology_label", - "namespace": "sample.diseases", + "namespace": "specimen_from_organism.diseases", "type": "string" }, { "name": "text", - "namespace": "sample.diseases", + "namespace": "specimen_from_organism.diseases", "type": "string" } ], - "name": "sample.diseases", + "name": "specimen_from_organism.diseases", "type": "record" }, "type": "array" @@ -652,27 +652,27 @@ }, { "name": "genus_species", - "namespace": "sample", + "namespace": "specimen_from_organism", "type": { "items": { "fields": [ { "name": "ontology", - "namespace": "sample.genus_species", + "namespace": "specimen_from_organism.genus_species", "type": "string" }, { "name": "ontology_label", - "namespace": "sample.genus_species", + "namespace": "specimen_from_organism.genus_species", "type": "string" }, { "name": "text", - "namespace": "sample.genus_species", + "namespace": "specimen_from_organism.genus_species", "type": "string" } ], - "name": "sample.genus_species", + "name": "specimen_from_organism.genus_species", "type": "record" }, "type": "array" @@ -680,86 +680,86 @@ }, { "name": "organ", - "namespace": "sample", + "namespace": "specimen_from_organism", "type": { "fields": [ { "name": "ontology", - "namespace": "sample.organ", + "namespace": "specimen_from_organism.organ", "type": "string" }, { "name": "ontology_label", - "namespace": "sample.organ", + "namespace": "specimen_from_organism.organ", "type": "string" }, { "name": "text", - "namespace": "sample.organ", + "namespace": "specimen_from_organism.organ", "type": "string" } ], - "name": "sample.organ", + "name": "specimen_from_organism.organ", "type": "record" } }, { "name": "organ_part", - "namespace": "sample", + "namespace": "specimen_from_organism", "type": { "fields": [ { "name": "ontology", - "namespace": "sample.organ_part", + "namespace": "specimen_from_organism.organ_part", "type": "string" }, { "name": "ontology_label", - "namespace": "sample.organ_part", + "namespace": "specimen_from_organism.organ_part", "type": "string" }, { "name": "text", - "namespace": "sample.organ_part", + "namespace": "specimen_from_organism.organ_part", "type": "string" } ], - "name": "sample.organ_part", + "name": "specimen_from_organism.organ_part", "type": "record" } }, { "name": "provenance", - "namespace": "sample", + "namespace": "specimen_from_organism", "type": { "fields": [ { "name": "document_id", - "namespace": "sample.provenance", + "namespace": "specimen_from_organism.provenance", "type": "string" }, { "name": "submission_date", - "namespace": "sample.provenance", + "namespace": "specimen_from_organism.provenance", "type": "string" }, { "name": "update_date", - "namespace": "sample.provenance", + "namespace": "specimen_from_organism.provenance", "type": "string" } ], - "name": "sample.provenance", + "name": "specimen_from_organism.provenance", "type": "record" } }, { "name": "schema_type", - "namespace": "sample", + "namespace": "specimen_from_organism", "type": "string" } ], - "name": "sample", + "name": "specimen_from_organism", "type": "record" } ]