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January 29, 2018 15:59
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| PUT gdc_from_graph | |
| { | |
| "settings": { | |
| "analysis": { | |
| "filter": { | |
| "edge_ngram": { | |
| "min_gram": "1", | |
| "side": "front", | |
| "type": "edge_ngram", | |
| "max_gram": "20" | |
| } | |
| }, | |
| "analyzer": { | |
| "autocomplete_analyzed": { | |
| "filter": [ | |
| "lowercase", | |
| "edge_ngram" | |
| ], | |
| "tokenizer": "standard" | |
| }, | |
| "autocomplete_prefix": { | |
| "filter": [ | |
| "lowercase", | |
| "edge_ngram" | |
| ], | |
| "tokenizer": "keyword" | |
| }, | |
| "lowercase_keyword": { | |
| "filter": [ | |
| "lowercase" | |
| ], | |
| "tokenizer": "keyword" | |
| } | |
| } | |
| } | |
| }, | |
| "mappings": { | |
| "case": { | |
| "properties": { | |
| "aliquot_ids": { | |
| "type": "keyword" | |
| }, | |
| "analyte_ids": { | |
| "type": "keyword" | |
| }, | |
| "annotations": { | |
| "type": "nested", | |
| "properties": { | |
| "annotation_id": { | |
| "type": "keyword" | |
| }, | |
| "case_id": { | |
| "type": "keyword" | |
| }, | |
| "case_submitter_id": { | |
| "type": "keyword" | |
| }, | |
| "category": { | |
| "type": "keyword" | |
| }, | |
| "classification": { | |
| "type": "keyword" | |
| }, | |
| "created_datetime": { | |
| "type": "keyword" | |
| }, | |
| "creator": { | |
| "type": "keyword" | |
| }, | |
| "entity_id": { | |
| "type": "keyword" | |
| }, | |
| "entity_submitter_id": { | |
| "type": "keyword" | |
| }, | |
| "entity_type": { | |
| "type": "keyword" | |
| }, | |
| "legacy_created_datetime": { | |
| "type": "keyword" | |
| }, | |
| "legacy_updated_datetime": { | |
| "type": "keyword" | |
| }, | |
| "notes": { | |
| "type": "keyword" | |
| }, | |
| "state": { | |
| "type": "keyword" | |
| }, | |
| "status": { | |
| "type": "keyword" | |
| }, | |
| "submitter_id": { | |
| "type": "keyword" | |
| }, | |
| "updated_datetime": { | |
| "type": "keyword" | |
| } | |
| } | |
| }, | |
| "case_autocomplete": { | |
| "type": "keyword", | |
| "fields": { | |
| "analyzed": { | |
| "type": "text", | |
| "analyzer": "autocomplete_analyzed", | |
| "search_analyzer": "lowercase_keyword" | |
| }, | |
| "lowercase": { | |
| "type": "text", | |
| "analyzer": "lowercase_keyword" | |
| }, | |
| "prefix": { | |
| "type": "text", | |
| "analyzer": "autocomplete_prefix", | |
| "search_analyzer": "lowercase_keyword" | |
| } | |
| } | |
| }, | |
| "case_id": { | |
| "type": "keyword", | |
| "copy_to": [ | |
| "case_autocomplete" | |
| ] | |
| }, | |
| "created_datetime": { | |
| "type": "keyword" | |
| }, | |
| "days_to_index": { | |
| "type": "long" | |
| }, | |
| "demographic": { | |
| "properties": { | |
| "created_datetime": { | |
| "type": "keyword" | |
| }, | |
| "demographic_id": { | |
| "type": "keyword" | |
| }, | |
| "ethnicity": { | |
| "type": "keyword" | |
| }, | |
| "gender": { | |
| "type": "keyword" | |
| }, | |
| "race": { | |
| "type": "keyword" | |
| }, | |
| "state": { | |
| "type": "keyword" | |
| }, | |
| "submitter_id": { | |
| "type": "keyword" | |
| }, | |
| "updated_datetime": { | |
| "type": "keyword" | |
| }, | |
| "year_of_birth": { | |
| "type": "long" | |
| }, | |
| "year_of_death": { | |
| "type": "long" | |
| } | |
| } | |
| }, | |
| "diagnoses": { | |
| "type": "nested", | |
| "properties": { | |
| "age_at_diagnosis": { | |
| "type": "long" | |
| }, | |
| "ajcc_clinical_m": { | |
| "type": "keyword" | |
| }, | |
| "ajcc_clinical_n": { | |
| "type": "keyword" | |
| }, | |
| "ajcc_clinical_stage": { | |
| "type": "keyword" | |
| }, | |
| "ajcc_clinical_t": { | |
| "type": "keyword" | |
| }, | |
| "ajcc_pathologic_m": { | |
| "type": "keyword" | |
| }, | |
| "ajcc_pathologic_n": { | |
| "type": "keyword" | |
| }, | |
| "ajcc_pathologic_stage": { | |
| "type": "keyword" | |
| }, | |
| "ajcc_pathologic_t": { | |
| "type": "keyword" | |
| }, | |
| "ann_arbor_b_symptoms": { | |
| "type": "keyword" | |
| }, | |
| "ann_arbor_clinical_stage": { | |
| "type": "keyword" | |
| }, | |
| "ann_arbor_extranodal_involvement": { | |
| "type": "keyword" | |
| }, | |
| "ann_arbor_pathologic_stage": { | |
| "type": "keyword" | |
| }, | |
| "burkitt_lymphoma_clinical_variant": { | |
| "type": "keyword" | |
| }, | |
| "cause_of_death": { | |
| "type": "keyword" | |
| }, | |
| "circumferential_resection_margin": { | |
| "type": "long" | |
| }, | |
| "classification_of_tumor": { | |
| "type": "keyword" | |
| }, | |
| "colon_polyps_history": { | |
| "type": "keyword" | |
| }, | |
| "created_datetime": { | |
| "type": "keyword" | |
| }, | |
| "days_to_birth": { | |
| "type": "long" | |
| }, | |
| "days_to_death": { | |
| "type": "long" | |
| }, | |
| "days_to_hiv_diagnosis": { | |
| "type": "long" | |
| }, | |
| "days_to_last_follow_up": { | |
| "type": "long" | |
| }, | |
| "days_to_last_known_disease_status": { | |
| "type": "long" | |
| }, | |
| "days_to_new_event": { | |
| "type": "long" | |
| }, | |
| "days_to_recurrence": { | |
| "type": "long" | |
| }, | |
| "diagnosis_id": { | |
| "type": "keyword" | |
| }, | |
| "figo_stage": { | |
| "type": "keyword" | |
| }, | |
| "hiv_positive": { | |
| "type": "keyword" | |
| }, | |
| "hpv_positive_type": { | |
| "type": "keyword" | |
| }, | |
| "hpv_status": { | |
| "type": "keyword" | |
| }, | |
| "last_known_disease_status": { | |
| "type": "keyword" | |
| }, | |
| "laterality": { | |
| "type": "keyword" | |
| }, | |
| "ldh_level_at_diagnosis": { | |
| "type": "long" | |
| }, | |
| "ldh_normal_range_upper": { | |
| "type": "long" | |
| }, | |
| "lymph_nodes_positive": { | |
| "type": "long" | |
| }, | |
| "lymphatic_invasion_present": { | |
| "type": "keyword" | |
| }, | |
| "method_of_diagnosis": { | |
| "type": "keyword" | |
| }, | |
| "morphology": { | |
| "type": "keyword" | |
| }, | |
| "new_event_anatomic_site": { | |
| "type": "keyword" | |
| }, | |
| "new_event_type": { | |
| "type": "keyword" | |
| }, | |
| "perineural_invasion_present": { | |
| "type": "keyword" | |
| }, | |
| "primary_diagnosis": { | |
| "type": "keyword" | |
| }, | |
| "prior_malignancy": { | |
| "type": "keyword" | |
| }, | |
| "prior_treatment": { | |
| "type": "keyword" | |
| }, | |
| "progression_or_recurrence": { | |
| "type": "keyword" | |
| }, | |
| "residual_disease": { | |
| "type": "keyword" | |
| }, | |
| "site_of_resection_or_biopsy": { | |
| "type": "keyword" | |
| }, | |
| "state": { | |
| "type": "keyword" | |
| }, | |
| "submitter_id": { | |
| "type": "keyword" | |
| }, | |
| "tissue_or_organ_of_origin": { | |
| "type": "keyword" | |
| }, | |
| "treatments": { | |
| "type": "nested", | |
| "properties": { | |
| "created_datetime": { | |
| "type": "keyword" | |
| }, | |
| "days_to_treatment": { | |
| "type": "long" | |
| }, | |
| "days_to_treatment_end": { | |
| "type": "long" | |
| }, | |
| "days_to_treatment_start": { | |
| "type": "long" | |
| }, | |
| "state": { | |
| "type": "keyword" | |
| }, | |
| "submitter_id": { | |
| "type": "keyword" | |
| }, | |
| "therapeutic_agents": { | |
| "type": "keyword" | |
| }, | |
| "treatment_anatomic_site": { | |
| "type": "keyword" | |
| }, | |
| "treatment_id": { | |
| "type": "keyword" | |
| }, | |
| "treatment_intent_type": { | |
| "type": "keyword" | |
| }, | |
| "treatment_or_therapy": { | |
| "type": "keyword" | |
| }, | |
| "treatment_outcome": { | |
| "type": "keyword" | |
| }, | |
| "treatment_type": { | |
| "type": "keyword" | |
| }, | |
| "updated_datetime": { | |
| "type": "keyword" | |
| } | |
| } | |
| }, | |
| "tumor_grade": { | |
| "type": "keyword" | |
| }, | |
| "tumor_stage": { | |
| "type": "keyword" | |
| }, | |
| "updated_datetime": { | |
| "type": "keyword" | |
| }, | |
| "vascular_invasion_present": { | |
| "type": "keyword" | |
| }, | |
| "vital_status": { | |
| "type": "keyword" | |
| }, | |
| "year_of_diagnosis": { | |
| "type": "long" | |
| } | |
| } | |
| }, | |
| "disease_type": { | |
| "type": "keyword" | |
| }, | |
| "exposures": { | |
| "type": "nested", | |
| "properties": { | |
| "alcohol_history": { | |
| "type": "keyword" | |
| }, | |
| "alcohol_intensity": { | |
| "type": "keyword" | |
| }, | |
| "bmi": { | |
| "type": "long" | |
| }, | |
| "cigarettes_per_day": { | |
| "type": "long" | |
| }, | |
| "created_datetime": { | |
| "type": "keyword" | |
| }, | |
| "exposure_id": { | |
| "type": "keyword" | |
| }, | |
| "height": { | |
| "type": "long" | |
| }, | |
| "pack_years_smoked": { | |
| "type": "long" | |
| }, | |
| "state": { | |
| "type": "keyword" | |
| }, | |
| "submitter_id": { | |
| "type": "keyword" | |
| }, | |
| "tobacco_smoking_onset_year": { | |
| "type": "long" | |
| }, | |
| "tobacco_smoking_quit_year": { | |
| "type": "long" | |
| }, | |
| "tobacco_smoking_status": { | |
| "type": "keyword" | |
| }, | |
| "updated_datetime": { | |
| "type": "keyword" | |
| }, | |
| "weight": { | |
| "type": "long" | |
| }, | |
| "years_smoked": { | |
| "type": "long" | |
| } | |
| } | |
| }, | |
| "family_histories": { | |
| "type": "nested", | |
| "properties": { | |
| "created_datetime": { | |
| "type": "keyword" | |
| }, | |
| "family_history_id": { | |
| "type": "keyword" | |
| }, | |
| "relationship_age_at_diagnosis": { | |
| "type": "long" | |
| }, | |
| "relationship_gender": { | |
| "type": "keyword" | |
| }, | |
| "relationship_primary_diagnosis": { | |
| "type": "keyword" | |
| }, | |
| "relationship_type": { | |
| "type": "keyword" | |
| }, | |
| "relative_with_cancer_history": { | |
| "type": "keyword" | |
| }, | |
| "state": { | |
| "type": "keyword" | |
| }, | |
| "submitter_id": { | |
| "type": "keyword" | |
| }, | |
| "updated_datetime": { | |
| "type": "keyword" | |
| } | |
| } | |
| }, | |
| "files": { | |
| "type": "nested", | |
| "properties": { | |
| "access": { | |
| "type": "keyword" | |
| }, | |
| "acl": { | |
| "type": "keyword" | |
| }, | |
| "analysis": { | |
| "properties": { | |
| "analysis_id": { | |
| "type": "keyword" | |
| }, | |
| "analysis_type": { | |
| "type": "keyword" | |
| }, | |
| "created_datetime": { | |
| "type": "keyword" | |
| }, | |
| "input_files": { | |
| "type": "nested", | |
| "properties": { | |
| "access": { | |
| "type": "keyword" | |
| }, | |
| "created_datetime": { | |
| "type": "keyword" | |
| }, | |
| "data_category": { | |
| "type": "keyword" | |
| }, | |
| "data_format": { | |
| "type": "keyword" | |
| }, | |
| "data_type": { | |
| "type": "keyword" | |
| }, | |
| "error_type": { | |
| "type": "keyword" | |
| }, | |
| "experimental_strategy": { | |
| "type": "keyword" | |
| }, | |
| "file_id": { | |
| "type": "keyword" | |
| }, | |
| "file_name": { | |
| "type": "keyword" | |
| }, | |
| "file_size": { | |
| "type": "long" | |
| }, | |
| "file_state": { | |
| "type": "keyword" | |
| }, | |
| "md5sum": { | |
| "type": "keyword" | |
| }, | |
| "platform": { | |
| "type": "keyword" | |
| }, | |
| "revision": { | |
| "type": "long" | |
| }, | |
| "state": { | |
| "type": "keyword" | |
| }, | |
| "state_comment": { | |
| "type": "keyword" | |
| }, | |
| "submitter_id": { | |
| "type": "keyword" | |
| }, | |
| "updated_datetime": { | |
| "type": "keyword" | |
| } | |
| } | |
| }, | |
| "metadata": { | |
| "properties": { | |
| "read_groups": { | |
| "type": "nested", | |
| "properties": { | |
| "RIN": { | |
| "type": "long" | |
| }, | |
| "adapter_name": { | |
| "type": "keyword" | |
| }, | |
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| "type": "keyword" | |
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| "base_caller_name": { | |
| "type": "keyword" | |
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| "type": "keyword" | |
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| "created_datetime": { | |
| "type": "keyword" | |
| }, | |
| "experiment_name": { | |
| "type": "keyword" | |
| }, | |
| "flow_cell_barcode": { | |
| "type": "keyword" | |
| }, | |
| "includes_spike_ins": { | |
| "type": "keyword" | |
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| "instrument_model": { | |
| "type": "keyword" | |
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| "type": "keyword" | |
| }, | |
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| "library_preparation_kit_catalog_number": { | |
| "type": "keyword" | |
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| "type": "keyword" | |
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| "library_preparation_kit_version": { | |
| "type": "keyword" | |
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| "library_selection": { | |
| "type": "keyword" | |
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| "type": "keyword" | |
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| "type": "keyword" | |
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| "platform": { | |
| "type": "keyword" | |
| }, | |
| "read_group_id": { | |
| "type": "keyword" | |
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| "read_group_name": { | |
| "type": "keyword" | |
| }, | |
| "read_group_qcs": { | |
| "type": "nested", | |
| "properties": { | |
| "adapter_content": { | |
| "type": "keyword" | |
| }, | |
| "basic_statistics": { | |
| "type": "keyword" | |
| }, | |
| "created_datetime": { | |
| "type": "keyword" | |
| }, | |
| "encoding": { | |
| "type": "keyword" | |
| }, | |
| "fastq_name": { | |
| "type": "keyword" | |
| }, | |
| "kmer_content": { | |
| "type": "keyword" | |
| }, | |
| "overrepresented_sequences": { | |
| "type": "keyword" | |
| }, | |
| "per_base_n_content": { | |
| "type": "keyword" | |
| }, | |
| "per_base_sequence_content": { | |
| "type": "keyword" | |
| }, | |
| "per_base_sequence_quality": { | |
| "type": "keyword" | |
| }, | |
| "per_sequence_gc_content": { | |
| "type": "keyword" | |
| }, | |
| "per_sequence_quality_score": { | |
| "type": "keyword" | |
| }, | |
| "per_tile_sequence_quality": { | |
| "type": "keyword" | |
| }, | |
| "percent_gc_content": { | |
| "type": "long" | |
| }, | |
| "read_group_qc_id": { | |
| "type": "keyword" | |
| }, | |
| "sequence_duplication_levels": { | |
| "type": "keyword" | |
| }, | |
| "sequence_length_distribution": { | |
| "type": "keyword" | |
| }, | |
| "state": { | |
| "type": "keyword" | |
| }, | |
| "submitter_id": { | |
| "type": "keyword" | |
| }, | |
| "total_sequences": { | |
| "type": "long" | |
| }, | |
| "updated_datetime": { | |
| "type": "keyword" | |
| }, | |
| "workflow_end_datetime": { | |
| "type": "keyword" | |
| }, | |
| "workflow_link": { | |
| "type": "keyword" | |
| }, | |
| "workflow_start_datetime": { | |
| "type": "keyword" | |
| }, | |
| "workflow_type": { | |
| "type": "keyword" | |
| }, | |
| "workflow_version": { | |
| "type": "keyword" | |
| } | |
| } | |
| }, | |
| "read_length": { | |
| "type": "long" | |
| }, | |
| "sequencing_center": { | |
| "type": "keyword" | |
| }, | |
| "sequencing_date": { | |
| "type": "keyword" | |
| }, | |
| "size_selection_range": { | |
| "type": "keyword" | |
| }, | |
| "spike_ins_concentration": { | |
| "type": "keyword" | |
| }, | |
| "spike_ins_fasta": { | |
| "type": "keyword" | |
| }, | |
| "state": { | |
| "type": "keyword" | |
| }, | |
| "submitter_id": { | |
| "type": "keyword" | |
| }, | |
| "target_capture_kit_catalog_number": { | |
| "type": "keyword" | |
| }, | |
| "target_capture_kit_name": { | |
| "type": "keyword" | |
| }, | |
| "target_capture_kit_target_region": { | |
| "type": "keyword" | |
| }, | |
| "target_capture_kit_vendor": { | |
| "type": "keyword" | |
| }, | |
| "target_capture_kit_version": { | |
| "type": "keyword" | |
| }, | |
| "to_trim_adapter_sequence": { | |
| "type": "keyword" | |
| }, | |
| "updated_datetime": { | |
| "type": "keyword" | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| "state": { | |
| "type": "keyword" | |
| }, | |
| "submitter_id": { | |
| "type": "keyword" | |
| }, | |
| "updated_datetime": { | |
| "type": "keyword" | |
| }, | |
| "workflow_end_datetime": { | |
| "type": "keyword" | |
| }, | |
| "workflow_link": { | |
| "type": "keyword" | |
| }, | |
| "workflow_start_datetime": { | |
| "type": "keyword" | |
| }, | |
| "workflow_type": { | |
| "type": "keyword" | |
| }, | |
| "workflow_version": { | |
| "type": "keyword" | |
| } | |
| } | |
| }, | |
| "archive": { | |
| "properties": { | |
| "archive_id": { | |
| "type": "keyword" | |
| }, | |
| "created_datetime": { | |
| "type": "keyword" | |
| }, | |
| "data_category": { | |
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| "data_format": { | |
| "type": "keyword" | |
| }, | |
| "data_type": { | |
| "type": "keyword" | |
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| "error_type": { | |
| "type": "keyword" | |
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| "file_name": { | |
| "type": "keyword" | |
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| "type": "long" | |
| }, | |
| "file_state": { | |
| "type": "keyword" | |
| }, | |
| "md5sum": { | |
| "type": "keyword" | |
| }, | |
| "revision": { | |
| "type": "long" | |
| }, | |
| "state": { | |
| "type": "keyword" | |
| }, | |
| "state_comment": { | |
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| } | |
| } | |
| } | |
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