From 78dfa40c8b6e5bce44b215814df44f68838037ab Mon Sep 17 00:00:00 2001 From: ian-whaling Date: Mon, 27 Jan 2025 22:14:06 -0800 Subject: [PATCH 01/13] calculated property started --- src/igvfd/types/file_set.py | 62 ++++++++++++++++++++++++++----------- 1 file changed, 44 insertions(+), 18 deletions(-) diff --git a/src/igvfd/types/file_set.py b/src/igvfd/types/file_set.py index a42329c63..ca514552e 100644 --- a/src/igvfd/types/file_set.py +++ b/src/igvfd/types/file_set.py @@ -89,7 +89,9 @@ class FileSet(Item): Path('samples.disease_terms', include=['@id', 'term_name', 'status']), Path('samples.targeted_sample_term', include=['@id', 'term_name', 'status']), Path('samples.modifications', include=['@id', 'modality', 'status']), - Path('samples.treatments', include=['@id', 'treatment_term_name', 'status']), + Path('samples.treatments', include=['@id', 'purpose', 'treatment_type', 'summary', 'status']), + Path('samples.construct_library_sets.integrated_content_files', include=[ + '@id', 'accession', 'file_set_type', 'summary', 'status', 'content_type', 'integrated_content_files']), Path('publications', include=['@id', 'publication_identifiers', 'status']), ] @@ -747,12 +749,9 @@ class MeasurementSet(FileSet): Path('control_file_sets', include=['@id', 'accession', 'aliases', 'status']), Path('related_multiome_datasets', include=['@id', 'accession', 'status']), Path('auxiliary_sets', include=['@id', 'accession', 'aliases', 'file_set_type', 'status']), - Path('samples.treatments', include=['@id', 'purpose', 'treatment_type', 'summary', 'status']), Path('samples.cell_fate_change_treatments', include=['@id', 'purpose', 'treatment_type', 'summary', 'status']), - Path('samples.disease_terms', include=['@id', 'term_name', 'status']), - Path('samples.modifications', include=['@id', 'modality', 'status']), Path('samples.construct_library_sets.small_scale_gene_list', include=[ - '@id', 'file_set_type', 'accession', 'small_scale_gene_list', 'summary', 'geneid', 'symbol', 'name', 'status']), + '@id', 'small_scale_gene_list', 'summary', 'geneid', 'symbol', 'name', 'status']), Path('files.sequencing_platform', include=['@id', 'term_name', 'status']), Path('targeted_genes', include=['@id', 'geneid', 'symbol', 'name', 'synonyms', 'status']), Path('functional_assay_mechanisms', include=['@id', 'term_id', 'term_name', 'status']) @@ -1180,22 +1179,49 @@ class ConstructLibrarySet(FileSet): set_status_up = FileSet.set_status_up + [] set_status_down = FileSet.set_status_down + [] - @calculated_property(schema={ - 'title': 'Applied to Samples', - 'description': 'The samples that link to this construct library set.', - 'type': 'array', - 'minItems': 1, - 'uniqueItems': True, - 'items': { - 'title': 'Applied to Sample', - 'type': ['string', 'object'], - 'linkFrom': 'Sample.construct_library_sets', - }, - 'notSubmittable': True - }) + @calculated_property(define=True, + schema={ + 'title': 'Applied to Samples', + 'description': 'The samples that link to this construct library set.', + 'type': 'array', + 'minItems': 1, + 'uniqueItems': True, + 'items': { + 'title': 'Applied to Sample', + 'type': ['string', 'object'], + 'linkFrom': 'Sample.construct_library_sets', + }, + 'notSubmittable': True + }) def applied_to_samples(self, request, applied_to_samples): return paths_filtered_by_status(request, applied_to_samples) + @calculated_property( + condition='applied_to_samples', + schema={ + 'title': 'File Sets', + 'description': 'The file sets with samples that integrate this construct library set.', + 'type': 'array', + 'minItems': 1, + 'uniqueItems': True, + 'items': { + 'title': 'File Set', + 'type': ['string', 'object'], + 'linkTo': 'FileSet', + }, + 'notSubmittable': True + }) + def file_sets(self, request, applied_to_samples=None): + file_sets = [] + for sample in applied_to_samples: + sample_object = request.embed(sample, + '@@object_with_select_calculated_properties?' + 'field=file_sets' + ) + file_sets = file_sets + sample_object.get('file_sets', []) + if file_sets: + return file_sets + @calculated_property( schema={ 'title': 'Summary', From a4f4b6136ad1f6f60ac06f95cb50b67c5014de8f Mon Sep 17 00:00:00 2001 From: ian-whaling Date: Mon, 27 Jan 2025 22:30:04 -0800 Subject: [PATCH 02/13] moved around some embedding --- src/igvfd/types/file_set.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/igvfd/types/file_set.py b/src/igvfd/types/file_set.py index ca514552e..ee5ec61f1 100644 --- a/src/igvfd/types/file_set.py +++ b/src/igvfd/types/file_set.py @@ -1166,6 +1166,7 @@ class ConstructLibrarySet(FileSet): Path('orf_list', include=['@id', 'orf_id', 'genes', 'aliases', 'status']), Path('orf_list.genes', include=['@id', 'symbol', 'status']), Path('publications', include=['@id', 'publication_identifiers', 'status']), + Path('file_sets', include=['@id', '@type', 'accession', 'summary', 'status']), ] audit_inherit = [ 'award', From 36e9f85beafa5815f24cde2b9c29ddbb787c62bb Mon Sep 17 00:00:00 2001 From: ian-whaling Date: Wed, 29 Jan 2025 12:38:19 -0800 Subject: [PATCH 03/13] embed instead of calculate --- src/igvfd/types/file_set.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/igvfd/types/file_set.py b/src/igvfd/types/file_set.py index ee5ec61f1..eb6d27eba 100644 --- a/src/igvfd/types/file_set.py +++ b/src/igvfd/types/file_set.py @@ -1161,12 +1161,12 @@ class ConstructLibrarySet(FileSet): Path('applied_to_samples.targeted_sample_term', include=['@id', 'term_name', 'status']), Path('applied_to_samples.modifications', include=['@id', 'modality', 'summary', 'status']), Path('applied_to_samples.treatments', include=['@id', 'treatment_term_name', 'summary', 'status']), + Path('applied_to_samples.file_sets', include=['@id', '@type', 'accession', 'aliases', 'summary', 'status']), Path('large_scale_gene_list', include=['@id', 'accession', 'aliases', 'status']), Path('large_scale_loci_list', include=['@id', 'accession', 'aliases', 'status']), Path('orf_list', include=['@id', 'orf_id', 'genes', 'aliases', 'status']), Path('orf_list.genes', include=['@id', 'symbol', 'status']), Path('publications', include=['@id', 'publication_identifiers', 'status']), - Path('file_sets', include=['@id', '@type', 'accession', 'summary', 'status']), ] audit_inherit = [ 'award', From 49976ae92083637b36ac5c59a1902144459ab303 Mon Sep 17 00:00:00 2001 From: ian-whaling Date: Wed, 29 Jan 2025 12:42:28 -0800 Subject: [PATCH 04/13] mappings --- src/igvfd/mappings/analysis_set.json | 364 +++++++++++++++++- src/igvfd/mappings/auxiliary_set.json | 364 +++++++++++++++++- src/igvfd/mappings/construct_library_set.json | 302 ++++++++++++++- src/igvfd/mappings/curated_set.json | 364 +++++++++++++++++- src/igvfd/mappings/measurement_set.json | 171 +++++++- src/igvfd/mappings/model_set.json | 364 +++++++++++++++++- src/igvfd/mappings/prediction_set.json | 171 +++++++- src/igvfd/types/file_set.py | 27 +- 8 files changed, 2106 insertions(+), 21 deletions(-) diff --git a/src/igvfd/mappings/analysis_set.json b/src/igvfd/mappings/analysis_set.json index df56d518e..7564a8f77 100644 --- a/src/igvfd/mappings/analysis_set.json +++ b/src/igvfd/mappings/analysis_set.json @@ -1673,7 +1673,369 @@ "type": "keyword" }, "construct_library_sets": { - "type": "keyword" + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "applied_to_samples": { + "type": "keyword" + }, + "associated_phenotypes": { + "type": "keyword" + }, + "average_guide_coverage": { + "store": true, + "type": "float" + }, + "average_insert_size": { + "store": true, + "type": "float" + }, + "award": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "control_file_sets": { + "type": "keyword" + }, + "control_for": { + "type": "keyword" + }, + "control_type": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "exon": { + "type": "keyword" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { + "type": "keyword" + }, + "guide_type": { + "type": "keyword" + }, + "input_for": { + "type": "keyword" + }, + "integrated_content_files": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "analysis_step_version": { + "type": "keyword" + }, + "anvil_url": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assembly": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "barcode_map_for": { + "type": "keyword" + }, + "cell_type_annotation": { + "type": "keyword" + }, + "checkfiles_version": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "content_md5sum": { + "type": "keyword" + }, + "content_type": { + "type": "keyword" + }, + "controlled_access": { + "store": true, + "type": "boolean" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "derived_from": { + "type": "keyword" + }, + "derived_manually": { + "store": true, + "type": "boolean" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "external": { + "store": true, + "type": "boolean" + }, + "file_format": { + "type": "keyword" + }, + "file_format_specifications": { + "type": "keyword" + }, + "file_format_type": { + "type": "keyword" + }, + "file_set": { + "type": "keyword" + }, + "file_size": { + "store": true, + "type": "long" + }, + "gene_list_for": { + "type": "keyword" + }, + "href": { + "type": "keyword" + }, + "input_file_for": { + "type": "keyword" + }, + "integrated_in": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "loci_list_for": { + "type": "keyword" + }, + "md5sum": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "s3_uri": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "source_url": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_file_name": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "transcriptome_annotation": { + "type": "keyword" + }, + "upload_credentials": { + "properties": {}, + "type": "object" + }, + "upload_status": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "validation_error_detail": { + "type": "keyword" + }, + "workflow": { + "type": "keyword" + } + }, + "type": "object" + }, + "lab": { + "type": "keyword" + }, + "large_scale_gene_list": { + "type": "keyword" + }, + "large_scale_loci_list": { + "type": "keyword" + }, + "lot_id": { + "type": "keyword" + }, + "lower_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "lower_bound_insert_size": { + "store": true, + "type": "long" + }, + "notes": { + "type": "text" + }, + "orf_list": { + "type": "keyword" + }, + "product_id": { + "type": "keyword" + }, + "publications": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "scope": { + "type": "keyword" + }, + "selection_criteria": { + "type": "keyword" + }, + "small_scale_gene_list": { + "type": "keyword" + }, + "small_scale_loci_list": { + "properties": { + "assembly": { + "type": "keyword" + }, + "chromosome": { + "type": "keyword" + }, + "end": { + "store": true, + "type": "long" + }, + "start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_files_timestamp": { + "type": "date" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "targeton": { + "type": "keyword" + }, + "tile": { + "properties": { + "tile_end": { + "store": true, + "type": "long" + }, + "tile_id": { + "type": "keyword" + }, + "tile_start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "tiling_modality": { + "type": "keyword" + }, + "upper_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "upper_bound_insert_size": { + "store": true, + "type": "long" + }, + "uuid": { + "type": "keyword" + } + }, + "type": "object" }, "creation_timestamp": { "type": "date" diff --git a/src/igvfd/mappings/auxiliary_set.json b/src/igvfd/mappings/auxiliary_set.json index 8820a3995..ca46b89b7 100644 --- a/src/igvfd/mappings/auxiliary_set.json +++ b/src/igvfd/mappings/auxiliary_set.json @@ -1428,7 +1428,369 @@ "type": "keyword" }, "construct_library_sets": { - "type": "keyword" + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "applied_to_samples": { + "type": "keyword" + }, + "associated_phenotypes": { + "type": "keyword" + }, + "average_guide_coverage": { + "store": true, + "type": "float" + }, + "average_insert_size": { + "store": true, + "type": "float" + }, + "award": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "control_file_sets": { + "type": "keyword" + }, + "control_for": { + "type": "keyword" + }, + "control_type": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "exon": { + "type": "keyword" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { + "type": "keyword" + }, + "guide_type": { + "type": "keyword" + }, + "input_for": { + "type": "keyword" + }, + "integrated_content_files": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "analysis_step_version": { + "type": "keyword" + }, + "anvil_url": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assembly": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "barcode_map_for": { + "type": "keyword" + }, + "cell_type_annotation": { + "type": "keyword" + }, + "checkfiles_version": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "content_md5sum": { + "type": "keyword" + }, + "content_type": { + "type": "keyword" + }, + "controlled_access": { + "store": true, + "type": "boolean" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "derived_from": { + "type": "keyword" + }, + "derived_manually": { + "store": true, + "type": "boolean" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "external": { + "store": true, + "type": "boolean" + }, + "file_format": { + "type": "keyword" + }, + "file_format_specifications": { + "type": "keyword" + }, + "file_format_type": { + "type": "keyword" + }, + "file_set": { + "type": "keyword" + }, + "file_size": { + "store": true, + "type": "long" + }, + "gene_list_for": { + "type": "keyword" + }, + "href": { + "type": "keyword" + }, + "input_file_for": { + "type": "keyword" + }, + "integrated_in": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "loci_list_for": { + "type": "keyword" + }, + "md5sum": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "s3_uri": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "source_url": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_file_name": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "transcriptome_annotation": { + "type": "keyword" + }, + "upload_credentials": { + "properties": {}, + "type": "object" + }, + "upload_status": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "validation_error_detail": { + "type": "keyword" + }, + "workflow": { + "type": "keyword" + } + }, + "type": "object" + }, + "lab": { + "type": "keyword" + }, + "large_scale_gene_list": { + "type": "keyword" + }, + "large_scale_loci_list": { + "type": "keyword" + }, + "lot_id": { + "type": "keyword" + }, + "lower_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "lower_bound_insert_size": { + "store": true, + "type": "long" + }, + "notes": { + "type": "text" + }, + "orf_list": { + "type": "keyword" + }, + "product_id": { + "type": "keyword" + }, + "publications": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "scope": { + "type": "keyword" + }, + "selection_criteria": { + "type": "keyword" + }, + "small_scale_gene_list": { + "type": "keyword" + }, + "small_scale_loci_list": { + "properties": { + "assembly": { + "type": "keyword" + }, + "chromosome": { + "type": "keyword" + }, + "end": { + "store": true, + "type": "long" + }, + "start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_files_timestamp": { + "type": "date" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "targeton": { + "type": "keyword" + }, + "tile": { + "properties": { + "tile_end": { + "store": true, + "type": "long" + }, + "tile_id": { + "type": "keyword" + }, + "tile_start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "tiling_modality": { + "type": "keyword" + }, + "upper_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "upper_bound_insert_size": { + "store": true, + "type": "long" + }, + "uuid": { + "type": "keyword" + } + }, + "type": "object" }, "creation_timestamp": { "type": "date" diff --git a/src/igvfd/mappings/construct_library_set.json b/src/igvfd/mappings/construct_library_set.json index 27393fdb5..c4674520f 100644 --- a/src/igvfd/mappings/construct_library_set.json +++ b/src/igvfd/mappings/construct_library_set.json @@ -436,7 +436,307 @@ "type": "boolean" }, "file_sets": { - "type": "keyword" + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "applied_to_samples": { + "type": "keyword" + }, + "assay_term": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assemblies": { + "type": "keyword" + }, + "assessed_genes": { + "type": "keyword" + }, + "associated_phenotypes": { + "type": "keyword" + }, + "auxiliary_sets": { + "type": "keyword" + }, + "average_guide_coverage": { + "store": true, + "type": "float" + }, + "average_insert_size": { + "store": true, + "type": "float" + }, + "award": { + "type": "keyword" + }, + "barcode_map": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "control_file_sets": { + "type": "keyword" + }, + "control_for": { + "type": "keyword" + }, + "control_type": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "demultiplexed_sample": { + "type": "keyword" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "donors": { + "type": "keyword" + }, + "exon": { + "type": "keyword" + }, + "external_image_data_url": { + "type": "keyword" + }, + "external_image_url": { + "type": "keyword" + }, + "external_input_data": { + "type": "keyword" + }, + "externally_hosted": { + "store": true, + "type": "boolean" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { + "type": "keyword" + }, + "functional_assay_mechanisms": { + "type": "keyword" + }, + "guide_type": { + "type": "keyword" + }, + "input_file_sets": { + "type": "keyword" + }, + "input_for": { + "type": "keyword" + }, + "integrated_content_files": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "large_scale_gene_list": { + "type": "keyword" + }, + "large_scale_loci_list": { + "type": "keyword" + }, + "lot_id": { + "type": "keyword" + }, + "lower_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "lower_bound_insert_size": { + "store": true, + "type": "long" + }, + "measurement_sets": { + "type": "keyword" + }, + "model_name": { + "type": "keyword" + }, + "model_version": { + "type": "keyword" + }, + "model_zoo_location": { + "type": "keyword" + }, + "multiome_size": { + "store": true, + "type": "long" + }, + "notes": { + "type": "text" + }, + "onlist_files": { + "type": "keyword" + }, + "onlist_method": { + "type": "keyword" + }, + "orf_list": { + "type": "keyword" + }, + "prediction_objects": { + "type": "keyword" + }, + "preferred_assay_title": { + "type": "keyword" + }, + "product_id": { + "type": "keyword" + }, + "protocols": { + "type": "keyword" + }, + "publications": { + "type": "keyword" + }, + "related_multiome_datasets": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "sample_summary": { + "type": "keyword" + }, + "samples": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "scope": { + "type": "keyword" + }, + "selection_criteria": { + "type": "keyword" + }, + "sequencing_library_types": { + "type": "keyword" + }, + "small_scale_gene_list": { + "type": "keyword" + }, + "small_scale_loci_list": { + "properties": { + "assembly": { + "type": "keyword" + }, + "chromosome": { + "type": "keyword" + }, + "end": { + "store": true, + "type": "long" + }, + "start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "software_version": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_files_timestamp": { + "type": "date" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "targeted_genes": { + "type": "keyword" + }, + "targeton": { + "type": "keyword" + }, + "taxa": { + "type": "keyword" + }, + "tile": { + "properties": { + "tile_end": { + "store": true, + "type": "long" + }, + "tile_id": { + "type": "keyword" + }, + "tile_start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "tiling_modality": { + "type": "keyword" + }, + "transcriptome_annotations": { + "type": "keyword" + }, + "upper_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "upper_bound_insert_size": { + "store": true, + "type": "long" + }, + "url": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "workflows": { + "type": "keyword" + } + }, + "type": "object" }, "growth_medium": { "type": "keyword" diff --git a/src/igvfd/mappings/curated_set.json b/src/igvfd/mappings/curated_set.json index a1281de86..73916731d 100644 --- a/src/igvfd/mappings/curated_set.json +++ b/src/igvfd/mappings/curated_set.json @@ -1288,7 +1288,369 @@ "type": "keyword" }, "construct_library_sets": { - "type": "keyword" + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "applied_to_samples": { + "type": "keyword" + }, + "associated_phenotypes": { + "type": "keyword" + }, + "average_guide_coverage": { + "store": true, + "type": "float" + }, + "average_insert_size": { + "store": true, + "type": "float" + }, + "award": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "control_file_sets": { + "type": "keyword" + }, + "control_for": { + "type": "keyword" + }, + "control_type": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "exon": { + "type": "keyword" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { + "type": "keyword" + }, + "guide_type": { + "type": "keyword" + }, + "input_for": { + "type": "keyword" + }, + "integrated_content_files": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "analysis_step_version": { + "type": "keyword" + }, + "anvil_url": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assembly": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "barcode_map_for": { + "type": "keyword" + }, + "cell_type_annotation": { + "type": "keyword" + }, + "checkfiles_version": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "content_md5sum": { + "type": "keyword" + }, + "content_type": { + "type": "keyword" + }, + "controlled_access": { + "store": true, + "type": "boolean" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "derived_from": { + "type": "keyword" + }, + "derived_manually": { + "store": true, + "type": "boolean" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "external": { + "store": true, + "type": "boolean" + }, + "file_format": { + "type": "keyword" + }, + "file_format_specifications": { + "type": "keyword" + }, + "file_format_type": { + "type": "keyword" + }, + "file_set": { + "type": "keyword" + }, + "file_size": { + "store": true, + "type": "long" + }, + "gene_list_for": { + "type": "keyword" + }, + "href": { + "type": "keyword" + }, + "input_file_for": { + "type": "keyword" + }, + "integrated_in": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "loci_list_for": { + "type": "keyword" + }, + "md5sum": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "s3_uri": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "source_url": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_file_name": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "transcriptome_annotation": { + "type": "keyword" + }, + "upload_credentials": { + "properties": {}, + "type": "object" + }, + "upload_status": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "validation_error_detail": { + "type": "keyword" + }, + "workflow": { + "type": "keyword" + } + }, + "type": "object" + }, + "lab": { + "type": "keyword" + }, + "large_scale_gene_list": { + "type": "keyword" + }, + "large_scale_loci_list": { + "type": "keyword" + }, + "lot_id": { + "type": "keyword" + }, + "lower_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "lower_bound_insert_size": { + "store": true, + "type": "long" + }, + "notes": { + "type": "text" + }, + "orf_list": { + "type": "keyword" + }, + "product_id": { + "type": "keyword" + }, + "publications": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "scope": { + "type": "keyword" + }, + "selection_criteria": { + "type": "keyword" + }, + "small_scale_gene_list": { + "type": "keyword" + }, + "small_scale_loci_list": { + "properties": { + "assembly": { + "type": "keyword" + }, + "chromosome": { + "type": "keyword" + }, + "end": { + "store": true, + "type": "long" + }, + "start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_files_timestamp": { + "type": "date" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "targeton": { + "type": "keyword" + }, + "tile": { + "properties": { + "tile_end": { + "store": true, + "type": "long" + }, + "tile_id": { + "type": "keyword" + }, + "tile_start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "tiling_modality": { + "type": "keyword" + }, + "upper_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "upper_bound_insert_size": { + "store": true, + "type": "long" + }, + "uuid": { + "type": "keyword" + } + }, + "type": "object" }, "creation_timestamp": { "type": "date" diff --git a/src/igvfd/mappings/measurement_set.json b/src/igvfd/mappings/measurement_set.json index 795026b7a..db7d56f7e 100644 --- a/src/igvfd/mappings/measurement_set.json +++ b/src/igvfd/mappings/measurement_set.json @@ -2260,7 +2260,176 @@ "type": "keyword" }, "integrated_content_files": { - "type": "keyword" + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "analysis_step_version": { + "type": "keyword" + }, + "anvil_url": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assembly": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "barcode_map_for": { + "type": "keyword" + }, + "cell_type_annotation": { + "type": "keyword" + }, + "checkfiles_version": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "content_md5sum": { + "type": "keyword" + }, + "content_type": { + "type": "keyword" + }, + "controlled_access": { + "store": true, + "type": "boolean" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "derived_from": { + "type": "keyword" + }, + "derived_manually": { + "store": true, + "type": "boolean" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "external": { + "store": true, + "type": "boolean" + }, + "file_format": { + "type": "keyword" + }, + "file_format_specifications": { + "type": "keyword" + }, + "file_format_type": { + "type": "keyword" + }, + "file_set": { + "type": "keyword" + }, + "file_size": { + "store": true, + "type": "long" + }, + "gene_list_for": { + "type": "keyword" + }, + "href": { + "type": "keyword" + }, + "input_file_for": { + "type": "keyword" + }, + "integrated_in": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "loci_list_for": { + "type": "keyword" + }, + "md5sum": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "s3_uri": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "source_url": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_file_name": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "transcriptome_annotation": { + "type": "keyword" + }, + "upload_credentials": { + "properties": {}, + "type": "object" + }, + "upload_status": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "validation_error_detail": { + "type": "keyword" + }, + "workflow": { + "type": "keyword" + } + }, + "type": "object" }, "lab": { "type": "keyword" diff --git a/src/igvfd/mappings/model_set.json b/src/igvfd/mappings/model_set.json index 4af06ee9d..543318d55 100644 --- a/src/igvfd/mappings/model_set.json +++ b/src/igvfd/mappings/model_set.json @@ -1709,7 +1709,369 @@ "type": "keyword" }, "construct_library_sets": { - "type": "keyword" + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "applied_to_samples": { + "type": "keyword" + }, + "associated_phenotypes": { + "type": "keyword" + }, + "average_guide_coverage": { + "store": true, + "type": "float" + }, + "average_insert_size": { + "store": true, + "type": "float" + }, + "award": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "control_file_sets": { + "type": "keyword" + }, + "control_for": { + "type": "keyword" + }, + "control_type": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "exon": { + "type": "keyword" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { + "type": "keyword" + }, + "guide_type": { + "type": "keyword" + }, + "input_for": { + "type": "keyword" + }, + "integrated_content_files": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "analysis_step_version": { + "type": "keyword" + }, + "anvil_url": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assembly": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "barcode_map_for": { + "type": "keyword" + }, + "cell_type_annotation": { + "type": "keyword" + }, + "checkfiles_version": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "content_md5sum": { + "type": "keyword" + }, + "content_type": { + "type": "keyword" + }, + "controlled_access": { + "store": true, + "type": "boolean" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "derived_from": { + "type": "keyword" + }, + "derived_manually": { + "store": true, + "type": "boolean" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "external": { + "store": true, + "type": "boolean" + }, + "file_format": { + "type": "keyword" + }, + "file_format_specifications": { + "type": "keyword" + }, + "file_format_type": { + "type": "keyword" + }, + "file_set": { + "type": "keyword" + }, + "file_size": { + "store": true, + "type": "long" + }, + "gene_list_for": { + "type": "keyword" + }, + "href": { + "type": "keyword" + }, + "input_file_for": { + "type": "keyword" + }, + "integrated_in": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "loci_list_for": { + "type": "keyword" + }, + "md5sum": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "s3_uri": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "source_url": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_file_name": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "transcriptome_annotation": { + "type": "keyword" + }, + "upload_credentials": { + "properties": {}, + "type": "object" + }, + "upload_status": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "validation_error_detail": { + "type": "keyword" + }, + "workflow": { + "type": "keyword" + } + }, + "type": "object" + }, + "lab": { + "type": "keyword" + }, + "large_scale_gene_list": { + "type": "keyword" + }, + "large_scale_loci_list": { + "type": "keyword" + }, + "lot_id": { + "type": "keyword" + }, + "lower_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "lower_bound_insert_size": { + "store": true, + "type": "long" + }, + "notes": { + "type": "text" + }, + "orf_list": { + "type": "keyword" + }, + "product_id": { + "type": "keyword" + }, + "publications": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "scope": { + "type": "keyword" + }, + "selection_criteria": { + "type": "keyword" + }, + "small_scale_gene_list": { + "type": "keyword" + }, + "small_scale_loci_list": { + "properties": { + "assembly": { + "type": "keyword" + }, + "chromosome": { + "type": "keyword" + }, + "end": { + "store": true, + "type": "long" + }, + "start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_files_timestamp": { + "type": "date" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "targeton": { + "type": "keyword" + }, + "tile": { + "properties": { + "tile_end": { + "store": true, + "type": "long" + }, + "tile_id": { + "type": "keyword" + }, + "tile_start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "tiling_modality": { + "type": "keyword" + }, + "upper_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "upper_bound_insert_size": { + "store": true, + "type": "long" + }, + "uuid": { + "type": "keyword" + } + }, + "type": "object" }, "creation_timestamp": { "type": "date" diff --git a/src/igvfd/mappings/prediction_set.json b/src/igvfd/mappings/prediction_set.json index 3de7bca5d..031ec3def 100644 --- a/src/igvfd/mappings/prediction_set.json +++ b/src/igvfd/mappings/prediction_set.json @@ -1814,7 +1814,176 @@ "type": "keyword" }, "integrated_content_files": { - "type": "keyword" + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "analysis_step_version": { + "type": "keyword" + }, + "anvil_url": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assembly": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "barcode_map_for": { + "type": "keyword" + }, + "cell_type_annotation": { + "type": "keyword" + }, + "checkfiles_version": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "content_md5sum": { + "type": "keyword" + }, + "content_type": { + "type": "keyword" + }, + "controlled_access": { + "store": true, + "type": "boolean" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "derived_from": { + "type": "keyword" + }, + "derived_manually": { + "store": true, + "type": "boolean" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "external": { + "store": true, + "type": "boolean" + }, + "file_format": { + "type": "keyword" + }, + "file_format_specifications": { + "type": "keyword" + }, + "file_format_type": { + "type": "keyword" + }, + "file_set": { + "type": "keyword" + }, + "file_size": { + "store": true, + "type": "long" + }, + "gene_list_for": { + "type": "keyword" + }, + "href": { + "type": "keyword" + }, + "input_file_for": { + "type": "keyword" + }, + "integrated_in": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "loci_list_for": { + "type": "keyword" + }, + "md5sum": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "s3_uri": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "source_url": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_file_name": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "transcriptome_annotation": { + "type": "keyword" + }, + "upload_credentials": { + "properties": {}, + "type": "object" + }, + "upload_status": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "validation_error_detail": { + "type": "keyword" + }, + "workflow": { + "type": "keyword" + } + }, + "type": "object" }, "lab": { "type": "keyword" diff --git a/src/igvfd/types/file_set.py b/src/igvfd/types/file_set.py index eb6d27eba..2d57a58b4 100644 --- a/src/igvfd/types/file_set.py +++ b/src/igvfd/types/file_set.py @@ -1180,20 +1180,19 @@ class ConstructLibrarySet(FileSet): set_status_up = FileSet.set_status_up + [] set_status_down = FileSet.set_status_down + [] - @calculated_property(define=True, - schema={ - 'title': 'Applied to Samples', - 'description': 'The samples that link to this construct library set.', - 'type': 'array', - 'minItems': 1, - 'uniqueItems': True, - 'items': { - 'title': 'Applied to Sample', - 'type': ['string', 'object'], - 'linkFrom': 'Sample.construct_library_sets', - }, - 'notSubmittable': True - }) + @calculated_property(schema={ + 'title': 'Applied to Samples', + 'description': 'The samples that link to this construct library set.', + 'type': 'array', + 'minItems': 1, + 'uniqueItems': True, + 'items': { + 'title': 'Applied to Sample', + 'type': ['string', 'object'], + 'linkFrom': 'Sample.construct_library_sets', + }, + 'notSubmittable': True + }) def applied_to_samples(self, request, applied_to_samples): return paths_filtered_by_status(request, applied_to_samples) From 0519449d97b4bed3591ccff666c25ed53e587c38 Mon Sep 17 00:00:00 2001 From: ian-whaling Date: Wed, 29 Jan 2025 15:07:18 -0800 Subject: [PATCH 05/13] change calculated property and embedding for file sets --- src/igvfd/mappings/alignment_file.json | 6 + src/igvfd/mappings/analysis_set.json | 845 ++++++++++-------- src/igvfd/mappings/auxiliary_set.json | 845 ++++++++++-------- src/igvfd/mappings/configuration_file.json | 6 + src/igvfd/mappings/construct_library_set.json | 9 + src/igvfd/mappings/curated_set.json | 842 +++++++++-------- .../genome_browser_annotation_file.json | 6 + src/igvfd/mappings/image_file.json | 6 + src/igvfd/mappings/in_vitro_system.json | 6 + src/igvfd/mappings/index_file.json | 6 + src/igvfd/mappings/matrix_file.json | 6 + src/igvfd/mappings/measurement_set.json | 737 +++++++++++++-- src/igvfd/mappings/model_file.json | 6 + src/igvfd/mappings/model_set.json | 845 ++++++++++-------- src/igvfd/mappings/multiplexed_sample.json | 6 + src/igvfd/mappings/prediction_set.json | 652 ++++++++++---- src/igvfd/mappings/primary_cell.json | 6 + src/igvfd/mappings/reference_file.json | 6 + src/igvfd/mappings/sequence_file.json | 6 + src/igvfd/mappings/signal_file.json | 6 + src/igvfd/mappings/tabular_file.json | 6 + src/igvfd/mappings/technical_sample.json | 6 + src/igvfd/mappings/tissue.json | 6 + src/igvfd/mappings/whole_organism.json | 6 + src/igvfd/searches/configs/analysis_set.py | 6 + src/igvfd/searches/configs/auxiliary_set.py | 6 + .../searches/configs/construct_library_set.py | 3 + src/igvfd/searches/configs/file_set.py | 6 + src/igvfd/searches/configs/measurement_set.py | 11 +- src/igvfd/searches/configs/model_set.py | 29 + src/igvfd/searches/configs/prediction_set.py | 6 + src/igvfd/types/file_set.py | 32 +- 32 files changed, 3267 insertions(+), 1709 deletions(-) diff --git a/src/igvfd/mappings/alignment_file.json b/src/igvfd/mappings/alignment_file.json index 60db838be..196971fa3 100644 --- a/src/igvfd/mappings/alignment_file.json +++ b/src/igvfd/mappings/alignment_file.json @@ -345,6 +345,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1402,6 +1405,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/analysis_set.json b/src/igvfd/mappings/analysis_set.json index 7564a8f77..e24f4eb20 100644 --- a/src/igvfd/mappings/analysis_set.json +++ b/src/igvfd/mappings/analysis_set.json @@ -301,6 +301,481 @@ "copy_to": "_fuzzy", "type": "keyword" }, + "construct_library_sets": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "applied_to_samples": { + "type": "keyword" + }, + "assay_term": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assemblies": { + "type": "keyword" + }, + "assessed_genes": { + "type": "keyword" + }, + "associated_phenotypes": { + "type": "keyword" + }, + "auxiliary_sets": { + "type": "keyword" + }, + "average_guide_coverage": { + "store": true, + "type": "float" + }, + "average_insert_size": { + "store": true, + "type": "float" + }, + "award": { + "type": "keyword" + }, + "barcode_map": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "construct_library_sets": { + "type": "keyword" + }, + "control_file_sets": { + "type": "keyword" + }, + "control_for": { + "type": "keyword" + }, + "control_type": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "demultiplexed_sample": { + "type": "keyword" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "donors": { + "type": "keyword" + }, + "exon": { + "type": "keyword" + }, + "external_image_data_url": { + "type": "keyword" + }, + "external_image_url": { + "type": "keyword" + }, + "external_input_data": { + "type": "keyword" + }, + "externally_hosted": { + "store": true, + "type": "boolean" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { + "type": "keyword" + }, + "functional_assay_mechanisms": { + "type": "keyword" + }, + "guide_type": { + "type": "keyword" + }, + "input_file_sets": { + "type": "keyword" + }, + "input_for": { + "type": "keyword" + }, + "integrated_content_files": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "analysis_step_version": { + "type": "keyword" + }, + "anvil_url": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assembly": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "barcode_map_for": { + "type": "keyword" + }, + "cell_type_annotation": { + "type": "keyword" + }, + "checkfiles_version": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "content_md5sum": { + "type": "keyword" + }, + "content_type": { + "type": "keyword" + }, + "controlled_access": { + "store": true, + "type": "boolean" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "derived_from": { + "type": "keyword" + }, + "derived_manually": { + "store": true, + "type": "boolean" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "external": { + "store": true, + "type": "boolean" + }, + "file_format": { + "type": "keyword" + }, + "file_format_specifications": { + "type": "keyword" + }, + "file_format_type": { + "type": "keyword" + }, + "file_set": { + "type": "keyword" + }, + "file_size": { + "store": true, + "type": "long" + }, + "gene_list_for": { + "type": "keyword" + }, + "href": { + "type": "keyword" + }, + "input_file_for": { + "type": "keyword" + }, + "integrated_in": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "loci_list_for": { + "type": "keyword" + }, + "md5sum": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "s3_uri": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "source_url": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_file_name": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "transcriptome_annotation": { + "type": "keyword" + }, + "upload_credentials": { + "properties": {}, + "type": "object" + }, + "upload_status": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "validation_error_detail": { + "type": "keyword" + }, + "workflow": { + "type": "keyword" + } + }, + "type": "object" + }, + "lab": { + "type": "keyword" + }, + "large_scale_gene_list": { + "type": "keyword" + }, + "large_scale_loci_list": { + "type": "keyword" + }, + "lot_id": { + "type": "keyword" + }, + "lower_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "lower_bound_insert_size": { + "store": true, + "type": "long" + }, + "measurement_sets": { + "type": "keyword" + }, + "model_name": { + "type": "keyword" + }, + "model_version": { + "type": "keyword" + }, + "model_zoo_location": { + "type": "keyword" + }, + "multiome_size": { + "store": true, + "type": "long" + }, + "notes": { + "type": "text" + }, + "onlist_files": { + "type": "keyword" + }, + "onlist_method": { + "type": "keyword" + }, + "orf_list": { + "type": "keyword" + }, + "prediction_objects": { + "type": "keyword" + }, + "preferred_assay_title": { + "type": "keyword" + }, + "product_id": { + "type": "keyword" + }, + "protocols": { + "type": "keyword" + }, + "publications": { + "type": "keyword" + }, + "related_multiome_datasets": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "sample_summary": { + "type": "keyword" + }, + "samples": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "scope": { + "type": "keyword" + }, + "selection_criteria": { + "type": "keyword" + }, + "sequencing_library_types": { + "type": "keyword" + }, + "small_scale_gene_list": { + "type": "keyword" + }, + "small_scale_loci_list": { + "properties": { + "assembly": { + "type": "keyword" + }, + "chromosome": { + "type": "keyword" + }, + "end": { + "store": true, + "type": "long" + }, + "start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "software_version": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_files_timestamp": { + "type": "date" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "targeted_genes": { + "type": "keyword" + }, + "targeton": { + "type": "keyword" + }, + "taxa": { + "type": "keyword" + }, + "tile": { + "properties": { + "tile_end": { + "store": true, + "type": "long" + }, + "tile_id": { + "type": "keyword" + }, + "tile_start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "tiling_modality": { + "type": "keyword" + }, + "transcriptome_annotations": { + "type": "keyword" + }, + "upper_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "upper_bound_insert_size": { + "store": true, + "type": "long" + }, + "url": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "workflows": { + "type": "keyword" + } + }, + "type": "object" + }, "control_for": { "properties": { "@id": { @@ -358,6 +833,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1156,6 +1634,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1673,369 +2154,7 @@ "type": "keyword" }, "construct_library_sets": { - "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "accession": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "alternate_accessions": { - "type": "keyword" - }, - "applied_to_samples": { - "type": "keyword" - }, - "associated_phenotypes": { - "type": "keyword" - }, - "average_guide_coverage": { - "store": true, - "type": "float" - }, - "average_insert_size": { - "store": true, - "type": "float" - }, - "award": { - "type": "keyword" - }, - "collections": { - "type": "keyword" - }, - "control_file_sets": { - "type": "keyword" - }, - "control_for": { - "type": "keyword" - }, - "control_type": { - "type": "keyword" - }, - "creation_timestamp": { - "type": "date" - }, - "description": { - "type": "text" - }, - "documents": { - "type": "keyword" - }, - "exon": { - "type": "keyword" - }, - "file_set_type": { - "type": "keyword" - }, - "files": { - "type": "keyword" - }, - "guide_type": { - "type": "keyword" - }, - "input_for": { - "type": "keyword" - }, - "integrated_content_files": { - "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "accession": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "alternate_accessions": { - "type": "keyword" - }, - "analysis_step_version": { - "type": "keyword" - }, - "anvil_url": { - "type": "keyword" - }, - "assay_titles": { - "type": "keyword" - }, - "assembly": { - "type": "keyword" - }, - "award": { - "type": "keyword" - }, - "barcode_map_for": { - "type": "keyword" - }, - "cell_type_annotation": { - "type": "keyword" - }, - "checkfiles_version": { - "type": "keyword" - }, - "collections": { - "type": "keyword" - }, - "content_md5sum": { - "type": "keyword" - }, - "content_type": { - "type": "keyword" - }, - "controlled_access": { - "store": true, - "type": "boolean" - }, - "creation_timestamp": { - "type": "date" - }, - "dbxrefs": { - "type": "keyword" - }, - "derived_from": { - "type": "keyword" - }, - "derived_manually": { - "store": true, - "type": "boolean" - }, - "description": { - "type": "text" - }, - "documents": { - "type": "keyword" - }, - "external": { - "store": true, - "type": "boolean" - }, - "file_format": { - "type": "keyword" - }, - "file_format_specifications": { - "type": "keyword" - }, - "file_format_type": { - "type": "keyword" - }, - "file_set": { - "type": "keyword" - }, - "file_size": { - "store": true, - "type": "long" - }, - "gene_list_for": { - "type": "keyword" - }, - "href": { - "type": "keyword" - }, - "input_file_for": { - "type": "keyword" - }, - "integrated_in": { - "type": "keyword" - }, - "lab": { - "type": "keyword" - }, - "loci_list_for": { - "type": "keyword" - }, - "md5sum": { - "type": "keyword" - }, - "notes": { - "type": "text" - }, - "release_timestamp": { - "type": "date" - }, - "revoke_detail": { - "type": "keyword" - }, - "s3_uri": { - "type": "keyword" - }, - "schema_version": { - "type": "keyword" - }, - "source_url": { - "type": "keyword" - }, - "sources": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" - }, - "submitted_file_name": { - "type": "keyword" - }, - "submitter_comment": { - "type": "keyword" - }, - "summary": { - "type": "keyword" - }, - "transcriptome_annotation": { - "type": "keyword" - }, - "upload_credentials": { - "properties": {}, - "type": "object" - }, - "upload_status": { - "type": "keyword" - }, - "uuid": { - "type": "keyword" - }, - "validation_error_detail": { - "type": "keyword" - }, - "workflow": { - "type": "keyword" - } - }, - "type": "object" - }, - "lab": { - "type": "keyword" - }, - "large_scale_gene_list": { - "type": "keyword" - }, - "large_scale_loci_list": { - "type": "keyword" - }, - "lot_id": { - "type": "keyword" - }, - "lower_bound_guide_coverage": { - "store": true, - "type": "long" - }, - "lower_bound_insert_size": { - "store": true, - "type": "long" - }, - "notes": { - "type": "text" - }, - "orf_list": { - "type": "keyword" - }, - "product_id": { - "type": "keyword" - }, - "publications": { - "type": "keyword" - }, - "release_timestamp": { - "type": "date" - }, - "revoke_detail": { - "type": "keyword" - }, - "schema_version": { - "type": "keyword" - }, - "scope": { - "type": "keyword" - }, - "selection_criteria": { - "type": "keyword" - }, - "small_scale_gene_list": { - "type": "keyword" - }, - "small_scale_loci_list": { - "properties": { - "assembly": { - "type": "keyword" - }, - "chromosome": { - "type": "keyword" - }, - "end": { - "store": true, - "type": "long" - }, - "start": { - "store": true, - "type": "long" - } - }, - "type": "object" - }, - "sources": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" - }, - "submitted_files_timestamp": { - "type": "date" - }, - "submitter_comment": { - "type": "keyword" - }, - "summary": { - "type": "keyword" - }, - "targeton": { - "type": "keyword" - }, - "tile": { - "properties": { - "tile_end": { - "store": true, - "type": "long" - }, - "tile_id": { - "type": "keyword" - }, - "tile_start": { - "store": true, - "type": "long" - } - }, - "type": "object" - }, - "tiling_modality": { - "type": "keyword" - }, - "upper_bound_guide_coverage": { - "store": true, - "type": "long" - }, - "upper_bound_insert_size": { - "store": true, - "type": "long" - }, - "uuid": { - "type": "keyword" - } - }, - "type": "object" + "type": "keyword" }, "creation_timestamp": { "type": "date" diff --git a/src/igvfd/mappings/auxiliary_set.json b/src/igvfd/mappings/auxiliary_set.json index ca46b89b7..6f0252f97 100644 --- a/src/igvfd/mappings/auxiliary_set.json +++ b/src/igvfd/mappings/auxiliary_set.json @@ -300,6 +300,481 @@ "copy_to": "_fuzzy", "type": "keyword" }, + "construct_library_sets": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "applied_to_samples": { + "type": "keyword" + }, + "assay_term": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assemblies": { + "type": "keyword" + }, + "assessed_genes": { + "type": "keyword" + }, + "associated_phenotypes": { + "type": "keyword" + }, + "auxiliary_sets": { + "type": "keyword" + }, + "average_guide_coverage": { + "store": true, + "type": "float" + }, + "average_insert_size": { + "store": true, + "type": "float" + }, + "award": { + "type": "keyword" + }, + "barcode_map": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "construct_library_sets": { + "type": "keyword" + }, + "control_file_sets": { + "type": "keyword" + }, + "control_for": { + "type": "keyword" + }, + "control_type": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "demultiplexed_sample": { + "type": "keyword" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "donors": { + "type": "keyword" + }, + "exon": { + "type": "keyword" + }, + "external_image_data_url": { + "type": "keyword" + }, + "external_image_url": { + "type": "keyword" + }, + "external_input_data": { + "type": "keyword" + }, + "externally_hosted": { + "store": true, + "type": "boolean" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { + "type": "keyword" + }, + "functional_assay_mechanisms": { + "type": "keyword" + }, + "guide_type": { + "type": "keyword" + }, + "input_file_sets": { + "type": "keyword" + }, + "input_for": { + "type": "keyword" + }, + "integrated_content_files": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "analysis_step_version": { + "type": "keyword" + }, + "anvil_url": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assembly": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "barcode_map_for": { + "type": "keyword" + }, + "cell_type_annotation": { + "type": "keyword" + }, + "checkfiles_version": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "content_md5sum": { + "type": "keyword" + }, + "content_type": { + "type": "keyword" + }, + "controlled_access": { + "store": true, + "type": "boolean" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "derived_from": { + "type": "keyword" + }, + "derived_manually": { + "store": true, + "type": "boolean" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "external": { + "store": true, + "type": "boolean" + }, + "file_format": { + "type": "keyword" + }, + "file_format_specifications": { + "type": "keyword" + }, + "file_format_type": { + "type": "keyword" + }, + "file_set": { + "type": "keyword" + }, + "file_size": { + "store": true, + "type": "long" + }, + "gene_list_for": { + "type": "keyword" + }, + "href": { + "type": "keyword" + }, + "input_file_for": { + "type": "keyword" + }, + "integrated_in": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "loci_list_for": { + "type": "keyword" + }, + "md5sum": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "s3_uri": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "source_url": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_file_name": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "transcriptome_annotation": { + "type": "keyword" + }, + "upload_credentials": { + "properties": {}, + "type": "object" + }, + "upload_status": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "validation_error_detail": { + "type": "keyword" + }, + "workflow": { + "type": "keyword" + } + }, + "type": "object" + }, + "lab": { + "type": "keyword" + }, + "large_scale_gene_list": { + "type": "keyword" + }, + "large_scale_loci_list": { + "type": "keyword" + }, + "lot_id": { + "type": "keyword" + }, + "lower_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "lower_bound_insert_size": { + "store": true, + "type": "long" + }, + "measurement_sets": { + "type": "keyword" + }, + "model_name": { + "type": "keyword" + }, + "model_version": { + "type": "keyword" + }, + "model_zoo_location": { + "type": "keyword" + }, + "multiome_size": { + "store": true, + "type": "long" + }, + "notes": { + "type": "text" + }, + "onlist_files": { + "type": "keyword" + }, + "onlist_method": { + "type": "keyword" + }, + "orf_list": { + "type": "keyword" + }, + "prediction_objects": { + "type": "keyword" + }, + "preferred_assay_title": { + "type": "keyword" + }, + "product_id": { + "type": "keyword" + }, + "protocols": { + "type": "keyword" + }, + "publications": { + "type": "keyword" + }, + "related_multiome_datasets": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "sample_summary": { + "type": "keyword" + }, + "samples": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "scope": { + "type": "keyword" + }, + "selection_criteria": { + "type": "keyword" + }, + "sequencing_library_types": { + "type": "keyword" + }, + "small_scale_gene_list": { + "type": "keyword" + }, + "small_scale_loci_list": { + "properties": { + "assembly": { + "type": "keyword" + }, + "chromosome": { + "type": "keyword" + }, + "end": { + "store": true, + "type": "long" + }, + "start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "software_version": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_files_timestamp": { + "type": "date" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "targeted_genes": { + "type": "keyword" + }, + "targeton": { + "type": "keyword" + }, + "taxa": { + "type": "keyword" + }, + "tile": { + "properties": { + "tile_end": { + "store": true, + "type": "long" + }, + "tile_id": { + "type": "keyword" + }, + "tile_start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "tiling_modality": { + "type": "keyword" + }, + "transcriptome_annotations": { + "type": "keyword" + }, + "upper_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "upper_bound_insert_size": { + "store": true, + "type": "long" + }, + "url": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "workflows": { + "type": "keyword" + } + }, + "type": "object" + }, "control_for": { "properties": { "@id": { @@ -357,6 +832,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1118,6 +1596,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1428,369 +1909,7 @@ "type": "keyword" }, "construct_library_sets": { - "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "accession": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "alternate_accessions": { - "type": "keyword" - }, - "applied_to_samples": { - "type": "keyword" - }, - "associated_phenotypes": { - "type": "keyword" - }, - "average_guide_coverage": { - "store": true, - "type": "float" - }, - "average_insert_size": { - "store": true, - "type": "float" - }, - "award": { - "type": "keyword" - }, - "collections": { - "type": "keyword" - }, - "control_file_sets": { - "type": "keyword" - }, - "control_for": { - "type": "keyword" - }, - "control_type": { - "type": "keyword" - }, - "creation_timestamp": { - "type": "date" - }, - "description": { - "type": "text" - }, - "documents": { - "type": "keyword" - }, - "exon": { - "type": "keyword" - }, - "file_set_type": { - "type": "keyword" - }, - "files": { - "type": "keyword" - }, - "guide_type": { - "type": "keyword" - }, - "input_for": { - "type": "keyword" - }, - "integrated_content_files": { - "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "accession": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "alternate_accessions": { - "type": "keyword" - }, - "analysis_step_version": { - "type": "keyword" - }, - "anvil_url": { - "type": "keyword" - }, - "assay_titles": { - "type": "keyword" - }, - "assembly": { - "type": "keyword" - }, - "award": { - "type": "keyword" - }, - "barcode_map_for": { - "type": "keyword" - }, - "cell_type_annotation": { - "type": "keyword" - }, - "checkfiles_version": { - "type": "keyword" - }, - "collections": { - "type": "keyword" - }, - "content_md5sum": { - "type": "keyword" - }, - "content_type": { - "type": "keyword" - }, - "controlled_access": { - "store": true, - "type": "boolean" - }, - "creation_timestamp": { - "type": "date" - }, - "dbxrefs": { - "type": "keyword" - }, - "derived_from": { - "type": "keyword" - }, - "derived_manually": { - "store": true, - "type": "boolean" - }, - "description": { - "type": "text" - }, - "documents": { - "type": "keyword" - }, - "external": { - "store": true, - "type": "boolean" - }, - "file_format": { - "type": "keyword" - }, - "file_format_specifications": { - "type": "keyword" - }, - "file_format_type": { - "type": "keyword" - }, - "file_set": { - "type": "keyword" - }, - "file_size": { - "store": true, - "type": "long" - }, - "gene_list_for": { - "type": "keyword" - }, - "href": { - "type": "keyword" - }, - "input_file_for": { - "type": "keyword" - }, - "integrated_in": { - "type": "keyword" - }, - "lab": { - "type": "keyword" - }, - "loci_list_for": { - "type": "keyword" - }, - "md5sum": { - "type": "keyword" - }, - "notes": { - "type": "text" - }, - "release_timestamp": { - "type": "date" - }, - "revoke_detail": { - "type": "keyword" - }, - "s3_uri": { - "type": "keyword" - }, - "schema_version": { - "type": "keyword" - }, - "source_url": { - "type": "keyword" - }, - "sources": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" - }, - "submitted_file_name": { - "type": "keyword" - }, - "submitter_comment": { - "type": "keyword" - }, - "summary": { - "type": "keyword" - }, - "transcriptome_annotation": { - "type": "keyword" - }, - "upload_credentials": { - "properties": {}, - "type": "object" - }, - "upload_status": { - "type": "keyword" - }, - "uuid": { - "type": "keyword" - }, - "validation_error_detail": { - "type": "keyword" - }, - "workflow": { - "type": "keyword" - } - }, - "type": "object" - }, - "lab": { - "type": "keyword" - }, - "large_scale_gene_list": { - "type": "keyword" - }, - "large_scale_loci_list": { - "type": "keyword" - }, - "lot_id": { - "type": "keyword" - }, - "lower_bound_guide_coverage": { - "store": true, - "type": "long" - }, - "lower_bound_insert_size": { - "store": true, - "type": "long" - }, - "notes": { - "type": "text" - }, - "orf_list": { - "type": "keyword" - }, - "product_id": { - "type": "keyword" - }, - "publications": { - "type": "keyword" - }, - "release_timestamp": { - "type": "date" - }, - "revoke_detail": { - "type": "keyword" - }, - "schema_version": { - "type": "keyword" - }, - "scope": { - "type": "keyword" - }, - "selection_criteria": { - "type": "keyword" - }, - "small_scale_gene_list": { - "type": "keyword" - }, - "small_scale_loci_list": { - "properties": { - "assembly": { - "type": "keyword" - }, - "chromosome": { - "type": "keyword" - }, - "end": { - "store": true, - "type": "long" - }, - "start": { - "store": true, - "type": "long" - } - }, - "type": "object" - }, - "sources": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" - }, - "submitted_files_timestamp": { - "type": "date" - }, - "submitter_comment": { - "type": "keyword" - }, - "summary": { - "type": "keyword" - }, - "targeton": { - "type": "keyword" - }, - "tile": { - "properties": { - "tile_end": { - "store": true, - "type": "long" - }, - "tile_id": { - "type": "keyword" - }, - "tile_start": { - "store": true, - "type": "long" - } - }, - "type": "object" - }, - "tiling_modality": { - "type": "keyword" - }, - "upper_bound_guide_coverage": { - "store": true, - "type": "long" - }, - "upper_bound_insert_size": { - "store": true, - "type": "long" - }, - "uuid": { - "type": "keyword" - } - }, - "type": "object" + "type": "keyword" }, "creation_timestamp": { "type": "date" diff --git a/src/igvfd/mappings/configuration_file.json b/src/igvfd/mappings/configuration_file.json index c130dd069..c4b95ef74 100644 --- a/src/igvfd/mappings/configuration_file.json +++ b/src/igvfd/mappings/configuration_file.json @@ -332,6 +332,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1385,6 +1388,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/construct_library_set.json b/src/igvfd/mappings/construct_library_set.json index c4674520f..22bd19623 100644 --- a/src/igvfd/mappings/construct_library_set.json +++ b/src/igvfd/mappings/construct_library_set.json @@ -490,6 +490,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1425,6 +1428,9 @@ "copy_to": "_fuzzy", "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1485,6 +1491,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/curated_set.json b/src/igvfd/mappings/curated_set.json index 73916731d..0d7761a07 100644 --- a/src/igvfd/mappings/curated_set.json +++ b/src/igvfd/mappings/curated_set.json @@ -301,6 +301,481 @@ "copy_to": "_fuzzy", "type": "keyword" }, + "construct_library_sets": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "applied_to_samples": { + "type": "keyword" + }, + "assay_term": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assemblies": { + "type": "keyword" + }, + "assessed_genes": { + "type": "keyword" + }, + "associated_phenotypes": { + "type": "keyword" + }, + "auxiliary_sets": { + "type": "keyword" + }, + "average_guide_coverage": { + "store": true, + "type": "float" + }, + "average_insert_size": { + "store": true, + "type": "float" + }, + "award": { + "type": "keyword" + }, + "barcode_map": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "construct_library_sets": { + "type": "keyword" + }, + "control_file_sets": { + "type": "keyword" + }, + "control_for": { + "type": "keyword" + }, + "control_type": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "demultiplexed_sample": { + "type": "keyword" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "donors": { + "type": "keyword" + }, + "exon": { + "type": "keyword" + }, + "external_image_data_url": { + "type": "keyword" + }, + "external_image_url": { + "type": "keyword" + }, + "external_input_data": { + "type": "keyword" + }, + "externally_hosted": { + "store": true, + "type": "boolean" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { + "type": "keyword" + }, + "functional_assay_mechanisms": { + "type": "keyword" + }, + "guide_type": { + "type": "keyword" + }, + "input_file_sets": { + "type": "keyword" + }, + "input_for": { + "type": "keyword" + }, + "integrated_content_files": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "analysis_step_version": { + "type": "keyword" + }, + "anvil_url": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assembly": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "barcode_map_for": { + "type": "keyword" + }, + "cell_type_annotation": { + "type": "keyword" + }, + "checkfiles_version": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "content_md5sum": { + "type": "keyword" + }, + "content_type": { + "type": "keyword" + }, + "controlled_access": { + "store": true, + "type": "boolean" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "derived_from": { + "type": "keyword" + }, + "derived_manually": { + "store": true, + "type": "boolean" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "external": { + "store": true, + "type": "boolean" + }, + "file_format": { + "type": "keyword" + }, + "file_format_specifications": { + "type": "keyword" + }, + "file_format_type": { + "type": "keyword" + }, + "file_set": { + "type": "keyword" + }, + "file_size": { + "store": true, + "type": "long" + }, + "gene_list_for": { + "type": "keyword" + }, + "href": { + "type": "keyword" + }, + "input_file_for": { + "type": "keyword" + }, + "integrated_in": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "loci_list_for": { + "type": "keyword" + }, + "md5sum": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "s3_uri": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "source_url": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_file_name": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "transcriptome_annotation": { + "type": "keyword" + }, + "upload_credentials": { + "properties": {}, + "type": "object" + }, + "upload_status": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "validation_error_detail": { + "type": "keyword" + }, + "workflow": { + "type": "keyword" + } + }, + "type": "object" + }, + "lab": { + "type": "keyword" + }, + "large_scale_gene_list": { + "type": "keyword" + }, + "large_scale_loci_list": { + "type": "keyword" + }, + "lot_id": { + "type": "keyword" + }, + "lower_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "lower_bound_insert_size": { + "store": true, + "type": "long" + }, + "measurement_sets": { + "type": "keyword" + }, + "model_name": { + "type": "keyword" + }, + "model_version": { + "type": "keyword" + }, + "model_zoo_location": { + "type": "keyword" + }, + "multiome_size": { + "store": true, + "type": "long" + }, + "notes": { + "type": "text" + }, + "onlist_files": { + "type": "keyword" + }, + "onlist_method": { + "type": "keyword" + }, + "orf_list": { + "type": "keyword" + }, + "prediction_objects": { + "type": "keyword" + }, + "preferred_assay_title": { + "type": "keyword" + }, + "product_id": { + "type": "keyword" + }, + "protocols": { + "type": "keyword" + }, + "publications": { + "type": "keyword" + }, + "related_multiome_datasets": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "sample_summary": { + "type": "keyword" + }, + "samples": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "scope": { + "type": "keyword" + }, + "selection_criteria": { + "type": "keyword" + }, + "sequencing_library_types": { + "type": "keyword" + }, + "small_scale_gene_list": { + "type": "keyword" + }, + "small_scale_loci_list": { + "properties": { + "assembly": { + "type": "keyword" + }, + "chromosome": { + "type": "keyword" + }, + "end": { + "store": true, + "type": "long" + }, + "start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "software_version": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_files_timestamp": { + "type": "date" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "targeted_genes": { + "type": "keyword" + }, + "targeton": { + "type": "keyword" + }, + "taxa": { + "type": "keyword" + }, + "tile": { + "properties": { + "tile_end": { + "store": true, + "type": "long" + }, + "tile_id": { + "type": "keyword" + }, + "tile_start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "tiling_modality": { + "type": "keyword" + }, + "transcriptome_annotations": { + "type": "keyword" + }, + "upper_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "upper_bound_insert_size": { + "store": true, + "type": "long" + }, + "url": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "workflows": { + "type": "keyword" + } + }, + "type": "object" + }, "control_for": { "properties": { "@id": { @@ -358,6 +833,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1288,369 +1766,7 @@ "type": "keyword" }, "construct_library_sets": { - "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "accession": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "alternate_accessions": { - "type": "keyword" - }, - "applied_to_samples": { - "type": "keyword" - }, - "associated_phenotypes": { - "type": "keyword" - }, - "average_guide_coverage": { - "store": true, - "type": "float" - }, - "average_insert_size": { - "store": true, - "type": "float" - }, - "award": { - "type": "keyword" - }, - "collections": { - "type": "keyword" - }, - "control_file_sets": { - "type": "keyword" - }, - "control_for": { - "type": "keyword" - }, - "control_type": { - "type": "keyword" - }, - "creation_timestamp": { - "type": "date" - }, - "description": { - "type": "text" - }, - "documents": { - "type": "keyword" - }, - "exon": { - "type": "keyword" - }, - "file_set_type": { - "type": "keyword" - }, - "files": { - "type": "keyword" - }, - "guide_type": { - "type": "keyword" - }, - "input_for": { - "type": "keyword" - }, - "integrated_content_files": { - "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "accession": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "alternate_accessions": { - "type": "keyword" - }, - "analysis_step_version": { - "type": "keyword" - }, - "anvil_url": { - "type": "keyword" - }, - "assay_titles": { - "type": "keyword" - }, - "assembly": { - "type": "keyword" - }, - "award": { - "type": "keyword" - }, - "barcode_map_for": { - "type": "keyword" - }, - "cell_type_annotation": { - "type": "keyword" - }, - "checkfiles_version": { - "type": "keyword" - }, - "collections": { - "type": "keyword" - }, - "content_md5sum": { - "type": "keyword" - }, - "content_type": { - "type": "keyword" - }, - "controlled_access": { - "store": true, - "type": "boolean" - }, - "creation_timestamp": { - "type": "date" - }, - "dbxrefs": { - "type": "keyword" - }, - "derived_from": { - "type": "keyword" - }, - "derived_manually": { - "store": true, - "type": "boolean" - }, - "description": { - "type": "text" - }, - "documents": { - "type": "keyword" - }, - "external": { - "store": true, - "type": "boolean" - }, - "file_format": { - "type": "keyword" - }, - "file_format_specifications": { - "type": "keyword" - }, - "file_format_type": { - "type": "keyword" - }, - "file_set": { - "type": "keyword" - }, - "file_size": { - "store": true, - "type": "long" - }, - "gene_list_for": { - "type": "keyword" - }, - "href": { - "type": "keyword" - }, - "input_file_for": { - "type": "keyword" - }, - "integrated_in": { - "type": "keyword" - }, - "lab": { - "type": "keyword" - }, - "loci_list_for": { - "type": "keyword" - }, - "md5sum": { - "type": "keyword" - }, - "notes": { - "type": "text" - }, - "release_timestamp": { - "type": "date" - }, - "revoke_detail": { - "type": "keyword" - }, - "s3_uri": { - "type": "keyword" - }, - "schema_version": { - "type": "keyword" - }, - "source_url": { - "type": "keyword" - }, - "sources": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" - }, - "submitted_file_name": { - "type": "keyword" - }, - "submitter_comment": { - "type": "keyword" - }, - "summary": { - "type": "keyword" - }, - "transcriptome_annotation": { - "type": "keyword" - }, - "upload_credentials": { - "properties": {}, - "type": "object" - }, - "upload_status": { - "type": "keyword" - }, - "uuid": { - "type": "keyword" - }, - "validation_error_detail": { - "type": "keyword" - }, - "workflow": { - "type": "keyword" - } - }, - "type": "object" - }, - "lab": { - "type": "keyword" - }, - "large_scale_gene_list": { - "type": "keyword" - }, - "large_scale_loci_list": { - "type": "keyword" - }, - "lot_id": { - "type": "keyword" - }, - "lower_bound_guide_coverage": { - "store": true, - "type": "long" - }, - "lower_bound_insert_size": { - "store": true, - "type": "long" - }, - "notes": { - "type": "text" - }, - "orf_list": { - "type": "keyword" - }, - "product_id": { - "type": "keyword" - }, - "publications": { - "type": "keyword" - }, - "release_timestamp": { - "type": "date" - }, - "revoke_detail": { - "type": "keyword" - }, - "schema_version": { - "type": "keyword" - }, - "scope": { - "type": "keyword" - }, - "selection_criteria": { - "type": "keyword" - }, - "small_scale_gene_list": { - "type": "keyword" - }, - "small_scale_loci_list": { - "properties": { - "assembly": { - "type": "keyword" - }, - "chromosome": { - "type": "keyword" - }, - "end": { - "store": true, - "type": "long" - }, - "start": { - "store": true, - "type": "long" - } - }, - "type": "object" - }, - "sources": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" - }, - "submitted_files_timestamp": { - "type": "date" - }, - "submitter_comment": { - "type": "keyword" - }, - "summary": { - "type": "keyword" - }, - "targeton": { - "type": "keyword" - }, - "tile": { - "properties": { - "tile_end": { - "store": true, - "type": "long" - }, - "tile_id": { - "type": "keyword" - }, - "tile_start": { - "store": true, - "type": "long" - } - }, - "type": "object" - }, - "tiling_modality": { - "type": "keyword" - }, - "upper_bound_guide_coverage": { - "store": true, - "type": "long" - }, - "upper_bound_insert_size": { - "store": true, - "type": "long" - }, - "uuid": { - "type": "keyword" - } - }, - "type": "object" + "type": "keyword" }, "creation_timestamp": { "type": "date" diff --git a/src/igvfd/mappings/genome_browser_annotation_file.json b/src/igvfd/mappings/genome_browser_annotation_file.json index bdbbc3343..911788c6e 100644 --- a/src/igvfd/mappings/genome_browser_annotation_file.json +++ b/src/igvfd/mappings/genome_browser_annotation_file.json @@ -422,6 +422,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1475,6 +1478,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/image_file.json b/src/igvfd/mappings/image_file.json index c7c405d51..90b85d4ea 100644 --- a/src/igvfd/mappings/image_file.json +++ b/src/igvfd/mappings/image_file.json @@ -332,6 +332,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1385,6 +1388,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/in_vitro_system.json b/src/igvfd/mappings/in_vitro_system.json index 527624185..1ec943993 100644 --- a/src/igvfd/mappings/in_vitro_system.json +++ b/src/igvfd/mappings/in_vitro_system.json @@ -632,6 +632,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1072,6 +1075,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/index_file.json b/src/igvfd/mappings/index_file.json index 78ede02e1..e0591c0f6 100644 --- a/src/igvfd/mappings/index_file.json +++ b/src/igvfd/mappings/index_file.json @@ -342,6 +342,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1399,6 +1402,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/matrix_file.json b/src/igvfd/mappings/matrix_file.json index d12fd4851..02de980e0 100644 --- a/src/igvfd/mappings/matrix_file.json +++ b/src/igvfd/mappings/matrix_file.json @@ -335,6 +335,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1392,6 +1395,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/measurement_set.json b/src/igvfd/mappings/measurement_set.json index db7d56f7e..febbecad1 100644 --- a/src/igvfd/mappings/measurement_set.json +++ b/src/igvfd/mappings/measurement_set.json @@ -266,99 +266,609 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, + "control_for": { + "type": "keyword" + }, + "control_type": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "donors": { + "type": "keyword" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { + "type": "keyword" + }, + "input_for": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "measurement_sets": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "publications": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "samples": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_files_timestamp": { + "type": "date" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "url": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + } + }, + "type": "object" + }, + "award": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "component": { + "type": "keyword" + }, + "contact_pi": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "description": { + "type": "text" + }, + "email": { + "type": "keyword" + }, + "first_name": { + "type": "keyword" + }, + "groups": { + "type": "keyword" + }, + "job_title": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "last_name": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "schema_version": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submits_for": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "title": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "viewing_groups": { + "type": "keyword" + } + }, + "type": "object" + }, + "creation_timestamp": { + "type": "date" + }, + "description": { + "type": "text" + }, + "end_date": { + "type": "keyword" + }, + "name": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "pis": { + "type": "keyword" + }, + "project": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "start_date": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "title": { + "type": "keyword" + }, + "url": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "viewing_group": { + "type": "keyword" + } + }, + "type": "object" + }, + "collections": { + "copy_to": "_fuzzy", + "type": "keyword" + }, + "construct_library_sets": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "applied_to_samples": { + "type": "keyword" + }, + "assay_term": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assemblies": { + "type": "keyword" + }, + "assessed_genes": { + "type": "keyword" + }, + "associated_phenotypes": { + "type": "keyword" + }, + "auxiliary_sets": { + "type": "keyword" + }, + "average_guide_coverage": { + "store": true, + "type": "float" + }, + "average_insert_size": { + "store": true, + "type": "float" + }, + "award": { + "type": "keyword" + }, + "barcode_map": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "construct_library_sets": { + "type": "keyword" + }, + "control_file_sets": { + "type": "keyword" + }, "control_for": { "type": "keyword" }, - "control_type": { + "control_type": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "demultiplexed_sample": { + "type": "keyword" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "donors": { + "type": "keyword" + }, + "exon": { + "type": "keyword" + }, + "external_image_data_url": { + "type": "keyword" + }, + "external_image_url": { + "type": "keyword" + }, + "external_input_data": { + "type": "keyword" + }, + "externally_hosted": { + "store": true, + "type": "boolean" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { + "type": "keyword" + }, + "functional_assay_mechanisms": { + "type": "keyword" + }, + "guide_type": { + "type": "keyword" + }, + "input_file_sets": { + "type": "keyword" + }, + "input_for": { + "type": "keyword" + }, + "integrated_content_files": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "analysis_step_version": { + "type": "keyword" + }, + "anvil_url": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assembly": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "barcode_map_for": { + "type": "keyword" + }, + "cell_type_annotation": { + "type": "keyword" + }, + "checkfiles_version": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "content_md5sum": { + "type": "keyword" + }, + "content_type": { + "type": "keyword" + }, + "controlled_access": { + "store": true, + "type": "boolean" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "derived_from": { + "type": "keyword" + }, + "derived_manually": { + "store": true, + "type": "boolean" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "external": { + "store": true, + "type": "boolean" + }, + "file_format": { + "type": "keyword" + }, + "file_format_specifications": { + "type": "keyword" + }, + "file_format_type": { + "type": "keyword" + }, + "file_set": { + "type": "keyword" + }, + "file_size": { + "store": true, + "type": "long" + }, + "gene_list_for": { + "type": "keyword" + }, + "href": { + "type": "keyword" + }, + "input_file_for": { + "type": "keyword" + }, + "integrated_in": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "loci_list_for": { + "type": "keyword" + }, + "md5sum": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "s3_uri": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "source_url": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_file_name": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "transcriptome_annotation": { + "type": "keyword" + }, + "upload_credentials": { + "properties": {}, + "type": "object" + }, + "upload_status": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "validation_error_detail": { + "type": "keyword" + }, + "workflow": { + "type": "keyword" + } + }, + "type": "object" + }, + "lab": { "type": "keyword" }, - "creation_timestamp": { - "type": "date" - }, - "dbxrefs": { + "large_scale_gene_list": { "type": "keyword" }, - "description": { - "type": "text" - }, - "documents": { + "large_scale_loci_list": { "type": "keyword" }, - "donors": { + "lot_id": { "type": "keyword" }, - "file_set_type": { - "type": "keyword" + "lower_bound_guide_coverage": { + "store": true, + "type": "long" }, - "files": { + "lower_bound_insert_size": { + "store": true, + "type": "long" + }, + "measurement_sets": { "type": "keyword" }, - "input_for": { + "model_name": { "type": "keyword" }, - "lab": { + "model_version": { "type": "keyword" }, - "measurement_sets": { + "model_zoo_location": { "type": "keyword" }, + "multiome_size": { + "store": true, + "type": "long" + }, "notes": { "type": "text" }, - "publications": { + "onlist_files": { "type": "keyword" }, - "release_timestamp": { - "type": "date" + "onlist_method": { + "type": "keyword" }, - "revoke_detail": { + "orf_list": { "type": "keyword" }, - "samples": { + "prediction_objects": { "type": "keyword" }, - "schema_version": { + "preferred_assay_title": { "type": "keyword" }, - "status": { + "product_id": { "type": "keyword" }, - "submitted_by": { + "protocols": { "type": "keyword" }, - "submitted_files_timestamp": { - "type": "date" + "publications": { + "type": "keyword" }, - "submitter_comment": { + "related_multiome_datasets": { "type": "keyword" }, - "summary": { + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { "type": "keyword" }, - "url": { + "sample_summary": { "type": "keyword" }, - "uuid": { + "samples": { "type": "keyword" - } - }, - "type": "object" - }, - "award": { - "properties": { - "@id": { + }, + "schema_version": { "type": "keyword" }, - "@type": { + "scope": { "type": "keyword" }, - "aliases": { + "selection_criteria": { "type": "keyword" }, - "component": { + "sequencing_library_types": { "type": "keyword" }, - "contact_pi": { + "small_scale_gene_list": { "properties": { "@id": { "type": "keyword" @@ -372,39 +882,52 @@ "creation_timestamp": { "type": "date" }, - "description": { - "type": "text" - }, - "email": { + "dbxrefs": { "type": "keyword" }, - "first_name": { - "type": "keyword" + "description": { + "type": "text" }, - "groups": { + "geneid": { "type": "keyword" }, - "job_title": { + "geneid_with_version": { "type": "keyword" }, - "lab": { - "type": "keyword" + "locations": { + "properties": { + "assembly": { + "type": "keyword" + }, + "chromosome": { + "type": "keyword" + }, + "end": { + "store": true, + "type": "long" + }, + "start": { + "store": true, + "type": "long" + } + }, + "type": "object" }, - "last_name": { + "name": { "type": "keyword" }, "notes": { "type": "text" }, + "release_timestamp": { + "type": "date" + }, "schema_version": { "type": "keyword" }, "status": { "type": "keyword" }, - "submits_for": { - "type": "keyword" - }, "submitted_by": { "type": "keyword" }, @@ -414,76 +937,121 @@ "summary": { "type": "keyword" }, + "symbol": { + "type": "keyword" + }, + "synonyms": { + "type": "keyword" + }, + "taxa": { + "type": "keyword" + }, "title": { "type": "keyword" }, + "transcriptome_annotation": { + "type": "keyword" + }, "uuid": { "type": "keyword" }, - "viewing_groups": { + "version_number": { "type": "keyword" } }, "type": "object" }, - "creation_timestamp": { - "type": "date" - }, - "description": { - "type": "text" + "small_scale_loci_list": { + "properties": { + "assembly": { + "type": "keyword" + }, + "chromosome": { + "type": "keyword" + }, + "end": { + "store": true, + "type": "long" + }, + "start": { + "store": true, + "type": "long" + } + }, + "type": "object" }, - "end_date": { + "software_version": { "type": "keyword" }, - "name": { + "sources": { "type": "keyword" }, - "notes": { - "type": "text" - }, - "pis": { + "status": { "type": "keyword" }, - "project": { + "submitted_by": { "type": "keyword" }, - "schema_version": { + "submitted_files_timestamp": { + "type": "date" + }, + "submitter_comment": { "type": "keyword" }, - "start_date": { + "summary": { "type": "keyword" }, - "status": { + "targeted_genes": { "type": "keyword" }, - "submitted_by": { + "targeton": { "type": "keyword" }, - "submitter_comment": { + "taxa": { "type": "keyword" }, - "summary": { + "tile": { + "properties": { + "tile_end": { + "store": true, + "type": "long" + }, + "tile_id": { + "type": "keyword" + }, + "tile_start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "tiling_modality": { "type": "keyword" }, - "title": { + "transcriptome_annotations": { "type": "keyword" }, + "upper_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "upper_bound_insert_size": { + "store": true, + "type": "long" + }, "url": { "type": "keyword" }, "uuid": { "type": "keyword" }, - "viewing_group": { + "workflows": { "type": "keyword" } }, "type": "object" }, - "collections": { - "copy_to": "_fuzzy", - "type": "keyword" - }, "control_file_sets": { "properties": { "@id": { @@ -541,6 +1109,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -846,6 +1417,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1907,6 +2481,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/model_file.json b/src/igvfd/mappings/model_file.json index 43d4bbf49..daf744813 100644 --- a/src/igvfd/mappings/model_file.json +++ b/src/igvfd/mappings/model_file.json @@ -346,6 +346,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1399,6 +1402,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/model_set.json b/src/igvfd/mappings/model_set.json index 543318d55..173a3e225 100644 --- a/src/igvfd/mappings/model_set.json +++ b/src/igvfd/mappings/model_set.json @@ -396,6 +396,481 @@ "copy_to": "_fuzzy", "type": "keyword" }, + "construct_library_sets": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "applied_to_samples": { + "type": "keyword" + }, + "assay_term": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assemblies": { + "type": "keyword" + }, + "assessed_genes": { + "type": "keyword" + }, + "associated_phenotypes": { + "type": "keyword" + }, + "auxiliary_sets": { + "type": "keyword" + }, + "average_guide_coverage": { + "store": true, + "type": "float" + }, + "average_insert_size": { + "store": true, + "type": "float" + }, + "award": { + "type": "keyword" + }, + "barcode_map": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "construct_library_sets": { + "type": "keyword" + }, + "control_file_sets": { + "type": "keyword" + }, + "control_for": { + "type": "keyword" + }, + "control_type": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "demultiplexed_sample": { + "type": "keyword" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "donors": { + "type": "keyword" + }, + "exon": { + "type": "keyword" + }, + "external_image_data_url": { + "type": "keyword" + }, + "external_image_url": { + "type": "keyword" + }, + "external_input_data": { + "type": "keyword" + }, + "externally_hosted": { + "store": true, + "type": "boolean" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { + "type": "keyword" + }, + "functional_assay_mechanisms": { + "type": "keyword" + }, + "guide_type": { + "type": "keyword" + }, + "input_file_sets": { + "type": "keyword" + }, + "input_for": { + "type": "keyword" + }, + "integrated_content_files": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "analysis_step_version": { + "type": "keyword" + }, + "anvil_url": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assembly": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "barcode_map_for": { + "type": "keyword" + }, + "cell_type_annotation": { + "type": "keyword" + }, + "checkfiles_version": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "content_md5sum": { + "type": "keyword" + }, + "content_type": { + "type": "keyword" + }, + "controlled_access": { + "store": true, + "type": "boolean" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "derived_from": { + "type": "keyword" + }, + "derived_manually": { + "store": true, + "type": "boolean" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "external": { + "store": true, + "type": "boolean" + }, + "file_format": { + "type": "keyword" + }, + "file_format_specifications": { + "type": "keyword" + }, + "file_format_type": { + "type": "keyword" + }, + "file_set": { + "type": "keyword" + }, + "file_size": { + "store": true, + "type": "long" + }, + "gene_list_for": { + "type": "keyword" + }, + "href": { + "type": "keyword" + }, + "input_file_for": { + "type": "keyword" + }, + "integrated_in": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "loci_list_for": { + "type": "keyword" + }, + "md5sum": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "s3_uri": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "source_url": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_file_name": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "transcriptome_annotation": { + "type": "keyword" + }, + "upload_credentials": { + "properties": {}, + "type": "object" + }, + "upload_status": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "validation_error_detail": { + "type": "keyword" + }, + "workflow": { + "type": "keyword" + } + }, + "type": "object" + }, + "lab": { + "type": "keyword" + }, + "large_scale_gene_list": { + "type": "keyword" + }, + "large_scale_loci_list": { + "type": "keyword" + }, + "lot_id": { + "type": "keyword" + }, + "lower_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "lower_bound_insert_size": { + "store": true, + "type": "long" + }, + "measurement_sets": { + "type": "keyword" + }, + "model_name": { + "type": "keyword" + }, + "model_version": { + "type": "keyword" + }, + "model_zoo_location": { + "type": "keyword" + }, + "multiome_size": { + "store": true, + "type": "long" + }, + "notes": { + "type": "text" + }, + "onlist_files": { + "type": "keyword" + }, + "onlist_method": { + "type": "keyword" + }, + "orf_list": { + "type": "keyword" + }, + "prediction_objects": { + "type": "keyword" + }, + "preferred_assay_title": { + "type": "keyword" + }, + "product_id": { + "type": "keyword" + }, + "protocols": { + "type": "keyword" + }, + "publications": { + "type": "keyword" + }, + "related_multiome_datasets": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "sample_summary": { + "type": "keyword" + }, + "samples": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "scope": { + "type": "keyword" + }, + "selection_criteria": { + "type": "keyword" + }, + "sequencing_library_types": { + "type": "keyword" + }, + "small_scale_gene_list": { + "type": "keyword" + }, + "small_scale_loci_list": { + "properties": { + "assembly": { + "type": "keyword" + }, + "chromosome": { + "type": "keyword" + }, + "end": { + "store": true, + "type": "long" + }, + "start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "software_version": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_files_timestamp": { + "type": "date" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "targeted_genes": { + "type": "keyword" + }, + "targeton": { + "type": "keyword" + }, + "taxa": { + "type": "keyword" + }, + "tile": { + "properties": { + "tile_end": { + "store": true, + "type": "long" + }, + "tile_id": { + "type": "keyword" + }, + "tile_start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "tiling_modality": { + "type": "keyword" + }, + "transcriptome_annotations": { + "type": "keyword" + }, + "upper_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "upper_bound_insert_size": { + "store": true, + "type": "long" + }, + "url": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "workflows": { + "type": "keyword" + } + }, + "type": "object" + }, "control_for": { "properties": { "@id": { @@ -453,6 +928,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1184,6 +1662,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1709,369 +2190,7 @@ "type": "keyword" }, "construct_library_sets": { - "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "accession": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "alternate_accessions": { - "type": "keyword" - }, - "applied_to_samples": { - "type": "keyword" - }, - "associated_phenotypes": { - "type": "keyword" - }, - "average_guide_coverage": { - "store": true, - "type": "float" - }, - "average_insert_size": { - "store": true, - "type": "float" - }, - "award": { - "type": "keyword" - }, - "collections": { - "type": "keyword" - }, - "control_file_sets": { - "type": "keyword" - }, - "control_for": { - "type": "keyword" - }, - "control_type": { - "type": "keyword" - }, - "creation_timestamp": { - "type": "date" - }, - "description": { - "type": "text" - }, - "documents": { - "type": "keyword" - }, - "exon": { - "type": "keyword" - }, - "file_set_type": { - "type": "keyword" - }, - "files": { - "type": "keyword" - }, - "guide_type": { - "type": "keyword" - }, - "input_for": { - "type": "keyword" - }, - "integrated_content_files": { - "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "accession": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "alternate_accessions": { - "type": "keyword" - }, - "analysis_step_version": { - "type": "keyword" - }, - "anvil_url": { - "type": "keyword" - }, - "assay_titles": { - "type": "keyword" - }, - "assembly": { - "type": "keyword" - }, - "award": { - "type": "keyword" - }, - "barcode_map_for": { - "type": "keyword" - }, - "cell_type_annotation": { - "type": "keyword" - }, - "checkfiles_version": { - "type": "keyword" - }, - "collections": { - "type": "keyword" - }, - "content_md5sum": { - "type": "keyword" - }, - "content_type": { - "type": "keyword" - }, - "controlled_access": { - "store": true, - "type": "boolean" - }, - "creation_timestamp": { - "type": "date" - }, - "dbxrefs": { - "type": "keyword" - }, - "derived_from": { - "type": "keyword" - }, - "derived_manually": { - "store": true, - "type": "boolean" - }, - "description": { - "type": "text" - }, - "documents": { - "type": "keyword" - }, - "external": { - "store": true, - "type": "boolean" - }, - "file_format": { - "type": "keyword" - }, - "file_format_specifications": { - "type": "keyword" - }, - "file_format_type": { - "type": "keyword" - }, - "file_set": { - "type": "keyword" - }, - "file_size": { - "store": true, - "type": "long" - }, - "gene_list_for": { - "type": "keyword" - }, - "href": { - "type": "keyword" - }, - "input_file_for": { - "type": "keyword" - }, - "integrated_in": { - "type": "keyword" - }, - "lab": { - "type": "keyword" - }, - "loci_list_for": { - "type": "keyword" - }, - "md5sum": { - "type": "keyword" - }, - "notes": { - "type": "text" - }, - "release_timestamp": { - "type": "date" - }, - "revoke_detail": { - "type": "keyword" - }, - "s3_uri": { - "type": "keyword" - }, - "schema_version": { - "type": "keyword" - }, - "source_url": { - "type": "keyword" - }, - "sources": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" - }, - "submitted_file_name": { - "type": "keyword" - }, - "submitter_comment": { - "type": "keyword" - }, - "summary": { - "type": "keyword" - }, - "transcriptome_annotation": { - "type": "keyword" - }, - "upload_credentials": { - "properties": {}, - "type": "object" - }, - "upload_status": { - "type": "keyword" - }, - "uuid": { - "type": "keyword" - }, - "validation_error_detail": { - "type": "keyword" - }, - "workflow": { - "type": "keyword" - } - }, - "type": "object" - }, - "lab": { - "type": "keyword" - }, - "large_scale_gene_list": { - "type": "keyword" - }, - "large_scale_loci_list": { - "type": "keyword" - }, - "lot_id": { - "type": "keyword" - }, - "lower_bound_guide_coverage": { - "store": true, - "type": "long" - }, - "lower_bound_insert_size": { - "store": true, - "type": "long" - }, - "notes": { - "type": "text" - }, - "orf_list": { - "type": "keyword" - }, - "product_id": { - "type": "keyword" - }, - "publications": { - "type": "keyword" - }, - "release_timestamp": { - "type": "date" - }, - "revoke_detail": { - "type": "keyword" - }, - "schema_version": { - "type": "keyword" - }, - "scope": { - "type": "keyword" - }, - "selection_criteria": { - "type": "keyword" - }, - "small_scale_gene_list": { - "type": "keyword" - }, - "small_scale_loci_list": { - "properties": { - "assembly": { - "type": "keyword" - }, - "chromosome": { - "type": "keyword" - }, - "end": { - "store": true, - "type": "long" - }, - "start": { - "store": true, - "type": "long" - } - }, - "type": "object" - }, - "sources": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" - }, - "submitted_files_timestamp": { - "type": "date" - }, - "submitter_comment": { - "type": "keyword" - }, - "summary": { - "type": "keyword" - }, - "targeton": { - "type": "keyword" - }, - "tile": { - "properties": { - "tile_end": { - "store": true, - "type": "long" - }, - "tile_id": { - "type": "keyword" - }, - "tile_start": { - "store": true, - "type": "long" - } - }, - "type": "object" - }, - "tiling_modality": { - "type": "keyword" - }, - "upper_bound_guide_coverage": { - "store": true, - "type": "long" - }, - "upper_bound_insert_size": { - "store": true, - "type": "long" - }, - "uuid": { - "type": "keyword" - } - }, - "type": "object" + "type": "keyword" }, "creation_timestamp": { "type": "date" diff --git a/src/igvfd/mappings/multiplexed_sample.json b/src/igvfd/mappings/multiplexed_sample.json index 01703e9ea..b1b3312b3 100644 --- a/src/igvfd/mappings/multiplexed_sample.json +++ b/src/igvfd/mappings/multiplexed_sample.json @@ -509,6 +509,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -939,6 +942,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/prediction_set.json b/src/igvfd/mappings/prediction_set.json index 031ec3def..454a29d92 100644 --- a/src/igvfd/mappings/prediction_set.json +++ b/src/igvfd/mappings/prediction_set.json @@ -396,6 +396,481 @@ "copy_to": "_fuzzy", "type": "keyword" }, + "construct_library_sets": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "applied_to_samples": { + "type": "keyword" + }, + "assay_term": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assemblies": { + "type": "keyword" + }, + "assessed_genes": { + "type": "keyword" + }, + "associated_phenotypes": { + "type": "keyword" + }, + "auxiliary_sets": { + "type": "keyword" + }, + "average_guide_coverage": { + "store": true, + "type": "float" + }, + "average_insert_size": { + "store": true, + "type": "float" + }, + "award": { + "type": "keyword" + }, + "barcode_map": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "construct_library_sets": { + "type": "keyword" + }, + "control_file_sets": { + "type": "keyword" + }, + "control_for": { + "type": "keyword" + }, + "control_type": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "demultiplexed_sample": { + "type": "keyword" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "donors": { + "type": "keyword" + }, + "exon": { + "type": "keyword" + }, + "external_image_data_url": { + "type": "keyword" + }, + "external_image_url": { + "type": "keyword" + }, + "external_input_data": { + "type": "keyword" + }, + "externally_hosted": { + "store": true, + "type": "boolean" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { + "type": "keyword" + }, + "functional_assay_mechanisms": { + "type": "keyword" + }, + "guide_type": { + "type": "keyword" + }, + "input_file_sets": { + "type": "keyword" + }, + "input_for": { + "type": "keyword" + }, + "integrated_content_files": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "analysis_step_version": { + "type": "keyword" + }, + "anvil_url": { + "type": "keyword" + }, + "assay_titles": { + "type": "keyword" + }, + "assembly": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "barcode_map_for": { + "type": "keyword" + }, + "cell_type_annotation": { + "type": "keyword" + }, + "checkfiles_version": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "content_md5sum": { + "type": "keyword" + }, + "content_type": { + "type": "keyword" + }, + "controlled_access": { + "store": true, + "type": "boolean" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "type": "keyword" + }, + "derived_from": { + "type": "keyword" + }, + "derived_manually": { + "store": true, + "type": "boolean" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "external": { + "store": true, + "type": "boolean" + }, + "file_format": { + "type": "keyword" + }, + "file_format_specifications": { + "type": "keyword" + }, + "file_format_type": { + "type": "keyword" + }, + "file_set": { + "type": "keyword" + }, + "file_size": { + "store": true, + "type": "long" + }, + "gene_list_for": { + "type": "keyword" + }, + "href": { + "type": "keyword" + }, + "input_file_for": { + "type": "keyword" + }, + "integrated_in": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "loci_list_for": { + "type": "keyword" + }, + "md5sum": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "s3_uri": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "source_url": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_file_name": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "transcriptome_annotation": { + "type": "keyword" + }, + "upload_credentials": { + "properties": {}, + "type": "object" + }, + "upload_status": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "validation_error_detail": { + "type": "keyword" + }, + "workflow": { + "type": "keyword" + } + }, + "type": "object" + }, + "lab": { + "type": "keyword" + }, + "large_scale_gene_list": { + "type": "keyword" + }, + "large_scale_loci_list": { + "type": "keyword" + }, + "lot_id": { + "type": "keyword" + }, + "lower_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "lower_bound_insert_size": { + "store": true, + "type": "long" + }, + "measurement_sets": { + "type": "keyword" + }, + "model_name": { + "type": "keyword" + }, + "model_version": { + "type": "keyword" + }, + "model_zoo_location": { + "type": "keyword" + }, + "multiome_size": { + "store": true, + "type": "long" + }, + "notes": { + "type": "text" + }, + "onlist_files": { + "type": "keyword" + }, + "onlist_method": { + "type": "keyword" + }, + "orf_list": { + "type": "keyword" + }, + "prediction_objects": { + "type": "keyword" + }, + "preferred_assay_title": { + "type": "keyword" + }, + "product_id": { + "type": "keyword" + }, + "protocols": { + "type": "keyword" + }, + "publications": { + "type": "keyword" + }, + "related_multiome_datasets": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "sample_summary": { + "type": "keyword" + }, + "samples": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "scope": { + "type": "keyword" + }, + "selection_criteria": { + "type": "keyword" + }, + "sequencing_library_types": { + "type": "keyword" + }, + "small_scale_gene_list": { + "type": "keyword" + }, + "small_scale_loci_list": { + "properties": { + "assembly": { + "type": "keyword" + }, + "chromosome": { + "type": "keyword" + }, + "end": { + "store": true, + "type": "long" + }, + "start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "software_version": { + "type": "keyword" + }, + "sources": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitted_files_timestamp": { + "type": "date" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "targeted_genes": { + "type": "keyword" + }, + "targeton": { + "type": "keyword" + }, + "taxa": { + "type": "keyword" + }, + "tile": { + "properties": { + "tile_end": { + "store": true, + "type": "long" + }, + "tile_id": { + "type": "keyword" + }, + "tile_start": { + "store": true, + "type": "long" + } + }, + "type": "object" + }, + "tiling_modality": { + "type": "keyword" + }, + "transcriptome_annotations": { + "type": "keyword" + }, + "upper_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "upper_bound_insert_size": { + "store": true, + "type": "long" + }, + "url": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "workflows": { + "type": "keyword" + } + }, + "type": "object" + }, "control_for": { "properties": { "@id": { @@ -453,6 +928,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1780,6 +2258,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1814,176 +2295,7 @@ "type": "keyword" }, "integrated_content_files": { - "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "accession": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "alternate_accessions": { - "type": "keyword" - }, - "analysis_step_version": { - "type": "keyword" - }, - "anvil_url": { - "type": "keyword" - }, - "assay_titles": { - "type": "keyword" - }, - "assembly": { - "type": "keyword" - }, - "award": { - "type": "keyword" - }, - "barcode_map_for": { - "type": "keyword" - }, - "cell_type_annotation": { - "type": "keyword" - }, - "checkfiles_version": { - "type": "keyword" - }, - "collections": { - "type": "keyword" - }, - "content_md5sum": { - "type": "keyword" - }, - "content_type": { - "type": "keyword" - }, - "controlled_access": { - "store": true, - "type": "boolean" - }, - "creation_timestamp": { - "type": "date" - }, - "dbxrefs": { - "type": "keyword" - }, - "derived_from": { - "type": "keyword" - }, - "derived_manually": { - "store": true, - "type": "boolean" - }, - "description": { - "type": "text" - }, - "documents": { - "type": "keyword" - }, - "external": { - "store": true, - "type": "boolean" - }, - "file_format": { - "type": "keyword" - }, - "file_format_specifications": { - "type": "keyword" - }, - "file_format_type": { - "type": "keyword" - }, - "file_set": { - "type": "keyword" - }, - "file_size": { - "store": true, - "type": "long" - }, - "gene_list_for": { - "type": "keyword" - }, - "href": { - "type": "keyword" - }, - "input_file_for": { - "type": "keyword" - }, - "integrated_in": { - "type": "keyword" - }, - "lab": { - "type": "keyword" - }, - "loci_list_for": { - "type": "keyword" - }, - "md5sum": { - "type": "keyword" - }, - "notes": { - "type": "text" - }, - "release_timestamp": { - "type": "date" - }, - "revoke_detail": { - "type": "keyword" - }, - "s3_uri": { - "type": "keyword" - }, - "schema_version": { - "type": "keyword" - }, - "source_url": { - "type": "keyword" - }, - "sources": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" - }, - "submitted_file_name": { - "type": "keyword" - }, - "submitter_comment": { - "type": "keyword" - }, - "summary": { - "type": "keyword" - }, - "transcriptome_annotation": { - "type": "keyword" - }, - "upload_credentials": { - "properties": {}, - "type": "object" - }, - "upload_status": { - "type": "keyword" - }, - "uuid": { - "type": "keyword" - }, - "validation_error_detail": { - "type": "keyword" - }, - "workflow": { - "type": "keyword" - } - }, - "type": "object" + "type": "keyword" }, "lab": { "type": "keyword" diff --git a/src/igvfd/mappings/primary_cell.json b/src/igvfd/mappings/primary_cell.json index c84fca2f5..00ea930fd 100644 --- a/src/igvfd/mappings/primary_cell.json +++ b/src/igvfd/mappings/primary_cell.json @@ -515,6 +515,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -949,6 +952,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/reference_file.json b/src/igvfd/mappings/reference_file.json index d489138fe..fd21ae96d 100644 --- a/src/igvfd/mappings/reference_file.json +++ b/src/igvfd/mappings/reference_file.json @@ -349,6 +349,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1402,6 +1405,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/sequence_file.json b/src/igvfd/mappings/sequence_file.json index f62121f1d..b9fa4222a 100644 --- a/src/igvfd/mappings/sequence_file.json +++ b/src/igvfd/mappings/sequence_file.json @@ -349,6 +349,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1411,6 +1414,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/signal_file.json b/src/igvfd/mappings/signal_file.json index 1596d71de..5ab30a7d6 100644 --- a/src/igvfd/mappings/signal_file.json +++ b/src/igvfd/mappings/signal_file.json @@ -422,6 +422,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1479,6 +1482,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/tabular_file.json b/src/igvfd/mappings/tabular_file.json index 668c0c8fc..04760c9ab 100644 --- a/src/igvfd/mappings/tabular_file.json +++ b/src/igvfd/mappings/tabular_file.json @@ -432,6 +432,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1489,6 +1492,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/technical_sample.json b/src/igvfd/mappings/technical_sample.json index 019baa4e1..7ebd88de7 100644 --- a/src/igvfd/mappings/technical_sample.json +++ b/src/igvfd/mappings/technical_sample.json @@ -336,6 +336,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -567,6 +570,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/tissue.json b/src/igvfd/mappings/tissue.json index d496ae294..cb347f19d 100644 --- a/src/igvfd/mappings/tissue.json +++ b/src/igvfd/mappings/tissue.json @@ -515,6 +515,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -949,6 +952,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/mappings/whole_organism.json b/src/igvfd/mappings/whole_organism.json index d3cce9880..3cbe6e618 100644 --- a/src/igvfd/mappings/whole_organism.json +++ b/src/igvfd/mappings/whole_organism.json @@ -512,6 +512,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -946,6 +949,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, diff --git a/src/igvfd/searches/configs/analysis_set.py b/src/igvfd/searches/configs/analysis_set.py index 73bac2366..58514a644 100644 --- a/src/igvfd/searches/configs/analysis_set.py +++ b/src/igvfd/searches/configs/analysis_set.py @@ -22,6 +22,9 @@ def analysis_set(): 'files.transcriptome_annotation': { 'title': 'Transcriptome Annotation', }, + 'construct_library_sets.file_set_type': { + 'title': 'Construct Library Data' + }, 'donors.taxa': { 'title': 'Taxa', }, @@ -49,6 +52,9 @@ def analysis_set(): 'files.file_format': { 'title': 'File Format', }, + 'construct_library_sets.integrated_content_files.content_type': { + 'title': 'Construct Library Design' + }, 'collections': { 'title': 'Collections', }, diff --git a/src/igvfd/searches/configs/auxiliary_set.py b/src/igvfd/searches/configs/auxiliary_set.py index 15d53e8ca..215a0cb1c 100644 --- a/src/igvfd/searches/configs/auxiliary_set.py +++ b/src/igvfd/searches/configs/auxiliary_set.py @@ -19,6 +19,9 @@ def auxiliary_set(): 'files.transcriptome_annotation': { 'title': 'Transcriptome Annotation', }, + 'construct_library_sets.file_set_type': { + 'title': 'Construct Library Data' + }, 'donors.taxa': { 'title': 'Taxa' }, @@ -49,6 +52,9 @@ def auxiliary_set(): 'files.file_format': { 'title': 'File Format', }, + 'construct_library_sets.integrated_content_files.content_type': { + 'title': 'Construct Library Design' + }, 'lab.title': { 'title': 'Lab' }, diff --git a/src/igvfd/searches/configs/construct_library_set.py b/src/igvfd/searches/configs/construct_library_set.py index 9f54a1db2..8d7707a27 100644 --- a/src/igvfd/searches/configs/construct_library_set.py +++ b/src/igvfd/searches/configs/construct_library_set.py @@ -58,6 +58,9 @@ def construct_library_set(): 'applied_to_samples.treatments.treatment_term_name': { 'title': 'Treatment' }, + 'applied_to_samples.file_sets.file_set_type': { + 'title': 'File Set Type' + }, 'files.content_type': { 'title': 'File Types', }, diff --git a/src/igvfd/searches/configs/file_set.py b/src/igvfd/searches/configs/file_set.py index 820ebfc67..383fdd27f 100644 --- a/src/igvfd/searches/configs/file_set.py +++ b/src/igvfd/searches/configs/file_set.py @@ -16,6 +16,9 @@ def file_set(): 'transcriptome_annotation': { 'title': 'Transcriptome Annotation', }, + 'construct_library_sets.file_set_type': { + 'title': 'Construct Library Data' + }, 'donors.taxa': { 'title': 'Taxa' }, @@ -46,6 +49,9 @@ def file_set(): 'files.file_format': { 'title': 'File Format', }, + 'construct_library_sets.integrated_content_files.content_type': { + 'title': 'Construct Library Design' + }, 'collections': { 'title': 'Collections', }, diff --git a/src/igvfd/searches/configs/measurement_set.py b/src/igvfd/searches/configs/measurement_set.py index d7191b249..4117e5d63 100644 --- a/src/igvfd/searches/configs/measurement_set.py +++ b/src/igvfd/searches/configs/measurement_set.py @@ -22,10 +22,10 @@ def measurement_set(): 'auxiliary_sets.file_set_type': { 'title': 'Auxiliary Data' }, - 'samples.construct_library_sets.file_set_type': { + 'construct_library_sets.file_set_type': { 'title': 'Construct Library Data' }, - 'samples.construct_library_sets.small_scale_gene_list.symbol': { + 'construct_library_sets.small_scale_gene_list.symbol': { 'title': 'Investigated Gene' }, 'targeted_genes.symbol': { @@ -64,6 +64,9 @@ def measurement_set(): 'files.file_format': { 'title': 'File Format', }, + 'construct_library_sets.integrated_content_files.content_type': { + 'title': 'Construct Library Design' + }, 'collections': { 'title': 'Collections', }, @@ -104,9 +107,9 @@ def measurement_set(): 'control_type', 'functional_assay_mechanisms.term_name', 'auxiliary_sets.file_set_type', - 'samples.construct_library_sets.file_set_type', + 'construct_library_sets.file_set_type', 'targeted_genes.symbol', - 'samples.construct_library_sets.small_scale_gene_list.symbol', + 'construct_library_sets.small_scale_gene_list.symbol', 'files.sequencing_platform.term_name', ], }, diff --git a/src/igvfd/searches/configs/model_set.py b/src/igvfd/searches/configs/model_set.py index a15990d10..3dcb1f17d 100644 --- a/src/igvfd/searches/configs/model_set.py +++ b/src/igvfd/searches/configs/model_set.py @@ -16,14 +16,43 @@ def model_set(): 'assessed_genes': { 'title': 'Assessed Gene' }, + 'construct_library_sets.file_set_type': { + 'title': 'Construct Library Data' + }, + 'donors.taxa': { + 'title': 'Taxa', + }, + 'samples.classifications': { + 'title': 'Classification', + }, + 'samples.sample_terms.term_name': { + 'title': 'Sample', + }, + 'samples.targeted_sample_term.term_name': { + 'title': 'Cellular Transformation Target', + }, + 'samples.disease_terms.term_name': { + 'title': 'Disease', + }, + 'samples.modifications.modality': { + 'title': 'Modification' + }, + 'samples.treatments.treatment_term_name': { + 'title': 'Treatment' + }, 'files.content_type': { 'title': 'File Types', }, 'files.file_format': { 'title': 'File Format', }, +<<<<<<< HEAD 'software_versions.software.title': { 'title': 'Software', +======= + 'construct_library_sets.integrated_content_files.content_type': { + 'title': 'Construct Library Design' +>>>>>>> 87202e45 (change calculated property and embedding for file sets) }, 'collections': { 'title': 'Collections', diff --git a/src/igvfd/searches/configs/prediction_set.py b/src/igvfd/searches/configs/prediction_set.py index dc79e2a27..4971d3b04 100644 --- a/src/igvfd/searches/configs/prediction_set.py +++ b/src/igvfd/searches/configs/prediction_set.py @@ -43,12 +43,18 @@ def prediction_set(): 'samples.treatments.treatment_term_name': { 'title': 'Treatment' }, + 'construct_library_sets.file_set_type': { + 'title': 'Construct Library Data' + }, 'files.content_type': { 'title': 'File Type', }, 'files.file_format': { 'title': 'File Format', }, + 'construct_library_sets.integrated_content_files.content_type': { + 'title': 'Construct Library Design' + }, 'status': { 'title': 'Status' }, diff --git a/src/igvfd/types/file_set.py b/src/igvfd/types/file_set.py index 2d57a58b4..4b47ae201 100644 --- a/src/igvfd/types/file_set.py +++ b/src/igvfd/types/file_set.py @@ -75,7 +75,6 @@ class FileSet(Item): 'cell_fate_change_treatments', 'cellular_sub_pool', 'classifications', - 'construct_library_sets', 'disease_terms', 'modifications', 'sample_terms', @@ -90,7 +89,7 @@ class FileSet(Item): Path('samples.targeted_sample_term', include=['@id', 'term_name', 'status']), Path('samples.modifications', include=['@id', 'modality', 'status']), Path('samples.treatments', include=['@id', 'purpose', 'treatment_type', 'summary', 'status']), - Path('samples.construct_library_sets.integrated_content_files', include=[ + Path('construct_library_sets.integrated_content_files', include=[ '@id', 'accession', 'file_set_type', 'summary', 'status', 'content_type', 'integrated_content_files']), Path('publications', include=['@id', 'publication_identifiers', 'status']), ] @@ -192,6 +191,33 @@ def submitted_files_timestamp(self, request, files, auxiliary_sets=[]): def input_for(self, request, input_for): return paths_filtered_by_status(request, input_for) + @calculated_property( + condition='samples', + schema={ + 'title': 'Construct Library Sets', + 'description': 'The construct library sets associated with the samples of this file set.', + 'type': 'array', + 'minItems': 1, + 'uniqueItems': True, + 'items': { + 'title': 'Construct Library Set', + 'description': 'A construct library set associated with a sample of this file set.', + 'type': 'string', + 'linkTo': 'FileSet', + }, + 'notSubmittable': True + }) + def construct_library_sets(self, request, samples=None): + construct_library_sets = [] + for sample in samples: + sample_object = request.embed(sample, + '@@object_with_select_calculated_properties?' + 'field=construct_library_sets' + ) + construct_library_sets = construct_library_sets + sample_object.get('construct_library_sets', []) + if construct_library_sets: + return construct_library_sets + @collection( name='analysis-sets', @@ -750,7 +776,7 @@ class MeasurementSet(FileSet): Path('related_multiome_datasets', include=['@id', 'accession', 'status']), Path('auxiliary_sets', include=['@id', 'accession', 'aliases', 'file_set_type', 'status']), Path('samples.cell_fate_change_treatments', include=['@id', 'purpose', 'treatment_type', 'summary', 'status']), - Path('samples.construct_library_sets.small_scale_gene_list', include=[ + Path('construct_library_sets.small_scale_gene_list', include=[ '@id', 'small_scale_gene_list', 'summary', 'geneid', 'symbol', 'name', 'status']), Path('files.sequencing_platform', include=['@id', 'term_name', 'status']), Path('targeted_genes', include=['@id', 'geneid', 'symbol', 'name', 'synonyms', 'status']), From 43e21d555e9f2f5441e437815334806bdb3e048b Mon Sep 17 00:00:00 2001 From: ian-whaling Date: Mon, 17 Feb 2025 23:53:42 -0800 Subject: [PATCH 06/13] fixed calculation --- src/igvfd/mappings/analysis_set.json | 13 +++++++++--- src/igvfd/mappings/auxiliary_set.json | 13 +++++++++--- src/igvfd/mappings/construct_library_set.json | 2 +- src/igvfd/mappings/curated_set.json | 13 +++++++++--- src/igvfd/mappings/measurement_set.json | 9 +++++++- src/igvfd/mappings/model_set.json | 9 +++++++- src/igvfd/mappings/prediction_set.json | 9 +++++++- .../searches/configs/construct_library_set.py | 8 ++++++- src/igvfd/searches/configs/model_set.py | 4 +--- .../tests/fixtures/schemas/analysis_set.py | 11 ++++++++++ src/igvfd/tests/test_types_analysis_set.py | 20 ++++++++++++++++-- src/igvfd/types/file_set.py | 21 ++++++++++++++----- 12 files changed, 108 insertions(+), 24 deletions(-) diff --git a/src/igvfd/mappings/analysis_set.json b/src/igvfd/mappings/analysis_set.json index e24f4eb20..99506526c 100644 --- a/src/igvfd/mappings/analysis_set.json +++ b/src/igvfd/mappings/analysis_set.json @@ -1,6 +1,6 @@ { - "hash": "bc24d24de6fcfff86dd1f8d568b5d7c1", - "index_name": "analysis_set_bc24d24d", + "hash": "b9ce17dedb292618be8bb68148fecbed", + "index_name": "analysis_set_b9ce17de", "item_type": "analysis_set", "mapping": { "dynamic_templates": [ @@ -513,6 +513,10 @@ "store": true, "type": "long" }, + "filtered": { + "store": true, + "type": "boolean" + }, "gene_list_for": { "type": "keyword" }, @@ -537,6 +541,9 @@ "notes": { "type": "text" }, + "quality_metrics": { + "type": "keyword" + }, "release_timestamp": { "type": "date" }, @@ -704,7 +711,7 @@ }, "type": "object" }, - "software_version": { + "software_versions": { "type": "keyword" }, "sources": { diff --git a/src/igvfd/mappings/auxiliary_set.json b/src/igvfd/mappings/auxiliary_set.json index 6f0252f97..a97560999 100644 --- a/src/igvfd/mappings/auxiliary_set.json +++ b/src/igvfd/mappings/auxiliary_set.json @@ -1,6 +1,6 @@ { - "hash": "7c1ffe6188380b0f96155573211b3998", - "index_name": "auxiliary_set_7c1ffe61", + "hash": "170c9a644a75ee9fc586daf9c34d9605", + "index_name": "auxiliary_set_170c9a64", "item_type": "auxiliary_set", "mapping": { "dynamic_templates": [ @@ -512,6 +512,10 @@ "store": true, "type": "long" }, + "filtered": { + "store": true, + "type": "boolean" + }, "gene_list_for": { "type": "keyword" }, @@ -536,6 +540,9 @@ "notes": { "type": "text" }, + "quality_metrics": { + "type": "keyword" + }, "release_timestamp": { "type": "date" }, @@ -703,7 +710,7 @@ }, "type": "object" }, - "software_version": { + "software_versions": { "type": "keyword" }, "sources": { diff --git a/src/igvfd/mappings/construct_library_set.json b/src/igvfd/mappings/construct_library_set.json index 22bd19623..dd646eed5 100644 --- a/src/igvfd/mappings/construct_library_set.json +++ b/src/igvfd/mappings/construct_library_set.json @@ -669,7 +669,7 @@ }, "type": "object" }, - "software_version": { + "software_versions": { "type": "keyword" }, "sources": { diff --git a/src/igvfd/mappings/curated_set.json b/src/igvfd/mappings/curated_set.json index 0d7761a07..31b4de475 100644 --- a/src/igvfd/mappings/curated_set.json +++ b/src/igvfd/mappings/curated_set.json @@ -1,6 +1,6 @@ { - "hash": "048a5861694a1b0caf722d17fcb3962a", - "index_name": "curated_set_048a5861", + "hash": "a8481f51d6e8dafbb3d40ea909b6fe22", + "index_name": "curated_set_a8481f51", "item_type": "curated_set", "mapping": { "dynamic_templates": [ @@ -513,6 +513,10 @@ "store": true, "type": "long" }, + "filtered": { + "store": true, + "type": "boolean" + }, "gene_list_for": { "type": "keyword" }, @@ -537,6 +541,9 @@ "notes": { "type": "text" }, + "quality_metrics": { + "type": "keyword" + }, "release_timestamp": { "type": "date" }, @@ -704,7 +711,7 @@ }, "type": "object" }, - "software_version": { + "software_versions": { "type": "keyword" }, "sources": { diff --git a/src/igvfd/mappings/measurement_set.json b/src/igvfd/mappings/measurement_set.json index febbecad1..a69bab401 100644 --- a/src/igvfd/mappings/measurement_set.json +++ b/src/igvfd/mappings/measurement_set.json @@ -699,6 +699,10 @@ "store": true, "type": "long" }, + "filtered": { + "store": true, + "type": "boolean" + }, "gene_list_for": { "type": "keyword" }, @@ -723,6 +727,9 @@ "notes": { "type": "text" }, + "quality_metrics": { + "type": "keyword" + }, "release_timestamp": { "type": "date" }, @@ -980,7 +987,7 @@ }, "type": "object" }, - "software_version": { + "software_versions": { "type": "keyword" }, "sources": { diff --git a/src/igvfd/mappings/model_set.json b/src/igvfd/mappings/model_set.json index 173a3e225..b98bec297 100644 --- a/src/igvfd/mappings/model_set.json +++ b/src/igvfd/mappings/model_set.json @@ -608,6 +608,10 @@ "store": true, "type": "long" }, + "filtered": { + "store": true, + "type": "boolean" + }, "gene_list_for": { "type": "keyword" }, @@ -632,6 +636,9 @@ "notes": { "type": "text" }, + "quality_metrics": { + "type": "keyword" + }, "release_timestamp": { "type": "date" }, @@ -799,7 +806,7 @@ }, "type": "object" }, - "software_version": { + "software_versions": { "type": "keyword" }, "sources": { diff --git a/src/igvfd/mappings/prediction_set.json b/src/igvfd/mappings/prediction_set.json index 454a29d92..fc61afd6d 100644 --- a/src/igvfd/mappings/prediction_set.json +++ b/src/igvfd/mappings/prediction_set.json @@ -608,6 +608,10 @@ "store": true, "type": "long" }, + "filtered": { + "store": true, + "type": "boolean" + }, "gene_list_for": { "type": "keyword" }, @@ -632,6 +636,9 @@ "notes": { "type": "text" }, + "quality_metrics": { + "type": "keyword" + }, "release_timestamp": { "type": "date" }, @@ -799,7 +806,7 @@ }, "type": "object" }, - "software_version": { + "software_versions": { "type": "keyword" }, "sources": { diff --git a/src/igvfd/searches/configs/construct_library_set.py b/src/igvfd/searches/configs/construct_library_set.py index 8d7707a27..bad00eeb9 100644 --- a/src/igvfd/searches/configs/construct_library_set.py +++ b/src/igvfd/searches/configs/construct_library_set.py @@ -58,8 +58,14 @@ def construct_library_set(): 'applied_to_samples.treatments.treatment_term_name': { 'title': 'Treatment' }, + 'applied_to_samples.nucleic_acid_delivery': { + 'title': 'Nucleic Acid Delivery Method' + }, 'applied_to_samples.file_sets.file_set_type': { - 'title': 'File Set Type' + 'title': 'File Set Type Used In' + }, + 'applied_to_samples.file_sets.preferred_assay_title': { + 'title': 'Assay Used In' }, 'files.content_type': { 'title': 'File Types', diff --git a/src/igvfd/searches/configs/model_set.py b/src/igvfd/searches/configs/model_set.py index 3dcb1f17d..214e838f0 100644 --- a/src/igvfd/searches/configs/model_set.py +++ b/src/igvfd/searches/configs/model_set.py @@ -46,13 +46,11 @@ def model_set(): 'files.file_format': { 'title': 'File Format', }, -<<<<<<< HEAD 'software_versions.software.title': { 'title': 'Software', -======= + }, 'construct_library_sets.integrated_content_files.content_type': { 'title': 'Construct Library Design' ->>>>>>> 87202e45 (change calculated property and embedding for file sets) }, 'collections': { 'title': 'Collections', diff --git a/src/igvfd/tests/fixtures/schemas/analysis_set.py b/src/igvfd/tests/fixtures/schemas/analysis_set.py index 9ecb246bf..b09072f5a 100644 --- a/src/igvfd/tests/fixtures/schemas/analysis_set.py +++ b/src/igvfd/tests/fixtures/schemas/analysis_set.py @@ -102,6 +102,17 @@ def analysis_set_with_scrna_measurement_sets(testapp, award, lab, measurement_se return testapp.post_json('/analysis_set', item, status=201).json['@graph'][0] +@pytest.fixture +def analysis_set_with_CLS_input(testapp, award, lab, construct_library_set_reporter): + item = { + 'award': award['@id'], + 'lab': lab['@id'], + 'file_set_type': 'intermediate analysis', + 'input_file_sets': [construct_library_set_reporter['@id']] + } + return testapp.post_json('/analysis_set', item, status=201).json['@graph'][0] + + @pytest.fixture def analysis_set_v1(analysis_set_base, curated_set_genome, human_donor, in_vitro_cell_line): item = analysis_set_base.copy() diff --git a/src/igvfd/tests/test_types_analysis_set.py b/src/igvfd/tests/test_types_analysis_set.py index d7a93b32b..56d68de3a 100644 --- a/src/igvfd/tests/test_types_analysis_set.py +++ b/src/igvfd/tests/test_types_analysis_set.py @@ -59,7 +59,7 @@ def test_calculated_samples(testapp, measurement_set, analysis_set_base, primary assert set([sample['@id'] for sample in res.json.get('samples')]) == {in_vitro_cell_line['@id']} -def test_assay_titles(testapp, analysis_set_base, measurement_set_mpra, measurement_set_multiome, principal_analysis_set, measurement_set_no_files, base_auxiliary_set): +def test_assay_titles(testapp, analysis_set_base, measurement_set_mpra, measurement_set_multiome, principal_analysis_set, measurement_set_no_files, base_auxiliary_set, analysis_set_with_CLS_input, construct_library_set_reporter, primary_cell): testapp.patch_json( analysis_set_base['@id'], { @@ -107,9 +107,17 @@ def test_assay_titles(testapp, analysis_set_base, measurement_set_mpra, measurem ) res = testapp.get(principal_analysis_set['@id']) assert set(res.json.get('assay_titles')) == {'CRISPR FlowFISH screen'} + testapp.patch_json( + primary_cell['@id'], + { + 'construct_library_sets': [construct_library_set_reporter['@id']] + } + ) + res = testapp.get(analysis_set_with_CLS_input['@id']) + assert set(res.json.get('assay_titles')) == {'lentiMPRA'} -def test_analysis_set_summary(testapp, analysis_set_base, base_auxiliary_set, measurement_set_no_files, measurement_set_mpra, measurement_set_multiome, principal_analysis_set, tabular_file, gene_myc_hs, assay_term_atac, assay_term_crispr, primary_cell, crispr_modification): +def test_analysis_set_summary(testapp, analysis_set_base, base_auxiliary_set, measurement_set_no_files, measurement_set_mpra, measurement_set_multiome, principal_analysis_set, tabular_file, gene_myc_hs, assay_term_atac, assay_term_crispr, primary_cell, crispr_modification, construct_library_set_reporter, analysis_set_with_CLS_input): # With no input_file_sets and no files present, summary is based on analysis file_set_type only. res = testapp.get(analysis_set_base['@id']).json assert res.get('summary', '') == 'Unspecified assay' @@ -205,6 +213,14 @@ def test_analysis_set_summary(testapp, analysis_set_base, base_auxiliary_set, me ) res = testapp.get(analysis_set_base['@id']).json assert res.get('summary', '') == 'interference 10x multiome, SUPERSTARR, lentiMPRA targeting MYC: peaks' + testapp.patch_json( + primary_cell['@id'], + { + 'construct_library_sets': [construct_library_set_reporter['@id']] + } + ) + res = testapp.get(analysis_set_with_CLS_input['@id']).json + assert res.get('summary', '') == 'lentiMPRA reporter library' def test_protocols(testapp, analysis_set_base, measurement_set_with_protocols): diff --git a/src/igvfd/types/file_set.py b/src/igvfd/types/file_set.py index 4b47ae201..14cc6da7b 100644 --- a/src/igvfd/types/file_set.py +++ b/src/igvfd/types/file_set.py @@ -340,10 +340,10 @@ def summary(self, request, file_set_type, input_file_sets=[], files=[], assay_ti targeted_genes_phrase = '' if targeted_genes: targeted_genes_phrase = f'targeting {", ".join(targeted_genes)}' - # The file set types are only shown if the inputs are all Auxiliary Sets - # and the Measurement Sets related to the Auxiliary Sets are not CRISPR screens. + # The file set types are only shown if the inputs are all Auxiliary Sets or Construct Library Sets + # and the Measurement Sets related to the Auxiliary Sets or Construct Library Sets are not CRISPR screens. file_set_type_phrase = '' - if fileset_types and len(fileset_subclasses) == 1 and 'AuxiliarySet' in fileset_subclasses: + if fileset_types and len(fileset_subclasses) == 1 and ('AuxiliarySet' in fileset_subclasses or 'ConstructLibrarySet' in fileset_subclasses): if not (assay_terms and all(x in crispr_screen_terms for x in assay_terms)): file_set_type_phrase = ', '.join(fileset_types) @@ -404,6 +404,16 @@ def assay_titles(self, request, input_file_sets=None): preferred_assay_title = measurement_set_object.get('preferred_assay_title') if preferred_assay_title: assay_titles.add(preferred_assay_title) + elif 'ConstructLibrarySet' in file_set_object.get('@type'): + for sample in file_set_object.get('applied_to_samples', []): + sample_object = request.embed( + sample, '@@object_with_select_calculated_properties?field=file_sets') + for file_set in sample_object.get('file_sets', []): + file_set_object = request.embed( + file_set, '@@object_with_select_calculated_properties?field=preferred_assay_title') + preferred_assay_title = file_set_object.get('preferred_assay_title') + if preferred_assay_title: + assay_titles.add(preferred_assay_title) return list(assay_titles) @calculated_property( @@ -1180,14 +1190,15 @@ class ConstructLibrarySet(FileSet): Path('associated_phenotypes', include=['@id', 'term_id', 'term_name', 'status']), Path('small_scale_gene_list', include=['@id', 'geneid', 'symbol', 'name', 'synonyms', 'status']), Path('applied_to_samples', include=['@id', '@type', 'accession', - 'aliases', 'classifications', 'disease_terms', 'donors', 'sample_terms', 'targeted_sample_term', 'status', 'summary', 'modifications', 'treatments']), + 'aliases', 'classifications', 'disease_terms', 'donors', 'sample_terms', 'targeted_sample_term', 'status', 'summary', 'modifications', 'treatments', 'nucleic_acid_delivery']), Path('applied_to_samples.donors', include=['@id', 'taxa', 'status']), Path('applied_to_samples.disease_terms', include=['@id', 'term_name', 'status']), Path('applied_to_samples.sample_terms', include=['@id', 'term_name', 'status']), Path('applied_to_samples.targeted_sample_term', include=['@id', 'term_name', 'status']), Path('applied_to_samples.modifications', include=['@id', 'modality', 'summary', 'status']), Path('applied_to_samples.treatments', include=['@id', 'treatment_term_name', 'summary', 'status']), - Path('applied_to_samples.file_sets', include=['@id', '@type', 'accession', 'aliases', 'summary', 'status']), + Path('applied_to_samples.file_sets', include=[ + '@id', '@type', 'accession', 'aliases', 'summary', 'status', 'preferred_assay_title']), Path('large_scale_gene_list', include=['@id', 'accession', 'aliases', 'status']), Path('large_scale_loci_list', include=['@id', 'accession', 'aliases', 'status']), Path('orf_list', include=['@id', 'orf_id', 'genes', 'aliases', 'status']), From f1ca794790eddda4447c94b02958c994766dbd67 Mon Sep 17 00:00:00 2001 From: ian-whaling Date: Tue, 18 Feb 2025 00:01:48 -0800 Subject: [PATCH 07/13] test for construct_library_sets --- src/igvfd/tests/test_types_file_set.py | 27 ++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/src/igvfd/tests/test_types_file_set.py b/src/igvfd/tests/test_types_file_set.py index 1527aeba1..b281189ac 100644 --- a/src/igvfd/tests/test_types_file_set.py +++ b/src/igvfd/tests/test_types_file_set.py @@ -102,3 +102,30 @@ def test_input_for(testapp, principal_analysis_set, auxiliary_set_v5, measuremen assert res.json.get('input_for', []) == [principal_analysis_set['@id']] res = testapp.get(auxiliary_set_v5['@id']) assert res.json.get('input_for', []) == [principal_analysis_set['@id']] + + +def test_construct_library_sets(testapp, principal_analysis_set, measurement_set, construct_library_set_genome_wide, base_expression_construct_library_set, tissue): + testapp.patch_json( + tissue['@id'], + { + 'construct_library_sets': [construct_library_set_genome_wide['@id'], base_expression_construct_library_set['@id']] + } + ) + testapp.patch_json( + measurement_set['@id'], + { + 'samples': [tissue['@id']] + } + ) + res = testapp.get(measurement_set['@id']) + assert set([file_set['@id'] for file_set in res.json.get('construct_library_sets', [])] + ) == {construct_library_set_genome_wide['@id'], base_expression_construct_library_set['@id']} + testapp.patch_json( + principal_analysis_set['@id'], + { + 'input_file_sets': [measurement_set['@id']] + } + ) + res = testapp.get(principal_analysis_set['@id']) + assert set([file_set['@id'] for file_set in res.json.get('construct_library_sets', [])] + ) == {construct_library_set_genome_wide['@id'], base_expression_construct_library_set['@id']} From 77e528e43565fe48e98c513dc92b854765a718d5 Mon Sep 17 00:00:00 2001 From: ian-whaling Date: Tue, 18 Feb 2025 00:16:08 -0800 Subject: [PATCH 08/13] adjustments to type --- src/igvfd/mappings/analysis_set.json | 4 ++-- src/igvfd/mappings/auxiliary_set.json | 4 ++-- src/igvfd/mappings/curated_set.json | 4 ++-- src/igvfd/types/file_set.py | 7 ++++--- 4 files changed, 10 insertions(+), 9 deletions(-) diff --git a/src/igvfd/mappings/analysis_set.json b/src/igvfd/mappings/analysis_set.json index 99506526c..3ae8d479b 100644 --- a/src/igvfd/mappings/analysis_set.json +++ b/src/igvfd/mappings/analysis_set.json @@ -1,6 +1,6 @@ { - "hash": "b9ce17dedb292618be8bb68148fecbed", - "index_name": "analysis_set_b9ce17de", + "hash": "0bb377e8e3c237fe0defb35978b0da90", + "index_name": "analysis_set_0bb377e8", "item_type": "analysis_set", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/auxiliary_set.json b/src/igvfd/mappings/auxiliary_set.json index a97560999..bf88157bd 100644 --- a/src/igvfd/mappings/auxiliary_set.json +++ b/src/igvfd/mappings/auxiliary_set.json @@ -1,6 +1,6 @@ { - "hash": "170c9a644a75ee9fc586daf9c34d9605", - "index_name": "auxiliary_set_170c9a64", + "hash": "dbb37ac938db6c445c4974fb3f50e0d2", + "index_name": "auxiliary_set_dbb37ac9", "item_type": "auxiliary_set", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/curated_set.json b/src/igvfd/mappings/curated_set.json index 31b4de475..fb0ff3526 100644 --- a/src/igvfd/mappings/curated_set.json +++ b/src/igvfd/mappings/curated_set.json @@ -1,6 +1,6 @@ { - "hash": "a8481f51d6e8dafbb3d40ea909b6fe22", - "index_name": "curated_set_a8481f51", + "hash": "53bfd46919b7e5d335cf5ccc86ec9c71", + "index_name": "curated_set_53bfd469", "item_type": "curated_set", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/types/file_set.py b/src/igvfd/types/file_set.py index 14cc6da7b..b6e4de013 100644 --- a/src/igvfd/types/file_set.py +++ b/src/igvfd/types/file_set.py @@ -208,15 +208,16 @@ def input_for(self, request, input_for): 'notSubmittable': True }) def construct_library_sets(self, request, samples=None): - construct_library_sets = [] + construct_library_sets = set() for sample in samples: sample_object = request.embed(sample, '@@object_with_select_calculated_properties?' 'field=construct_library_sets' ) - construct_library_sets = construct_library_sets + sample_object.get('construct_library_sets', []) + if sample_object.get('construct_library_sets', []): + construct_library_sets = construct_library_sets | set(sample_object.get('construct_library_sets', [])) if construct_library_sets: - return construct_library_sets + return list(construct_library_sets) @collection( From a7f69c90b0a9b6f577f9cf14cb9a6d8dd3144926 Mon Sep 17 00:00:00 2001 From: ian-whaling Date: Tue, 18 Feb 2025 09:33:08 -0800 Subject: [PATCH 09/13] audit + mappings --- src/igvfd/audit/measurement_set.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/igvfd/audit/measurement_set.py b/src/igvfd/audit/measurement_set.py index e2108b5b0..434f95bb9 100644 --- a/src/igvfd/audit/measurement_set.py +++ b/src/igvfd/audit/measurement_set.py @@ -388,7 +388,7 @@ def audit_missing_construct_library_set(value, system): assay_term_name = value.get('assay_term').get('term_name') preferred_assay_title = value.get('preferred_assay_title') - construct_library_sets = value.get('samples')[0].get('construct_library_sets') + construct_library_sets = value.get('construct_library_sets') if (assay_term_name in expected_library_by_assay_term or preferred_assay_title in expected_library_by_preferred_assay_title) and not (value.get('control_for')): From 46cc9cfcaee3acd9f40c9947a353aa313aabd087 Mon Sep 17 00:00:00 2001 From: ian-whaling Date: Tue, 18 Feb 2025 11:18:50 -0800 Subject: [PATCH 10/13] remove file_sets --- src/igvfd/schemas/changelogs/analysis_set.md | 4 +++ src/igvfd/schemas/changelogs/auxiliary_set.md | 4 +++ src/igvfd/schemas/changelogs/curated_set.md | 4 +++ .../schemas/changelogs/measurement_set.md | 4 +++ src/igvfd/schemas/changelogs/model_set.md | 4 +++ .../schemas/changelogs/prediction_set.md | 4 +++ src/igvfd/types/file_set.py | 26 ------------------- 7 files changed, 24 insertions(+), 26 deletions(-) diff --git a/src/igvfd/schemas/changelogs/analysis_set.md b/src/igvfd/schemas/changelogs/analysis_set.md index cdb2df3c6..a7e364646 100644 --- a/src/igvfd/schemas/changelogs/analysis_set.md +++ b/src/igvfd/schemas/changelogs/analysis_set.md @@ -2,12 +2,16 @@ ### Minor changes since schema version 9 +<<<<<<< HEAD * Extend `collections` enum list to include `ACMG73`. * Extend `collections` enum list to include `Morphic`. * Extend `collections` enum list to include `StanfordFCC`. * Extend `collections` enum list to include `IGVF phase 1`. * Extend `collections` enum list to include `TOPMED Freeze 8`. * Extend `collections` enum list to include `Williams Syndrome Research`. +======= +* Add calculated property `construct_library_sets`. +>>>>>>> 8cee011f (remove file_sets) * Extend `collections` enum list to include `IGVF_catalog_beta_v0.5`. * Extend `status` enum list to include `preview`. * Rename calculated property `input_file_set_for` to `input_for`. diff --git a/src/igvfd/schemas/changelogs/auxiliary_set.md b/src/igvfd/schemas/changelogs/auxiliary_set.md index 8e8873c97..84fe75075 100644 --- a/src/igvfd/schemas/changelogs/auxiliary_set.md +++ b/src/igvfd/schemas/changelogs/auxiliary_set.md @@ -2,12 +2,16 @@ ### Minor changes since schema version 12 +<<<<<<< HEAD * Extend `collections` enum list to include `ACMG73`. * Extend `collections` enum list to include `Morphic`. * Extend `collections` enum list to include `StanfordFCC`. * Extend `collections` enum list to include `IGVF phase 1`. * Extend `collections` enum list to include `TOPMED Freeze 8`. * Extend `collections` enum list to include `Williams Syndrome Research`. +======= +* Add calculated property `construct_library_sets`. +>>>>>>> 8cee011f (remove file_sets) * Extend `collections` enum list to include `IGVF_catalog_beta_v0.5`. ### Schema version 12 diff --git a/src/igvfd/schemas/changelogs/curated_set.md b/src/igvfd/schemas/changelogs/curated_set.md index 680140dad..2bd5fa486 100644 --- a/src/igvfd/schemas/changelogs/curated_set.md +++ b/src/igvfd/schemas/changelogs/curated_set.md @@ -2,12 +2,16 @@ ### Minor changes since schema version 8 +<<<<<<< HEAD * Extend `collections` enum list to include `ACMG73`. * Extend `collections` enum list to include `Morphic`. * Extend `collections` enum list to include `StanfordFCC`. * Extend `collections` enum list to include `IGVF phase 1`. * Extend `collections` enum list to include `TOPMED Freeze 8`. * Extend `collections` enum list to include `Williams Syndrome Research`. +======= +* Add calculated property `construct_library_sets`. +>>>>>>> 8cee011f (remove file_sets) * Extend `collections` enum list to include `IGVF_catalog_beta_v0.5`. * Extend `status` enum list to include `preview`. * Rename calculated property `input_file_set_for` to `input_for`. diff --git a/src/igvfd/schemas/changelogs/measurement_set.md b/src/igvfd/schemas/changelogs/measurement_set.md index 718793683..f8c22bdf0 100644 --- a/src/igvfd/schemas/changelogs/measurement_set.md +++ b/src/igvfd/schemas/changelogs/measurement_set.md @@ -2,12 +2,16 @@ ### Minor changes since schema version 23 +<<<<<<< HEAD * Extend `collections` enum list to include `ACMG73`. * Extend `collections` enum list to include `Morphic`. * Extend `collections` enum list to include `StanfordFCC`. * Extend `collections` enum list to include `IGVF phase 1`. * Extend `collections` enum list to include `TOPMED Freeze 8`. * Extend `collections` enum list to include `Williams Syndrome Research`. +======= +* Add calculated property `construct_library_sets`. +>>>>>>> 8cee011f (remove file_sets) * Extend `preferred_assay_title` enum list to include `CRISPR MACS screen`. * Extend `preferred_assay_title` enum list to include `scMito-seq`. * Extend `preferred_assay_title` enum list to include `WGS`. diff --git a/src/igvfd/schemas/changelogs/model_set.md b/src/igvfd/schemas/changelogs/model_set.md index 822a1ef57..475319075 100644 --- a/src/igvfd/schemas/changelogs/model_set.md +++ b/src/igvfd/schemas/changelogs/model_set.md @@ -2,12 +2,16 @@ ### Minor changes since schema version 5 +<<<<<<< HEAD * Extend `collections` enum list to include `ACMG73`. * Extend `collections` enum list to include `Morphic`. * Extend `collections` enum list to include `StanfordFCC`. * Extend `collections` enum list to include `IGVF phase 1`. * Extend `collections` enum list to include `TOPMED Freeze 8`. * Extend `collections` enum list to include `Williams Syndrome Research`. +======= +* Add calculated property `construct_library_sets`. +>>>>>>> 8cee011f (remove file_sets) ### Schema version 5 diff --git a/src/igvfd/schemas/changelogs/prediction_set.md b/src/igvfd/schemas/changelogs/prediction_set.md index 5323a2625..4e5e15ba2 100644 --- a/src/igvfd/schemas/changelogs/prediction_set.md +++ b/src/igvfd/schemas/changelogs/prediction_set.md @@ -2,12 +2,16 @@ ### Minor changes since schema version 8 +<<<<<<< HEAD * Extend `collections` enum list to include `ACMG73`. * Extend `collections` enum list to include `Morphic`. * Extend `collections` enum list to include `StanfordFCC`. * Extend `collections` enum list to include `IGVF phase 1`. * Extend `collections` enum list to include `TOPMED Freeze 8`. * Extend `collections` enum list to include `Williams Syndrome Research`. +======= +* Add calculated property `construct_library_sets`. +>>>>>>> 8cee011f (remove file_sets) * Extend `collections` enum list to include `IGVF_catalog_beta_v0.5`. * Extend `status` enum list to include `preview`. * Rename calculated property `input_file_set_for` to `input_for`. diff --git a/src/igvfd/types/file_set.py b/src/igvfd/types/file_set.py index b6e4de013..ecfe99a9d 100644 --- a/src/igvfd/types/file_set.py +++ b/src/igvfd/types/file_set.py @@ -1234,32 +1234,6 @@ class ConstructLibrarySet(FileSet): def applied_to_samples(self, request, applied_to_samples): return paths_filtered_by_status(request, applied_to_samples) - @calculated_property( - condition='applied_to_samples', - schema={ - 'title': 'File Sets', - 'description': 'The file sets with samples that integrate this construct library set.', - 'type': 'array', - 'minItems': 1, - 'uniqueItems': True, - 'items': { - 'title': 'File Set', - 'type': ['string', 'object'], - 'linkTo': 'FileSet', - }, - 'notSubmittable': True - }) - def file_sets(self, request, applied_to_samples=None): - file_sets = [] - for sample in applied_to_samples: - sample_object = request.embed(sample, - '@@object_with_select_calculated_properties?' - 'field=file_sets' - ) - file_sets = file_sets + sample_object.get('file_sets', []) - if file_sets: - return file_sets - @calculated_property( schema={ 'title': 'Summary', From a4341189fc9febd93fd2872e6c482f50b40bec48 Mon Sep 17 00:00:00 2001 From: ian-whaling Date: Tue, 18 Feb 2025 13:25:36 -0800 Subject: [PATCH 11/13] changelog --- src/igvfd/schemas/changelogs/analysis_set.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/igvfd/schemas/changelogs/analysis_set.md b/src/igvfd/schemas/changelogs/analysis_set.md index a7e364646..24f8e13f1 100644 --- a/src/igvfd/schemas/changelogs/analysis_set.md +++ b/src/igvfd/schemas/changelogs/analysis_set.md @@ -2,16 +2,15 @@ ### Minor changes since schema version 9 -<<<<<<< HEAD +* Update calculation of `summary`. +* Update calculation of `assay_titles`. +* Add calculated property `construct_library_sets`. * Extend `collections` enum list to include `ACMG73`. * Extend `collections` enum list to include `Morphic`. * Extend `collections` enum list to include `StanfordFCC`. * Extend `collections` enum list to include `IGVF phase 1`. * Extend `collections` enum list to include `TOPMED Freeze 8`. * Extend `collections` enum list to include `Williams Syndrome Research`. -======= -* Add calculated property `construct_library_sets`. ->>>>>>> 8cee011f (remove file_sets) * Extend `collections` enum list to include `IGVF_catalog_beta_v0.5`. * Extend `status` enum list to include `preview`. * Rename calculated property `input_file_set_for` to `input_for`. From 0caad440bcc05a13b01476a77a100b8eb7c583df Mon Sep 17 00:00:00 2001 From: ian-whaling Date: Tue, 18 Feb 2025 14:45:50 -0800 Subject: [PATCH 12/13] mappings --- src/igvfd/mappings/alignment_file.json | 4 +- src/igvfd/mappings/configuration_file.json | 4 +- src/igvfd/mappings/construct_library_set.json | 4 +- .../genome_browser_annotation_file.json | 4 +- src/igvfd/mappings/image_file.json | 4 +- src/igvfd/mappings/index_file.json | 4 +- src/igvfd/mappings/matrix_file.json | 4 +- src/igvfd/mappings/measurement_set.json | 470 +----------------- src/igvfd/mappings/model_file.json | 4 +- src/igvfd/mappings/model_set.json | 4 +- src/igvfd/mappings/prediction_set.json | 4 +- src/igvfd/mappings/reference_file.json | 4 +- src/igvfd/mappings/sequence_file.json | 4 +- src/igvfd/mappings/signal_file.json | 4 +- src/igvfd/mappings/tabular_file.json | 4 +- 15 files changed, 37 insertions(+), 489 deletions(-) diff --git a/src/igvfd/mappings/alignment_file.json b/src/igvfd/mappings/alignment_file.json index 196971fa3..d818a50bb 100644 --- a/src/igvfd/mappings/alignment_file.json +++ b/src/igvfd/mappings/alignment_file.json @@ -1,6 +1,6 @@ { - "hash": "7f221dd2ce0c8f90adfd95ba7b025cab", - "index_name": "alignment_file_7f221dd2", + "hash": "d784165b95ad0795451e7e1a79b87936", + "index_name": "alignment_file_d784165b", "item_type": "alignment_file", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/configuration_file.json b/src/igvfd/mappings/configuration_file.json index c4b95ef74..ddb25cf38 100644 --- a/src/igvfd/mappings/configuration_file.json +++ b/src/igvfd/mappings/configuration_file.json @@ -1,6 +1,6 @@ { - "hash": "e775f0a39a668474b289dea153cbc696", - "index_name": "configuration_file_e775f0a3", + "hash": "447e775054e9a4836cb65a480a38faff", + "index_name": "configuration_file_447e7750", "item_type": "configuration_file", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/construct_library_set.json b/src/igvfd/mappings/construct_library_set.json index dd646eed5..da34bd1f6 100644 --- a/src/igvfd/mappings/construct_library_set.json +++ b/src/igvfd/mappings/construct_library_set.json @@ -1,6 +1,6 @@ { - "hash": "0d63cb7fe2f3b9b9fa42e83cded17bf3", - "index_name": "construct_library_set_0d63cb7f", + "hash": "7ea29280f399421a03d3a697a2b5365c", + "index_name": "construct_library_set_7ea29280", "item_type": "construct_library_set", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/genome_browser_annotation_file.json b/src/igvfd/mappings/genome_browser_annotation_file.json index 911788c6e..0c7070484 100644 --- a/src/igvfd/mappings/genome_browser_annotation_file.json +++ b/src/igvfd/mappings/genome_browser_annotation_file.json @@ -1,6 +1,6 @@ { - "hash": "e1e9c75f86974ee26d25c4e1f2ca89b3", - "index_name": "genome_browser_annotation_file_e1e9c75f", + "hash": "cec0bd8c3eb8479c820a3403ae775be6", + "index_name": "genome_browser_annotation_file_cec0bd8c", "item_type": "genome_browser_annotation_file", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/image_file.json b/src/igvfd/mappings/image_file.json index 90b85d4ea..e401dca8b 100644 --- a/src/igvfd/mappings/image_file.json +++ b/src/igvfd/mappings/image_file.json @@ -1,6 +1,6 @@ { - "hash": "454fc29f895f6bc3a44697623523ab66", - "index_name": "image_file_454fc29f", + "hash": "9d1370578fffd6d46ed2a425a3c2a68c", + "index_name": "image_file_9d137057", "item_type": "image_file", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/index_file.json b/src/igvfd/mappings/index_file.json index e0591c0f6..5835afc6e 100644 --- a/src/igvfd/mappings/index_file.json +++ b/src/igvfd/mappings/index_file.json @@ -1,6 +1,6 @@ { - "hash": "a147612e9013f900a3c1ac70cddd841e", - "index_name": "index_file_a147612e", + "hash": "be39bd35a8f339ff91c2abcb2408d874", + "index_name": "index_file_be39bd35", "item_type": "index_file", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/matrix_file.json b/src/igvfd/mappings/matrix_file.json index 02de980e0..7b165582b 100644 --- a/src/igvfd/mappings/matrix_file.json +++ b/src/igvfd/mappings/matrix_file.json @@ -1,6 +1,6 @@ { - "hash": "648d2fcde23db421f14ecbba94fe7153", - "index_name": "matrix_file_648d2fcd", + "hash": "8bfe66504f1c9d6cae853c37f5d7025a", + "index_name": "matrix_file_8bfe6650", "item_type": "matrix_file", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/measurement_set.json b/src/igvfd/mappings/measurement_set.json index a69bab401..ee8a75e34 100644 --- a/src/igvfd/mappings/measurement_set.json +++ b/src/igvfd/mappings/measurement_set.json @@ -1,6 +1,6 @@ { - "hash": "558f566d153d4d2e10fa9f67b0a335ad", - "index_name": "measurement_set_558f566d", + "hash": "fa707dbbe1e54b85c215b8b1f8f0097d", + "index_name": "measurement_set_fa707dbb", "item_type": "measurement_set", "mapping": { "dynamic_templates": [ @@ -886,6 +886,9 @@ "aliases": { "type": "keyword" }, + "collections": { + "type": "keyword" + }, "creation_timestamp": { "type": "date" }, @@ -935,6 +938,9 @@ "status": { "type": "keyword" }, + "study_sets": { + "type": "keyword" + }, "submitted_by": { "type": "keyword" }, @@ -2774,465 +2780,7 @@ "type": "keyword" }, "construct_library_sets": { - "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "accession": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "alternate_accessions": { - "type": "keyword" - }, - "applied_to_samples": { - "type": "keyword" - }, - "associated_phenotypes": { - "type": "keyword" - }, - "average_guide_coverage": { - "store": true, - "type": "float" - }, - "average_insert_size": { - "store": true, - "type": "float" - }, - "award": { - "type": "keyword" - }, - "collections": { - "type": "keyword" - }, - "control_file_sets": { - "type": "keyword" - }, - "control_for": { - "type": "keyword" - }, - "control_type": { - "type": "keyword" - }, - "creation_timestamp": { - "type": "date" - }, - "description": { - "type": "text" - }, - "documents": { - "type": "keyword" - }, - "exon": { - "type": "keyword" - }, - "file_set_type": { - "type": "keyword" - }, - "files": { - "type": "keyword" - }, - "guide_type": { - "type": "keyword" - }, - "input_for": { - "type": "keyword" - }, - "integrated_content_files": { - "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "accession": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "alternate_accessions": { - "type": "keyword" - }, - "analysis_step_version": { - "type": "keyword" - }, - "anvil_url": { - "type": "keyword" - }, - "assay_titles": { - "type": "keyword" - }, - "assembly": { - "type": "keyword" - }, - "award": { - "type": "keyword" - }, - "barcode_map_for": { - "type": "keyword" - }, - "cell_type_annotation": { - "type": "keyword" - }, - "checkfiles_version": { - "type": "keyword" - }, - "collections": { - "type": "keyword" - }, - "content_md5sum": { - "type": "keyword" - }, - "content_type": { - "type": "keyword" - }, - "controlled_access": { - "store": true, - "type": "boolean" - }, - "creation_timestamp": { - "type": "date" - }, - "dbxrefs": { - "type": "keyword" - }, - "derived_from": { - "type": "keyword" - }, - "derived_manually": { - "store": true, - "type": "boolean" - }, - "description": { - "type": "text" - }, - "documents": { - "type": "keyword" - }, - "external": { - "store": true, - "type": "boolean" - }, - "file_format": { - "type": "keyword" - }, - "file_format_specifications": { - "type": "keyword" - }, - "file_format_type": { - "type": "keyword" - }, - "file_set": { - "type": "keyword" - }, - "file_size": { - "store": true, - "type": "long" - }, - "gene_list_for": { - "type": "keyword" - }, - "href": { - "type": "keyword" - }, - "input_file_for": { - "type": "keyword" - }, - "integrated_in": { - "type": "keyword" - }, - "lab": { - "type": "keyword" - }, - "loci_list_for": { - "type": "keyword" - }, - "md5sum": { - "type": "keyword" - }, - "notes": { - "type": "text" - }, - "release_timestamp": { - "type": "date" - }, - "revoke_detail": { - "type": "keyword" - }, - "s3_uri": { - "type": "keyword" - }, - "schema_version": { - "type": "keyword" - }, - "source_url": { - "type": "keyword" - }, - "sources": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" - }, - "submitted_file_name": { - "type": "keyword" - }, - "submitter_comment": { - "type": "keyword" - }, - "summary": { - "type": "keyword" - }, - "transcriptome_annotation": { - "type": "keyword" - }, - "upload_credentials": { - "properties": {}, - "type": "object" - }, - "upload_status": { - "type": "keyword" - }, - "uuid": { - "type": "keyword" - }, - "validation_error_detail": { - "type": "keyword" - }, - "workflow": { - "type": "keyword" - } - }, - "type": "object" - }, - "lab": { - "type": "keyword" - }, - "large_scale_gene_list": { - "type": "keyword" - }, - "large_scale_loci_list": { - "type": "keyword" - }, - "lot_id": { - "type": "keyword" - }, - "lower_bound_guide_coverage": { - "store": true, - "type": "long" - }, - "lower_bound_insert_size": { - "store": true, - "type": "long" - }, - "notes": { - "type": "text" - }, - "orf_list": { - "type": "keyword" - }, - "product_id": { - "type": "keyword" - }, - "publications": { - "type": "keyword" - }, - "release_timestamp": { - "type": "date" - }, - "revoke_detail": { - "type": "keyword" - }, - "schema_version": { - "type": "keyword" - }, - "scope": { - "type": "keyword" - }, - "selection_criteria": { - "type": "keyword" - }, - "small_scale_gene_list": { - "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "collections": { - "type": "keyword" - }, - "creation_timestamp": { - "type": "date" - }, - "dbxrefs": { - "type": "keyword" - }, - "description": { - "type": "text" - }, - "geneid": { - "type": "keyword" - }, - "geneid_with_version": { - "type": "keyword" - }, - "locations": { - "properties": { - "assembly": { - "type": "keyword" - }, - "chromosome": { - "type": "keyword" - }, - "end": { - "store": true, - "type": "long" - }, - "start": { - "store": true, - "type": "long" - } - }, - "type": "object" - }, - "name": { - "type": "keyword" - }, - "notes": { - "type": "text" - }, - "release_timestamp": { - "type": "date" - }, - "schema_version": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "study_sets": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" - }, - "submitter_comment": { - "type": "keyword" - }, - "summary": { - "type": "keyword" - }, - "symbol": { - "type": "keyword" - }, - "synonyms": { - "type": "keyword" - }, - "taxa": { - "type": "keyword" - }, - "title": { - "type": "keyword" - }, - "transcriptome_annotation": { - "type": "keyword" - }, - "uuid": { - "type": "keyword" - }, - "version_number": { - "type": "keyword" - } - }, - "type": "object" - }, - "small_scale_loci_list": { - "properties": { - "assembly": { - "type": "keyword" - }, - "chromosome": { - "type": "keyword" - }, - "end": { - "store": true, - "type": "long" - }, - "start": { - "store": true, - "type": "long" - } - }, - "type": "object" - }, - "sources": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" - }, - "submitted_files_timestamp": { - "type": "date" - }, - "submitter_comment": { - "type": "keyword" - }, - "summary": { - "type": "keyword" - }, - "targeton": { - "type": "keyword" - }, - "tile": { - "properties": { - "tile_end": { - "store": true, - "type": "long" - }, - "tile_id": { - "type": "keyword" - }, - "tile_start": { - "store": true, - "type": "long" - } - }, - "type": "object" - }, - "tiling_modality": { - "type": "keyword" - }, - "upper_bound_guide_coverage": { - "store": true, - "type": "long" - }, - "upper_bound_insert_size": { - "store": true, - "type": "long" - }, - "uuid": { - "type": "keyword" - } - }, - "type": "object" + "type": "keyword" }, "creation_timestamp": { "type": "date" diff --git a/src/igvfd/mappings/model_file.json b/src/igvfd/mappings/model_file.json index daf744813..67b0064af 100644 --- a/src/igvfd/mappings/model_file.json +++ b/src/igvfd/mappings/model_file.json @@ -1,6 +1,6 @@ { - "hash": "bd275db53554d41c2fbe86b6f41d79ed", - "index_name": "model_file_bd275db5", + "hash": "08f42f395093e6bc091292bcdb90d6b4", + "index_name": "model_file_08f42f39", "item_type": "model_file", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/model_set.json b/src/igvfd/mappings/model_set.json index b98bec297..adba2f987 100644 --- a/src/igvfd/mappings/model_set.json +++ b/src/igvfd/mappings/model_set.json @@ -1,6 +1,6 @@ { - "hash": "21263baed14c4358d833513a91cd6973", - "index_name": "model_set_21263bae", + "hash": "9a92d8cddad37092d6e50a912a17db19", + "index_name": "model_set_9a92d8cd", "item_type": "model_set", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/prediction_set.json b/src/igvfd/mappings/prediction_set.json index fc61afd6d..94f3e3341 100644 --- a/src/igvfd/mappings/prediction_set.json +++ b/src/igvfd/mappings/prediction_set.json @@ -1,6 +1,6 @@ { - "hash": "b2fbca9c0ef0c7ecec59276b9b615655", - "index_name": "prediction_set_b2fbca9c", + "hash": "250c4be07b883a0101bfb246c22e8a7b", + "index_name": "prediction_set_250c4be0", "item_type": "prediction_set", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/reference_file.json b/src/igvfd/mappings/reference_file.json index fd21ae96d..af282d70c 100644 --- a/src/igvfd/mappings/reference_file.json +++ b/src/igvfd/mappings/reference_file.json @@ -1,6 +1,6 @@ { - "hash": "025fe7d97455288b51806d3ceb26049a", - "index_name": "reference_file_025fe7d9", + "hash": "ab4b8a53d9ea8b0fc335295c8544ee0d", + "index_name": "reference_file_ab4b8a53", "item_type": "reference_file", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/sequence_file.json b/src/igvfd/mappings/sequence_file.json index b9fa4222a..7e720ed0f 100644 --- a/src/igvfd/mappings/sequence_file.json +++ b/src/igvfd/mappings/sequence_file.json @@ -1,6 +1,6 @@ { - "hash": "eaa9f509cea03432d377ff7abefaef8b", - "index_name": "sequence_file_eaa9f509", + "hash": "a48edad850025cae67120cd5c5c1cc08", + "index_name": "sequence_file_a48edad8", "item_type": "sequence_file", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/signal_file.json b/src/igvfd/mappings/signal_file.json index 5ab30a7d6..d72db1679 100644 --- a/src/igvfd/mappings/signal_file.json +++ b/src/igvfd/mappings/signal_file.json @@ -1,6 +1,6 @@ { - "hash": "a0f988658275faf2705043bc171cf4bb", - "index_name": "signal_file_a0f98865", + "hash": "a7165aae756bdf0e05158d053005ae27", + "index_name": "signal_file_a7165aae", "item_type": "signal_file", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/tabular_file.json b/src/igvfd/mappings/tabular_file.json index 04760c9ab..862a144eb 100644 --- a/src/igvfd/mappings/tabular_file.json +++ b/src/igvfd/mappings/tabular_file.json @@ -1,6 +1,6 @@ { - "hash": "764a0fee11f02a6a14b56c9ad3c418a8", - "index_name": "tabular_file_764a0fee", + "hash": "cb0435e3e47c1fccaf0fa6260378439f", + "index_name": "tabular_file_cb0435e3", "item_type": "tabular_file", "mapping": { "dynamic_templates": [ From b1a98e8136347808d3590b6d4623a9ba5d99d779 Mon Sep 17 00:00:00 2001 From: ian-whaling Date: Tue, 18 Feb 2025 15:38:47 -0800 Subject: [PATCH 13/13] mappings --- src/igvfd/mappings/in_vitro_system.json | 4 ++-- src/igvfd/mappings/multiplexed_sample.json | 4 ++-- src/igvfd/mappings/primary_cell.json | 4 ++-- src/igvfd/mappings/technical_sample.json | 4 ++-- src/igvfd/mappings/tissue.json | 4 ++-- src/igvfd/mappings/whole_organism.json | 4 ++-- 6 files changed, 12 insertions(+), 12 deletions(-) diff --git a/src/igvfd/mappings/in_vitro_system.json b/src/igvfd/mappings/in_vitro_system.json index 1ec943993..72d55f1e3 100644 --- a/src/igvfd/mappings/in_vitro_system.json +++ b/src/igvfd/mappings/in_vitro_system.json @@ -1,6 +1,6 @@ { - "hash": "71c95c3b9a0f677e96aac42447e6309b", - "index_name": "in_vitro_system_71c95c3b", + "hash": "fa1e8769dddf9d6b871ba3551ef1acea", + "index_name": "in_vitro_system_fa1e8769", "item_type": "in_vitro_system", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/multiplexed_sample.json b/src/igvfd/mappings/multiplexed_sample.json index b1b3312b3..114acc807 100644 --- a/src/igvfd/mappings/multiplexed_sample.json +++ b/src/igvfd/mappings/multiplexed_sample.json @@ -1,6 +1,6 @@ { - "hash": "9a39ffe650996dd4828d918c9332f1d0", - "index_name": "multiplexed_sample_9a39ffe6", + "hash": "5182a7959c84e45854a0cb1f86c40480", + "index_name": "multiplexed_sample_5182a795", "item_type": "multiplexed_sample", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/primary_cell.json b/src/igvfd/mappings/primary_cell.json index 00ea930fd..ff6c547aa 100644 --- a/src/igvfd/mappings/primary_cell.json +++ b/src/igvfd/mappings/primary_cell.json @@ -1,6 +1,6 @@ { - "hash": "5695da5557a9fd66eb239d73ddbc07b3", - "index_name": "primary_cell_5695da55", + "hash": "51b272f869f13d46ffdef5d2abb4b841", + "index_name": "primary_cell_51b272f8", "item_type": "primary_cell", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/technical_sample.json b/src/igvfd/mappings/technical_sample.json index 7ebd88de7..eabe2ad49 100644 --- a/src/igvfd/mappings/technical_sample.json +++ b/src/igvfd/mappings/technical_sample.json @@ -1,6 +1,6 @@ { - "hash": "8838c29f2bbdda2bdf4ff0be8088d3d7", - "index_name": "technical_sample_8838c29f", + "hash": "745f109b9b3ba23e187d2e8502d86185", + "index_name": "technical_sample_745f109b", "item_type": "technical_sample", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/tissue.json b/src/igvfd/mappings/tissue.json index cb347f19d..729f7c53f 100644 --- a/src/igvfd/mappings/tissue.json +++ b/src/igvfd/mappings/tissue.json @@ -1,6 +1,6 @@ { - "hash": "f23841d1c69a561ac73c35927eb1195f", - "index_name": "tissue_f23841d1", + "hash": "95349f2c038569fc3d61345cf730b5b5", + "index_name": "tissue_95349f2c", "item_type": "tissue", "mapping": { "dynamic_templates": [ diff --git a/src/igvfd/mappings/whole_organism.json b/src/igvfd/mappings/whole_organism.json index 3cbe6e618..1b9c5e2e7 100644 --- a/src/igvfd/mappings/whole_organism.json +++ b/src/igvfd/mappings/whole_organism.json @@ -1,6 +1,6 @@ { - "hash": "635adf892bb32062a0d72038967d024b", - "index_name": "whole_organism_635adf89", + "hash": "77492da46f48723e6e08145731442254", + "index_name": "whole_organism_77492da4", "item_type": "whole_organism", "mapping": { "dynamic_templates": [