diff --git a/src/igvfd/mappings/alignment_file.json b/src/igvfd/mappings/alignment_file.json index c8c9b6053..53d074b33 100644 --- a/src/igvfd/mappings/alignment_file.json +++ b/src/igvfd/mappings/alignment_file.json @@ -1,6 +1,6 @@ { - "hash": "9a1f386a76d5f1df4f25e6da6d327295", - "index_name": "alignment_file_9a1f386a", + "hash": "f617309b794f2577e13c373373ba56f2", + "index_name": "alignment_file_f617309b", "item_type": "alignment_file", "mapping": { "dynamic_templates": [ @@ -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 5e1f7c2d7..856f9bdf7 100644 --- a/src/igvfd/mappings/analysis_set.json +++ b/src/igvfd/mappings/analysis_set.json @@ -1,6 +1,6 @@ { - "hash": "5bec85936f441634f48a3ac1f62dc5b9", - "index_name": "analysis_set_5bec8593", + "hash": "c7c00d1ca0390089c8d663b91db08ff3", + "index_name": "analysis_set_c7c00d1c", "item_type": "analysis_set", "mapping": { "dynamic_templates": [ @@ -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" }, @@ -1153,6 +1631,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1670,369 +2151,7 @@ "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 62711ee52..142ab9ada 100644 --- a/src/igvfd/mappings/auxiliary_set.json +++ b/src/igvfd/mappings/auxiliary_set.json @@ -1,6 +1,6 @@ { - "hash": "ebd9e961fa41a054837b0897b93c4344", - "index_name": "auxiliary_set_ebd9e961", + "hash": "97c731a802a9e7f2ce4dde7bac6293b8", + "index_name": "auxiliary_set_97c731a8", "item_type": "auxiliary_set", "mapping": { "dynamic_templates": [ @@ -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" }, @@ -1115,6 +1593,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1425,369 +1906,7 @@ "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 2dafe26a6..21c9ff501 100644 --- a/src/igvfd/mappings/configuration_file.json +++ b/src/igvfd/mappings/configuration_file.json @@ -1,6 +1,6 @@ { - "hash": "3f6c1b5a3eed8442ca0e105c6f510810", - "index_name": "configuration_file_3f6c1b5a", + "hash": "6fe084aa86305a9053c3520a56da40e6", + "index_name": "configuration_file_6fe084aa", "item_type": "configuration_file", "mapping": { "dynamic_templates": [ @@ -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 90fb514ba..1cc89a404 100644 --- a/src/igvfd/mappings/construct_library_set.json +++ b/src/igvfd/mappings/construct_library_set.json @@ -1,6 +1,6 @@ { - "hash": "f06cd62c6ae0639df3864f58971ffe66", - "index_name": "construct_library_set_f06cd62c", + "hash": "349b5bda5fdf54d38edfb9fbed1a105a", + "index_name": "construct_library_set_349b5bda", "item_type": "construct_library_set", "mapping": { "dynamic_templates": [ @@ -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 23e885b72..453d8f20f 100644 --- a/src/igvfd/mappings/curated_set.json +++ b/src/igvfd/mappings/curated_set.json @@ -1,6 +1,6 @@ { - "hash": "4e345953c3a89476cb0343e16e17fef9", - "index_name": "curated_set_4e345953", + "hash": "41cb20cf5958b19c7a691c881f26a6eb", + "index_name": "curated_set_41cb20cf", "item_type": "curated_set", "mapping": { "dynamic_templates": [ @@ -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" }, @@ -1285,369 +1763,7 @@ "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 e887b10c8..a2e20cb74 100644 --- a/src/igvfd/mappings/genome_browser_annotation_file.json +++ b/src/igvfd/mappings/genome_browser_annotation_file.json @@ -1,6 +1,6 @@ { - "hash": "1b877d9bbe2a5992f13d1593cef9518f", - "index_name": "genome_browser_annotation_file_1b877d9b", + "hash": "208c82a6b25262ab94fdcbe7f04ff0dc", + "index_name": "genome_browser_annotation_file_208c82a6", "item_type": "genome_browser_annotation_file", "mapping": { "dynamic_templates": [ @@ -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 204d3647b..d2682684b 100644 --- a/src/igvfd/mappings/image_file.json +++ b/src/igvfd/mappings/image_file.json @@ -1,6 +1,6 @@ { - "hash": "ff56c17904244518c7b5942eb2929550", - "index_name": "image_file_ff56c179", + "hash": "2a6e909e52297cba26415e8b69cdaaa0", + "index_name": "image_file_2a6e909e", "item_type": "image_file", "mapping": { "dynamic_templates": [ @@ -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 b0bede46c..e2a52e6ba 100644 --- a/src/igvfd/mappings/in_vitro_system.json +++ b/src/igvfd/mappings/in_vitro_system.json @@ -1,6 +1,6 @@ { - "hash": "12c8c8825d0899f88dc41f5f5517629c", - "index_name": "in_vitro_system_12c8c882", + "hash": "d94ec58ad262012efda25eb65f00c4ee", + "index_name": "in_vitro_system_d94ec58a", "item_type": "in_vitro_system", "mapping": { "dynamic_templates": [ @@ -626,6 +626,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1066,6 +1069,9 @@ "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 fedd0ba60..3a393152a 100644 --- a/src/igvfd/mappings/index_file.json +++ b/src/igvfd/mappings/index_file.json @@ -1,6 +1,6 @@ { - "hash": "3eab73137b1ae54747b432690ac4ea0e", - "index_name": "index_file_3eab7313", + "hash": "630e78c636a2ac45b68452b41aace43a", + "index_name": "index_file_630e78c6", "item_type": "index_file", "mapping": { "dynamic_templates": [ @@ -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 4312b53f6..d4051a32d 100644 --- a/src/igvfd/mappings/matrix_file.json +++ b/src/igvfd/mappings/matrix_file.json @@ -1,6 +1,6 @@ { - "hash": "56da2981f8ef77797ef7b1f3a12c7656", - "index_name": "matrix_file_56da2981", + "hash": "9419036be2c861c1d45e08ab1bc84204", + "index_name": "matrix_file_9419036b", "item_type": "matrix_file", "mapping": { "dynamic_templates": [ @@ -335,6 +335,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1388,6 +1391,9 @@ "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 08be404cd..fa0c9c395 100644 --- a/src/igvfd/mappings/measurement_set.json +++ b/src/igvfd/mappings/measurement_set.json @@ -1,6 +1,6 @@ { - "hash": "871f76f6359d225cab05a4fdcf185858", - "index_name": "measurement_set_871f76f6", + "hash": "41df9084b1355bebe4c7922d3895588b", + "index_name": "measurement_set_41df9084", "item_type": "measurement_set", "mapping": { "dynamic_templates": [ @@ -266,6 +266,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_for": { "type": "keyword" }, @@ -484,7 +487,7 @@ "copy_to": "_fuzzy", "type": "keyword" }, - "control_file_sets": { + "construct_library_sets": { "properties": { "@id": { "type": "keyword" @@ -493,11 +496,9 @@ "type": "keyword" }, "accession": { - "copy_to": "_exact", "type": "keyword" }, "aliases": { - "copy_to": "_exact", "type": "keyword" }, "alternate_accessions": { @@ -541,6 +542,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -603,7 +607,176 @@ "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" @@ -696,7 +869,97 @@ "type": "keyword" }, "small_scale_gene_list": { - "type": "keyword" + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "aliases": { + "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" + }, + "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": { @@ -789,7 +1052,7 @@ }, "type": "object" }, - "control_for": { + "control_file_sets": { "properties": { "@id": { "type": "keyword" @@ -846,6 +1109,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1094,24 +1360,7 @@ }, "type": "object" }, - "control_type": { - "type": "keyword" - }, - "creation_timestamp": { - "type": "date" - }, - "dbxrefs": { - "copy_to": "_exact", - "type": "keyword" - }, - "description": { - "copy_to": "_fuzzy", - "type": "text" - }, - "documents": { - "type": "keyword" - }, - "donors": { + "control_for": { "properties": { "@id": { "type": "keyword" @@ -1130,433 +1379,419 @@ "alternate_accessions": { "type": "keyword" }, - "award": { + "applied_to_samples": { "type": "keyword" }, - "collections": { + "assay_term": { "type": "keyword" }, - "creation_timestamp": { - "type": "date" - }, - "dbxrefs": { + "assay_titles": { "type": "keyword" }, - "description": { - "type": "text" - }, - "documents": { + "assemblies": { "type": "keyword" }, - "ethnicities": { + "assessed_genes": { "type": "keyword" }, - "genotype": { + "associated_phenotypes": { "type": "keyword" }, - "human_donor_identifiers": { + "auxiliary_sets": { "type": "keyword" }, - "individual_rodent": { + "average_guide_coverage": { "store": true, - "type": "boolean" + "type": "float" }, - "lab": { + "average_insert_size": { + "store": true, + "type": "float" + }, + "award": { "type": "keyword" }, - "lot_id": { + "barcode_map": { "type": "keyword" }, - "notes": { - "type": "text" + "collections": { + "type": "keyword" }, - "phenotypic_features": { + "construct_library_sets": { "type": "keyword" }, - "product_id": { + "control_file_sets": { "type": "keyword" }, - "publications": { + "control_for": { "type": "keyword" }, - "related_donors": { - "properties": { - "donor": { - "type": "keyword" - }, - "relationship_type": { - "type": "keyword" - } - }, - "type": "object" + "control_type": { + "type": "keyword" }, - "release_timestamp": { + "creation_timestamp": { "type": "date" }, - "revoke_detail": { + "dbxrefs": { "type": "keyword" }, - "rodent_identifier": { + "demultiplexed_sample": { "type": "keyword" }, - "schema_version": { - "type": "keyword" + "description": { + "type": "text" }, - "sex": { + "documents": { "type": "keyword" }, - "sources": { + "donors": { "type": "keyword" }, - "status": { + "exon": { "type": "keyword" }, - "strain": { + "external_image_data_url": { "type": "keyword" }, - "strain_background": { + "external_image_url": { "type": "keyword" }, - "submitted_by": { + "external_input_data": { "type": "keyword" }, - "submitter_comment": { + "externally_hosted": { + "store": true, + "type": "boolean" + }, + "file_set_type": { "type": "keyword" }, - "summary": { + "files": { "type": "keyword" }, - "taxa": { + "functional_assay_mechanisms": { "type": "keyword" }, - "url": { + "guide_type": { "type": "keyword" }, - "uuid": { + "input_file_sets": { "type": "keyword" }, - "virtual": { - "store": true, - "type": "boolean" - } - }, - "type": "object" - }, - "external_image_url": { - "type": "keyword" - }, - "externally_hosted": { - "store": true, - "type": "boolean" - }, - "file_set_type": { - "type": "keyword" - }, - "files": { - "properties": { - "@id": { + "input_for": { "type": "keyword" }, - "@type": { + "integrated_content_files": { "type": "keyword" }, - "accession": { - "copy_to": "_exact", + "lab": { "type": "keyword" }, - "aliases": { - "copy_to": "_exact", + "large_scale_gene_list": { "type": "keyword" }, - "alternate_accessions": { + "large_scale_loci_list": { "type": "keyword" }, - "analysis_step_version": { + "lot_id": { "type": "keyword" }, - "anvil_url": { + "lower_bound_guide_coverage": { + "store": true, + "type": "long" + }, + "lower_bound_insert_size": { + "store": true, + "type": "long" + }, + "measurement_sets": { "type": "keyword" }, - "assay_titles": { + "model_name": { "type": "keyword" }, - "assembly": { + "model_version": { "type": "keyword" }, - "award": { + "model_zoo_location": { "type": "keyword" }, - "barcode_map_for": { + "multiome_size": { + "store": true, + "type": "long" + }, + "notes": { + "type": "text" + }, + "onlist_files": { "type": "keyword" }, - "base_modifications": { + "onlist_method": { "type": "keyword" }, - "cell_type_annotation": { + "orf_list": { "type": "keyword" }, - "checkfiles_version": { + "prediction_objects": { "type": "keyword" }, - "collections": { + "preferred_assay_title": { "type": "keyword" }, - "content_md5sum": { + "product_id": { "type": "keyword" }, - "content_summary": { + "protocols": { "type": "keyword" }, - "content_type": { - "copy_to": "_fuzzy", + "publications": { "type": "keyword" }, - "controlled_access": { - "store": true, - "type": "boolean" + "related_multiome_datasets": { + "type": "keyword" }, - "creation_timestamp": { + "release_timestamp": { "type": "date" }, - "dbxrefs": { + "revoke_detail": { "type": "keyword" }, - "derived_from": { + "sample_summary": { "type": "keyword" }, - "derived_manually": { - "store": true, - "type": "boolean" - }, - "description": { - "type": "text" - }, - "documents": { + "samples": { "type": "keyword" }, - "external": { - "store": true, - "type": "boolean" - }, - "external_host_url": { + "schema_version": { "type": "keyword" }, - "externally_hosted": { - "store": true, - "type": "boolean" - }, - "file_format": { + "scope": { "type": "keyword" }, - "file_format_specifications": { + "selection_criteria": { "type": "keyword" }, - "file_format_type": { + "sequencing_library_types": { "type": "keyword" }, - "file_set": { + "small_scale_gene_list": { "type": "keyword" }, - "file_size": { - "store": true, - "type": "long" - }, - "filtered": { - "store": true, - "type": "boolean" + "small_scale_loci_list": { + "properties": { + "assembly": { + "type": "keyword" + }, + "chromosome": { + "type": "keyword" + }, + "end": { + "store": true, + "type": "long" + }, + "start": { + "store": true, + "type": "long" + } + }, + "type": "object" }, - "flowcell_id": { + "software_version": { "type": "keyword" }, - "gene_list_for": { + "sources": { "type": "keyword" }, - "href": { + "status": { "type": "keyword" }, - "illumina_read_type": { + "submitted_by": { "type": "keyword" }, - "index": { - "type": "keyword" + "submitted_files_timestamp": { + "type": "date" }, - "input_file_for": { + "submitter_comment": { "type": "keyword" }, - "integrated_in": { + "summary": { "type": "keyword" }, - "lab": { + "targeted_genes": { "type": "keyword" }, - "lane": { - "store": true, - "type": "long" + "targeton": { + "type": "keyword" }, - "loci_list_for": { + "taxa": { "type": "keyword" }, - "maximum_read_length": { - "store": true, - "type": "long" + "tile": { + "properties": { + "tile_end": { + "store": true, + "type": "long" + }, + "tile_id": { + "type": "keyword" + }, + "tile_start": { + "store": true, + "type": "long" + } + }, + "type": "object" }, - "md5sum": { + "tiling_modality": { "type": "keyword" }, - "mean_read_length": { - "store": true, - "type": "float" + "transcriptome_annotations": { + "type": "keyword" }, - "minimum_read_length": { + "upper_bound_guide_coverage": { "store": true, "type": "long" }, - "normalized": { + "upper_bound_insert_size": { "store": true, - "type": "boolean" + "type": "long" }, - "notes": { - "type": "text" + "url": { + "type": "keyword" }, - "principal_dimension": { + "uuid": { "type": "keyword" }, - "read_count": { - "store": true, - "type": "long" + "workflows": { + "type": "keyword" + } + }, + "type": "object" + }, + "control_type": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "dbxrefs": { + "copy_to": "_exact", + "type": "keyword" + }, + "description": { + "copy_to": "_fuzzy", + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "donors": { + "properties": { + "@id": { + "type": "keyword" }, - "read_names": { + "@type": { "type": "keyword" }, - "redacted": { - "store": true, - "type": "boolean" + "accession": { + "copy_to": "_exact", + "type": "keyword" }, - "reference_files": { + "aliases": { + "copy_to": "_exact", "type": "keyword" }, - "release_timestamp": { + "alternate_accessions": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "creation_timestamp": { "type": "date" }, - "revoke_detail": { + "dbxrefs": { "type": "keyword" }, - "s3_uri": { + "description": { + "type": "text" + }, + "documents": { "type": "keyword" }, - "schema_version": { + "ethnicities": { "type": "keyword" }, - "secondary_dimensions": { + "genotype": { "type": "keyword" }, - "seqspec_of": { + "human_donor_identifiers": { "type": "keyword" }, - "seqspecs": { + "individual_rodent": { + "store": true, + "type": "boolean" + }, + "lab": { "type": "keyword" }, - "sequencing_kit": { + "lot_id": { "type": "keyword" }, - "sequencing_platform": { + "notes": { + "type": "text" + }, + "phenotypic_features": { + "type": "keyword" + }, + "product_id": { + "type": "keyword" + }, + "publications": { + "type": "keyword" + }, + "related_donors": { "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "ancestors": { - "type": "keyword" - }, - "company": { - "type": "keyword" - }, - "creation_timestamp": { - "type": "date" - }, - "deprecated_ntr_terms": { - "type": "keyword" - }, - "description": { - "type": "text" - }, - "is_a": { - "type": "keyword" - }, - "name": { - "type": "keyword" - }, - "notes": { - "type": "text" - }, - "ontology": { - "type": "keyword" - }, - "release_timestamp": { - "type": "date" - }, - "schema_version": { - "type": "keyword" - }, - "sequencing_kits": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" - }, - "submitter_comment": { - "type": "keyword" - }, - "summary": { - "type": "keyword" - }, - "synonyms": { - "type": "keyword" - }, - "term_id": { - "type": "keyword" - }, - "term_name": { + "donor": { "type": "keyword" }, - "uuid": { + "relationship_type": { "type": "keyword" } }, "type": "object" }, - "sequencing_run": { - "store": true, - "type": "long" + "release_timestamp": { + "type": "date" }, - "source_url": { + "revoke_detail": { "type": "keyword" }, - "sources": { + "rodent_identifier": { "type": "keyword" }, - "start_view_position": { + "schema_version": { + "type": "keyword" + }, + "sex": { + "type": "keyword" + }, + "sources": { "type": "keyword" }, "status": { "type": "keyword" }, - "strand_specificity": { + "strain": { "type": "keyword" }, - "submitted_by": { + "strain_background": { "type": "keyword" }, - "submitted_file_name": { - "copy_to": "_fuzzy", + "submitted_by": { "type": "keyword" }, "submitter_comment": { @@ -1565,29 +1800,33 @@ "summary": { "type": "keyword" }, - "transcriptome_annotation": { + "taxa": { "type": "keyword" }, - "upload_credentials": { - "properties": {}, - "type": "object" - }, - "upload_status": { + "url": { "type": "keyword" }, "uuid": { "type": "keyword" }, - "validation_error_detail": { - "type": "keyword" - }, - "workflow": { - "type": "keyword" + "virtual": { + "store": true, + "type": "boolean" } }, "type": "object" }, - "functional_assay_mechanisms": { + "external_image_url": { + "type": "keyword" + }, + "externally_hosted": { + "store": true, + "type": "boolean" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { "properties": { "@id": { "type": "keyword" @@ -1595,417 +1834,394 @@ "@type": { "type": "keyword" }, + "accession": { + "copy_to": "_exact", + "type": "keyword" + }, "aliases": { + "copy_to": "_exact", "type": "keyword" }, - "ancestors": { + "alternate_accessions": { "type": "keyword" }, - "creation_timestamp": { - "type": "date" + "analysis_step_version": { + "type": "keyword" }, - "deprecated_ntr_terms": { + "anvil_url": { "type": "keyword" }, - "description": { - "type": "text" - }, - "is_a": { + "assay_titles": { "type": "keyword" }, - "name": { + "assembly": { "type": "keyword" }, - "notes": { - "type": "text" - }, - "ontology": { + "award": { "type": "keyword" }, - "release_timestamp": { - "type": "date" - }, - "schema_version": { + "barcode_map_for": { "type": "keyword" }, - "status": { + "base_modifications": { "type": "keyword" }, - "submitted_by": { + "cell_type_annotation": { "type": "keyword" }, - "submitter_comment": { + "checkfiles_version": { "type": "keyword" }, - "summary": { + "collections": { "type": "keyword" }, - "synonyms": { + "content_md5sum": { "type": "keyword" }, - "term_id": { + "content_summary": { "type": "keyword" }, - "term_name": { + "content_type": { "copy_to": "_fuzzy", "type": "keyword" }, - "uuid": { - "type": "keyword" - } - }, - "type": "object" - }, - "input_for": { - "type": "keyword" - }, - "lab": { - "properties": { - "@id": { - "type": "keyword" + "controlled_access": { + "store": true, + "type": "boolean" }, - "@type": { - "type": "keyword" + "creation_timestamp": { + "type": "date" }, - "aliases": { + "dbxrefs": { "type": "keyword" }, - "awards": { + "derived_from": { "type": "keyword" }, - "creation_timestamp": { - "type": "date" + "derived_manually": { + "store": true, + "type": "boolean" }, "description": { "type": "text" }, - "institute_label": { - "type": "keyword" - }, - "name": { + "documents": { "type": "keyword" }, - "notes": { - "type": "text" + "external": { + "store": true, + "type": "boolean" }, - "pi": { + "external_host_url": { "type": "keyword" }, - "schema_version": { - "type": "keyword" + "externally_hosted": { + "store": true, + "type": "boolean" }, - "status": { + "file_format": { "type": "keyword" }, - "submitted_by": { + "file_format_specifications": { "type": "keyword" }, - "submitter_comment": { + "file_format_type": { "type": "keyword" }, - "summary": { + "file_set": { "type": "keyword" }, - "title": { - "copy_to": "_fuzzy", - "type": "keyword" + "file_size": { + "store": true, + "type": "long" }, - "url": { - "type": "keyword" + "filtered": { + "store": true, + "type": "boolean" }, - "uuid": { - "type": "keyword" - } - }, - "type": "object" - }, - "multiome_size": { - "store": true, - "type": "long" - }, - "notes": { - "type": "text" - }, - "onlist_files": { - "type": "keyword" - }, - "onlist_method": { - "type": "keyword" - }, - "preferred_assay_title": { - "copy_to": "_fuzzy", - "type": "keyword" - }, - "protocols": { - "type": "keyword" - }, - "publications": { - "properties": { - "@id": { + "flowcell_id": { "type": "keyword" }, - "@type": { + "gene_list_for": { "type": "keyword" }, - "abstract": { + "href": { "type": "keyword" }, - "aliases": { + "illumina_read_type": { "type": "keyword" }, - "attachment": { - "properties": { - "download": { - "type": "keyword" - }, - "height": { - "store": true, - "type": "long" - }, - "href": { - "type": "keyword" - }, - "md5sum": { - "type": "keyword" - }, - "size": { - "store": true, - "type": "long" - }, - "type": { - "type": "keyword" - }, - "width": { - "store": true, - "type": "long" - } - }, - "type": "object" - }, - "authors": { + "index": { "type": "keyword" }, - "award": { + "input_file_for": { "type": "keyword" }, - "creation_timestamp": { - "type": "date" - }, - "date_published": { + "integrated_in": { "type": "keyword" }, - "date_revised": { + "lab": { "type": "keyword" }, - "description": { - "type": "text" + "lane": { + "store": true, + "type": "long" }, - "donors": { + "loci_list_for": { "type": "keyword" }, - "file_sets": { - "type": "keyword" + "maximum_read_length": { + "store": true, + "type": "long" }, - "issue": { + "md5sum": { "type": "keyword" }, - "journal": { - "type": "keyword" + "mean_read_length": { + "store": true, + "type": "float" }, - "lab": { - "type": "keyword" + "minimum_read_length": { + "store": true, + "type": "long" + }, + "normalized": { + "store": true, + "type": "boolean" }, "notes": { "type": "text" }, - "page": { - "type": "keyword" - }, - "publication_identifiers": { - "copy_to": "_exact", + "principal_dimension": { "type": "keyword" }, - "publication_year": { + "read_count": { "store": true, "type": "long" }, - "published_by": { - "type": "keyword" - }, - "release_timestamp": { - "type": "date" - }, - "samples": { - "type": "keyword" - }, - "schema_version": { - "type": "keyword" - }, - "software": { + "read_names": { "type": "keyword" }, - "software_versions": { - "type": "keyword" + "redacted": { + "store": true, + "type": "boolean" }, - "status": { + "reference_files": { "type": "keyword" }, - "submitted_by": { - "type": "keyword" + "release_timestamp": { + "type": "date" }, - "submitter_comment": { + "revoke_detail": { "type": "keyword" }, - "summary": { + "s3_uri": { "type": "keyword" }, - "title": { + "schema_version": { "type": "keyword" }, - "uuid": { + "secondary_dimensions": { "type": "keyword" }, - "volume": { + "seqspec_of": { "type": "keyword" }, - "workflows": { - "type": "keyword" - } - }, - "type": "object" - }, - "related_multiome_datasets": { - "properties": { - "@id": { + "seqspecs": { "type": "keyword" }, - "@type": { + "sequencing_kit": { "type": "keyword" }, - "accession": { - "copy_to": "_exact", - "type": "keyword" + "sequencing_platform": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "ancestors": { + "type": "keyword" + }, + "company": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "deprecated_ntr_terms": { + "type": "keyword" + }, + "description": { + "type": "text" + }, + "is_a": { + "type": "keyword" + }, + "name": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "ontology": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "schema_version": { + "type": "keyword" + }, + "sequencing_kits": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "synonyms": { + "type": "keyword" + }, + "term_id": { + "type": "keyword" + }, + "term_name": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + } + }, + "type": "object" }, - "aliases": { - "type": "keyword" + "sequencing_run": { + "store": true, + "type": "long" }, - "alternate_accessions": { + "source_url": { "type": "keyword" }, - "assay_term": { + "sources": { "type": "keyword" }, - "auxiliary_sets": { + "start_view_position": { "type": "keyword" }, - "award": { + "status": { "type": "keyword" }, - "collections": { + "strand_specificity": { "type": "keyword" }, - "control_file_sets": { + "submitted_by": { "type": "keyword" }, - "control_for": { + "submitted_file_name": { + "copy_to": "_fuzzy", "type": "keyword" }, - "control_type": { + "submitter_comment": { "type": "keyword" }, - "creation_timestamp": { - "type": "date" + "summary": { + "type": "keyword" }, - "dbxrefs": { + "transcriptome_annotation": { "type": "keyword" }, - "description": { - "type": "text" + "upload_credentials": { + "properties": {}, + "type": "object" }, - "documents": { + "upload_status": { "type": "keyword" }, - "donors": { + "uuid": { "type": "keyword" }, - "external_image_url": { + "validation_error_detail": { "type": "keyword" }, - "externally_hosted": { - "store": true, - "type": "boolean" - }, - "file_set_type": { + "workflow": { "type": "keyword" - }, - "files": { + } + }, + "type": "object" + }, + "functional_assay_mechanisms": { + "properties": { + "@id": { "type": "keyword" }, - "functional_assay_mechanisms": { + "@type": { "type": "keyword" }, - "input_for": { + "aliases": { "type": "keyword" }, - "lab": { + "ancestors": { "type": "keyword" }, - "multiome_size": { - "store": true, - "type": "long" - }, - "notes": { - "type": "text" + "creation_timestamp": { + "type": "date" }, - "onlist_files": { + "deprecated_ntr_terms": { "type": "keyword" }, - "onlist_method": { - "type": "keyword" + "description": { + "type": "text" }, - "preferred_assay_title": { + "is_a": { "type": "keyword" }, - "protocols": { + "name": { "type": "keyword" }, - "publications": { - "type": "keyword" + "notes": { + "type": "text" }, - "related_multiome_datasets": { + "ontology": { "type": "keyword" }, "release_timestamp": { "type": "date" }, - "revoke_detail": { - "type": "keyword" - }, - "samples": { - "type": "keyword" - }, "schema_version": { "type": "keyword" }, - "sequencing_library_types": { - "type": "keyword" - }, "status": { "type": "keyword" }, "submitted_by": { "type": "keyword" }, - "submitted_files_timestamp": { - "type": "date" - }, "submitter_comment": { "type": "keyword" }, "summary": { "type": "keyword" }, - "targeted_genes": { + "synonyms": { + "type": "keyword" + }, + "term_id": { + "type": "keyword" + }, + "term_name": { + "copy_to": "_fuzzy", "type": "keyword" }, "uuid": { @@ -2014,13 +2230,10 @@ }, "type": "object" }, - "release_timestamp": { - "type": "date" - }, - "revoke_detail": { + "input_for": { "type": "keyword" }, - "samples": { + "lab": { "properties": { "@id": { "type": "keyword" @@ -2028,165 +2241,406 @@ "@type": { "type": "keyword" }, - "accession": { - "copy_to": "_exact", + "aliases": { "type": "keyword" }, - "age": { + "awards": { "type": "keyword" }, - "age_units": { + "creation_timestamp": { + "type": "date" + }, + "description": { + "type": "text" + }, + "institute_label": { "type": "keyword" }, - "aliases": { - "copy_to": "_exact", + "name": { "type": "keyword" }, - "alternate_accessions": { + "notes": { + "type": "text" + }, + "pi": { "type": "keyword" }, - "award": { + "schema_version": { "type": "keyword" }, - "barcode_map": { + "status": { "type": "keyword" }, - "biomarkers": { + "submitted_by": { "type": "keyword" }, - "biosample_qualifiers": { + "submitter_comment": { "type": "keyword" }, - "ccf_id": { + "summary": { "type": "keyword" }, - "cell_fate_change_protocol": { + "title": { + "copy_to": "_fuzzy", "type": "keyword" }, - "cell_fate_change_treatments": { - "properties": { - "@id": { - "type": "keyword" - }, - "@type": { - "type": "keyword" - }, - "aliases": { - "type": "keyword" - }, - "amount": { - "store": true, - "type": "float" - }, - "amount_units": { - "type": "keyword" - }, - "award": { - "type": "keyword" - }, - "biosamples_treated": { - "type": "keyword" - }, - "creation_timestamp": { - "type": "date" - }, - "depletion": { - "store": true, - "type": "boolean" - }, - "description": { - "type": "text" - }, - "documents": { - "type": "keyword" - }, - "duration": { - "store": true, - "type": "float" - }, - "duration_units": { - "type": "keyword" - }, - "lab": { - "type": "keyword" - }, - "lot_id": { + "url": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + } + }, + "type": "object" + }, + "multiome_size": { + "store": true, + "type": "long" + }, + "notes": { + "type": "text" + }, + "onlist_files": { + "type": "keyword" + }, + "onlist_method": { + "type": "keyword" + }, + "preferred_assay_title": { + "copy_to": "_fuzzy", + "type": "keyword" + }, + "protocols": { + "type": "keyword" + }, + "publications": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "abstract": { + "type": "keyword" + }, + "aliases": { + "type": "keyword" + }, + "attachment": { + "properties": { + "download": { "type": "keyword" }, - "notes": { - "type": "text" - }, - "pH": { - "store": true, - "type": "float" - }, - "post_treatment_time": { + "height": { "store": true, - "type": "float" - }, - "post_treatment_time_units": { - "type": "keyword" - }, - "product_id": { - "type": "keyword" - }, - "purpose": { - "type": "keyword" - }, - "release_timestamp": { - "type": "date" - }, - "schema_version": { - "type": "keyword" - }, - "sources": { - "type": "keyword" - }, - "status": { - "type": "keyword" - }, - "submitted_by": { - "type": "keyword" + "type": "long" }, - "submitter_comment": { + "href": { "type": "keyword" }, - "summary": { + "md5sum": { "type": "keyword" }, - "temperature": { + "size": { "store": true, - "type": "float" - }, - "temperature_units": { - "type": "keyword" - }, - "treatment_term_id": { - "type": "keyword" - }, - "treatment_term_name": { - "type": "keyword" + "type": "long" }, - "treatment_type": { + "type": { "type": "keyword" }, - "uuid": { - "type": "keyword" + "width": { + "store": true, + "type": "long" } }, "type": "object" }, - "cellular_sub_pool": { + "authors": { "type": "keyword" }, - "classifications": { + "award": { + "type": "keyword" + }, + "creation_timestamp": { + "type": "date" + }, + "date_published": { + "type": "keyword" + }, + "date_revised": { + "type": "keyword" + }, + "description": { + "type": "text" + }, + "donors": { + "type": "keyword" + }, + "file_sets": { + "type": "keyword" + }, + "issue": { + "type": "keyword" + }, + "journal": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "notes": { + "type": "text" + }, + "page": { + "type": "keyword" + }, + "publication_identifiers": { + "copy_to": "_exact", + "type": "keyword" + }, + "publication_year": { + "store": true, + "type": "long" + }, + "published_by": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "samples": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "software": { + "type": "keyword" + }, + "software_versions": { + "type": "keyword" + }, + "status": { + "type": "keyword" + }, + "submitted_by": { + "type": "keyword" + }, + "submitter_comment": { + "type": "keyword" + }, + "summary": { + "type": "keyword" + }, + "title": { + "type": "keyword" + }, + "uuid": { + "type": "keyword" + }, + "volume": { + "type": "keyword" + }, + "workflows": { + "type": "keyword" + } + }, + "type": "object" + }, + "related_multiome_datasets": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { "copy_to": "_exact", "type": "keyword" }, + "aliases": { + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "assay_term": { + "type": "keyword" + }, + "auxiliary_sets": { + "type": "keyword" + }, + "award": { + "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" + }, + "description": { + "type": "text" + }, + "documents": { + "type": "keyword" + }, + "donors": { + "type": "keyword" + }, + "external_image_url": { + "type": "keyword" + }, + "externally_hosted": { + "store": true, + "type": "boolean" + }, + "file_set_type": { + "type": "keyword" + }, + "files": { + "type": "keyword" + }, + "functional_assay_mechanisms": { + "type": "keyword" + }, + "input_for": { + "type": "keyword" + }, + "lab": { + "type": "keyword" + }, + "multiome_size": { + "store": true, + "type": "long" + }, + "notes": { + "type": "text" + }, + "onlist_files": { + "type": "keyword" + }, + "onlist_method": { + "type": "keyword" + }, + "preferred_assay_title": { + "type": "keyword" + }, + "protocols": { + "type": "keyword" + }, + "publications": { + "type": "keyword" + }, + "related_multiome_datasets": { + "type": "keyword" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "samples": { + "type": "keyword" + }, + "schema_version": { + "type": "keyword" + }, + "sequencing_library_types": { + "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" + }, + "uuid": { + "type": "keyword" + } + }, + "type": "object" + }, + "release_timestamp": { + "type": "date" + }, + "revoke_detail": { + "type": "keyword" + }, + "samples": { + "properties": { + "@id": { + "type": "keyword" + }, + "@type": { + "type": "keyword" + }, + "accession": { + "copy_to": "_exact", + "type": "keyword" + }, + "age": { + "type": "keyword" + }, + "age_units": { + "type": "keyword" + }, + "aliases": { + "copy_to": "_exact", + "type": "keyword" + }, + "alternate_accessions": { + "type": "keyword" + }, + "award": { + "type": "keyword" + }, + "barcode_map": { + "type": "keyword" + }, + "biomarkers": { + "type": "keyword" + }, + "biosample_qualifiers": { + "type": "keyword" + }, + "ccf_id": { + "type": "keyword" + }, + "cell_fate_change_protocol": { + "type": "keyword" + }, + "cell_fate_change_treatments": { "properties": { "@id": { "type": "keyword" @@ -2194,399 +2648,74 @@ "@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": { + "amount": { "store": true, "type": "float" }, - "award": { - "type": "keyword" - }, - "collections": { - "type": "keyword" - }, - "control_file_sets": { + "amount_units": { "type": "keyword" }, - "control_for": { + "award": { "type": "keyword" }, - "control_type": { + "biosamples_treated": { "type": "keyword" }, "creation_timestamp": { "type": "date" }, + "depletion": { + "store": true, + "type": "boolean" + }, "description": { "type": "text" }, "documents": { "type": "keyword" }, - "exon": { - "type": "keyword" - }, - "file_set_type": { - "type": "keyword" - }, - "files": { - "type": "keyword" - }, - "guide_type": { - "type": "keyword" + "duration": { + "store": true, + "type": "float" }, - "input_for": { + "duration_units": { "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" + "notes": { + "type": "text" }, - "lower_bound_insert_size": { + "pH": { "store": true, - "type": "long" + "type": "float" }, - "notes": { - "type": "text" + "post_treatment_time": { + "store": true, + "type": "float" }, - "orf_list": { + "post_treatment_time_units": { "type": "keyword" }, "product_id": { "type": "keyword" }, - "publications": { + "purpose": { "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" - }, - "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" - }, - "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" }, @@ -2596,44 +2725,27 @@ "submitted_by": { "type": "keyword" }, - "submitted_files_timestamp": { - "type": "date" - }, "submitter_comment": { "type": "keyword" }, "summary": { "type": "keyword" }, - "targeton": { - "type": "keyword" + "temperature": { + "store": true, + "type": "float" }, - "tile": { - "properties": { - "tile_end": { - "store": true, - "type": "long" - }, - "tile_id": { - "type": "keyword" - }, - "tile_start": { - "store": true, - "type": "long" - } - }, - "type": "object" + "temperature_units": { + "type": "keyword" }, - "tiling_modality": { + "treatment_term_id": { "type": "keyword" }, - "upper_bound_guide_coverage": { - "store": true, - "type": "long" + "treatment_term_name": { + "type": "keyword" }, - "upper_bound_insert_size": { - "store": true, - "type": "long" + "treatment_type": { + "type": "keyword" }, "uuid": { "type": "keyword" @@ -2641,6 +2753,19 @@ }, "type": "object" }, + "cellular_sub_pool": { + "type": "keyword" + }, + "classifications": { + "copy_to": "_exact", + "type": "keyword" + }, + "collections": { + "type": "keyword" + }, + "construct_library_sets": { + "type": "keyword" + }, "creation_timestamp": { "type": "date" }, diff --git a/src/igvfd/mappings/model_file.json b/src/igvfd/mappings/model_file.json index 96bf61251..ec6b2a64a 100644 --- a/src/igvfd/mappings/model_file.json +++ b/src/igvfd/mappings/model_file.json @@ -1,6 +1,6 @@ { - "hash": "c66e2212e206fdd7580db1ba81610e9b", - "index_name": "model_file_c66e2212", + "hash": "ece69ef452ed1ea3598c1e317c115eb8", + "index_name": "model_file_ece69ef4", "item_type": "model_file", "mapping": { "dynamic_templates": [ @@ -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 de371828f..5a19aca07 100644 --- a/src/igvfd/mappings/model_set.json +++ b/src/igvfd/mappings/model_set.json @@ -1,6 +1,6 @@ { - "hash": "93ade25509c3bd6cbb092fe0bbf39aa2", - "index_name": "model_set_93ade255", + "hash": "1c624f733f2d772c61601bc7fcfb3eba", + "index_name": "model_set_1c624f73", "item_type": "model_set", "mapping": { "dynamic_templates": [ @@ -390,6 +390,481 @@ "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": { @@ -447,6 +922,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1175,6 +1653,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1700,369 +2181,7 @@ "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 76af35425..f9a077c0e 100644 --- a/src/igvfd/mappings/multiplexed_sample.json +++ b/src/igvfd/mappings/multiplexed_sample.json @@ -1,6 +1,6 @@ { - "hash": "89ef91693c2990c91c2588f32cd0cb78", - "index_name": "multiplexed_sample_89ef9169", + "hash": "6c4cd367ba86627f76a2dc5557db373a", + "index_name": "multiplexed_sample_6c4cd367", "item_type": "multiplexed_sample", "mapping": { "dynamic_templates": [ @@ -503,6 +503,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -933,6 +936,9 @@ "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 d2d0cd32c..5e41ac0cd 100644 --- a/src/igvfd/mappings/prediction_set.json +++ b/src/igvfd/mappings/prediction_set.json @@ -1,6 +1,6 @@ { - "hash": "fee679b6647cd31b5f4aa323c07a215d", - "index_name": "prediction_set_fee679b6", + "hash": "3a1326f62d19d30cb6d27a3a01fdad42", + "index_name": "prediction_set_3a1326f6", "item_type": "prediction_set", "mapping": { "dynamic_templates": [ @@ -390,6 +390,481 @@ "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": { @@ -447,6 +922,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1757,6 +2235,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1791,176 +2272,7 @@ "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 ff565f822..28714e6ed 100644 --- a/src/igvfd/mappings/primary_cell.json +++ b/src/igvfd/mappings/primary_cell.json @@ -1,6 +1,6 @@ { - "hash": "d94737ebce9786fc7648c981127d1e77", - "index_name": "primary_cell_d94737eb", + "hash": "4f909efcdcf747c4dee9d95f0f9469b9", + "index_name": "primary_cell_4f909efc", "item_type": "primary_cell", "mapping": { "dynamic_templates": [ @@ -509,6 +509,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -943,6 +946,9 @@ "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 1b727d30e..5196aa21a 100644 --- a/src/igvfd/mappings/reference_file.json +++ b/src/igvfd/mappings/reference_file.json @@ -1,6 +1,6 @@ { - "hash": "746cf1089ab0d3d21820928ca45f0a29", - "index_name": "reference_file_746cf108", + "hash": "8ab196c401a4f471b7b7a92496dc4a21", + "index_name": "reference_file_8ab196c4", "item_type": "reference_file", "mapping": { "dynamic_templates": [ @@ -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 15c8b8d52..fb9cc058e 100644 --- a/src/igvfd/mappings/sequence_file.json +++ b/src/igvfd/mappings/sequence_file.json @@ -1,6 +1,6 @@ { - "hash": "106fe9342fff0cc109f57ecb16641a3f", - "index_name": "sequence_file_106fe934", + "hash": "c85fddd3ff90ab59f9dcc49cb1eed254", + "index_name": "sequence_file_c85fddd3", "item_type": "sequence_file", "mapping": { "dynamic_templates": [ @@ -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 4a98df90f..dadff91e0 100644 --- a/src/igvfd/mappings/signal_file.json +++ b/src/igvfd/mappings/signal_file.json @@ -1,6 +1,6 @@ { - "hash": "5cae71fd2ef4ddec92ed9c3057a7921a", - "index_name": "signal_file_5cae71fd", + "hash": "ca824425e928f1cfa025ad3fb1c0307f", + "index_name": "signal_file_ca824425", "item_type": "signal_file", "mapping": { "dynamic_templates": [ @@ -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 68262d662..5d7ce3c92 100644 --- a/src/igvfd/mappings/tabular_file.json +++ b/src/igvfd/mappings/tabular_file.json @@ -1,6 +1,6 @@ { - "hash": "234c47c13cd9c7b0d7f8725954fc8f96", - "index_name": "tabular_file_234c47c1", + "hash": "7274bffeca8c7261824a73c3481b55e1", + "index_name": "tabular_file_7274bffe", "item_type": "tabular_file", "mapping": { "dynamic_templates": [ @@ -432,6 +432,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -1485,6 +1488,9 @@ "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 934c11d73..74a2af23d 100644 --- a/src/igvfd/mappings/technical_sample.json +++ b/src/igvfd/mappings/technical_sample.json @@ -1,6 +1,6 @@ { - "hash": "f997e6a5a000bce05f1f062264a42d30", - "index_name": "technical_sample_f997e6a5", + "hash": "be000c2fac5fe9fc0611a19e930c3a60", + "index_name": "technical_sample_be000c2f", "item_type": "technical_sample", "mapping": { "dynamic_templates": [ @@ -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 acaee7166..d2fbcbb3f 100644 --- a/src/igvfd/mappings/tissue.json +++ b/src/igvfd/mappings/tissue.json @@ -1,6 +1,6 @@ { - "hash": "150ee310e9442f985909c9fa5fb17007", - "index_name": "tissue_150ee310", + "hash": "25ac6c9fde6a72ed644f50b6829b8590", + "index_name": "tissue_25ac6c9f", "item_type": "tissue", "mapping": { "dynamic_templates": [ @@ -509,6 +509,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -943,6 +946,9 @@ "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 3d428fed2..c0d37efb3 100644 --- a/src/igvfd/mappings/whole_organism.json +++ b/src/igvfd/mappings/whole_organism.json @@ -1,6 +1,6 @@ { - "hash": "4b4e47d638fb6c52126e8599141e33ce", - "index_name": "whole_organism_4b4e47d6", + "hash": "7f612ead3f0ded2d20a8ffbb6c1dfb4d", + "index_name": "whole_organism_7f612ead", "item_type": "whole_organism", "mapping": { "dynamic_templates": [ @@ -506,6 +506,9 @@ "collections": { "type": "keyword" }, + "construct_library_sets": { + "type": "keyword" + }, "control_file_sets": { "type": "keyword" }, @@ -940,6 +943,9 @@ "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 75cb4fe8e..ed681d9c1 100644 --- a/src/igvfd/searches/configs/model_set.py +++ b/src/igvfd/searches/configs/model_set.py @@ -16,12 +16,39 @@ 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', }, + 'construct_library_sets.integrated_content_files.content_type': { + 'title': 'Construct Library Design' + }, '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 36e4c7994..5bc2dfbaa 100644 --- a/src/igvfd/types/file_set.py +++ b/src/igvfd/types/file_set.py @@ -74,7 +74,6 @@ class FileSet(Item): 'treatments', 'cell_fate_change_treatments', 'classifications', - 'construct_library_sets', 'disease_terms', 'modifications', 'sample_terms', @@ -89,7 +88,7 @@ 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']), ] @@ -191,6 +190,33 @@ 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', @@ -749,7 +775,7 @@ 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']),