diff --git a/jenkins-blood.planx-pla.net/etlMapping.yaml b/jenkins-blood.planx-pla.net/etlMapping.yaml index c7520bdd0..5d2564f38 100644 --- a/jenkins-blood.planx-pla.net/etlMapping.yaml +++ b/jenkins-blood.planx-pla.net/etlMapping.yaml @@ -1,139 +1,83 @@ + mappings: - - name: jenkins-blood.planx-pla.net_study - doc_type: study + - name: jenkins-blood.planx-pla.net_subject + doc_type: subject type: aggregator - root: study + root: subject props: - - name: project_id - name: submitter_id - - name: study_setup - - name: study_objective - - name: study_design - - name: study_description - - name: data_description - - name: associated_study - aggregated_props: - - name: _cases_count - path: cases - fn: count - - name: _biospecimens_count - path: cases.biospecimens - fn: count - - name: _samples_count - path: cases.biospecimens.samples - fn: count - - name: _aliquots_count - path: cases.biospecimens.samples.aliquots - fn: count - - name: _analytes_count - path: cases.biospecimens.samples.aliquots.analytes - fn: count - - name: _read_groups_count - path: cases.biospecimens.samples.aliquots.analytes.read_groups - fn: count - - name: _immunoassays_count - path: cases.biospecimens.samples.aliquots.analytes.immunoassays - fn: count - - name: _cell_images_count - path: cases.biospecimens.samples.aliquots.analytes.cell_images - fn: count - - name: _pcr_assays_count - path: cases.biospecimens.samples.aliquots.analytes.pcr_assays - fn: count - - name: _pcr_assay_files_count - path: cases.biospecimens.samples.aliquots.analytes.pcr_assays.pcr_assay_files - fn: count - - name: _mass_cytometry_assays_count - path: cases.biospecimens.samples.aliquots.analytes.mass_cytometry_assays - fn: count - - name: _mass_cytometry_images_count - path: cases.biospecimens.samples.aliquots.analytes.mass_cytometry_assays.mass_cytometry_images - fn: count - - name: _slide_images_count - path: cases.biospecimens.samples.aliquots.slide_images - fn: count - - name: _submitted_aligned_reads_files_count - path: cases.biospecimens.samples.aliquots.analytes.read_groups.submitted_aligned_reads_files - fn: count - - name: _submitted_methylations_count - path: cases.biospecimens.samples.aliquots.analytes.submitted_methylation_files - fn: count - - name: _submitted_somatic_mutations_count - path: cases.biospecimens.samples.aliquots.analytes.read_groups.submitted_somatic_mutations - fn: count - - name: _submitted_unaligned_reads_files_count - path: cases.biospecimens.samples.aliquots.analytes.read_groups.submitted_unaligned_reads_files - fn: count - parent_props: - - path: projects[project_code:code,project_name:name,project_investigator_affiliation:investigator_affiliation] - - name: jenkins-blood.planx-pla.net_case - doc_type: case - type: aggregator - root: case - props: - name: project_id - - name: submitter_id - - name: index_date - - name: lost_to_followup - flatten_props: - - path: demographics - props: - - name: gender - - name: days_to_birth - - name: race - - name: ethnicity + - name: sex + - name: age_value + - name: ancestry + - name: disease_description + - name: phenotype_present + - name: phenotype_absent + - name: disease_id + - name: solve_state + - name: congenital_status + - name: age_of_onset + - name: phenotype_group + - name: anvil_project_id +# flatten_props: aggregated_props: - - name: _biospecimens_count - path: biospecimens - fn: count + - name: sample_provider + path: samples + src: sample_provider + fn: set + - name: tissue_affected_status + path: samples + src: tissue_affected_status + fn: set + - name: tissue_type + path: samples + src: tissue_type + fn: set + - name: sample_type + path: samples + src: sample_type + fn: set + - name: original_material_type + path: samples + src: original_material_type + fn: set + - name: exome_capture_platform + path: samples.sequencings + src: exome_capture_platform + fn: set + - name: library_prep_kit_method + path: samples.sequencings + src: library_prep_kit_method + fn: set + - name: capture_region_bed_file + path: samples.sequencings + src: capture_region_bed_file + fn: set + - name: reference_genome_build + path: samples.sequencings + src: reference_genome_build + fn: set + - name: sequencing_assay + path: samples.sequencings + src: sequencing_assay + fn: set + - name: alignment_method + path: samples.sequencings + src: alignment_method + fn: set + - name: data_processing_pipeline + path: samples.sequencings + src: data_processing_pipeline + fn: set - name: _samples_count - path: biospecimens.samples - fn: count - - name: _aliquots_count - path: biospecimens.samples.aliquots - fn: count - - name: _analytes_count - path: biospecimens.samples.aliquots.analytes - fn: count - - name: _read_groups_count - path: biospecimens.samples.aliquots.analytes.read_groups - fn: count - - name: _immunoassays_count - path: biospecimens.samples.aliquots.analytes.immunoassays - fn: count - - name: _cell_images_count - path: biospecimens.samples.aliquots.analytes.cell_images - fn: count - - name: _pcr_assays_count - path: biospecimens.samples.aliquots.analytes.pcr_assays + path: samples fn: count - - name: _pcr_assay_files_count - path: biospecimens.samples.aliquots.analytes.pcr_assays.pcr_assay_files - fn: count - - name: _mass_cytometry_assays_count - path: biospecimens.samples.aliquots.analytes.mass_cytometry_assays - fn: count - - name: _mass_cytometry_images_count - path: biospecimens.samples.aliquots.analytes.mass_cytometry_assays.mass_cytometry_images - fn: count - - name: _slide_images_count - path: biospecimens.samples.aliquots.slide_images - fn: count - - name: _submitted_aligned_reads_files_count - path: biospecimens.samples.aliquots.analytes.read_groups.submitted_aligned_reads_files - fn: count - - name: _submitted_methylations_count - path: biospecimens.samples.aliquots.analytes.submitted_methylation_files - fn: count - - name: _submitted_somatic_mutations_count - path: biospecimens.samples.aliquots.analytes.read_groups.submitted_somatic_mutations - fn: count - - name: _submitted_unaligned_reads_files_count - path: biospecimens.samples.aliquots.analytes.read_groups.submitted_unaligned_reads_files + - name: _sequencings_count + path: samples.sequencings fn: count joining_props: - index: file - join_on: _case_id + join_on: _subject_id props: - name: data_format src: data_format @@ -141,199 +85,26 @@ mappings: - name: data_type src: data_type fn: set - - name: jenkins-blood.planx-pla.net_biospecimen - doc_type: biospecimen - type: aggregator - root: biospecimen - props: - - name: project_id - - name: submitter_id - - name: biospecimen_anatomic_site - - name: biospecimen_type - - name: blood_tube_type - - name: days_to_collection - - name: days_to_procurement - - name: method_of_procurement - - name: procured_or_purchased - - name: tissue_type - - name: disease_type - - name: shipping_temperature - - name: tumor_code - - name: tumor_morphology - - name: days_to_collection_other - - name: days_to_procurement_other - - name: biospecimen_volume - - name: blood_draw_method - - name: clinical_site - - name: primary_site - - name: tumor_descriptor - - name: procurement_temperature - - name: metastatic_bone - - name: metastatic_visceral - - name: metastatic_lymph_node - - name: biospecimen_weight - flatten_props: - - path: samples - props: - - name: composition - - name: hours_to_fractionation_lower - - name: hours_to_fractionation_upper - - name: blood_fractionation_method - - name: sample_volume - - name: storage_agitation - - name: storage_agitation_hours - sorted_by: updated_datetime, desc - - name: jenkins-blood.planx-pla.net_aliquot - doc_type: aliquot - type: aggregator - root: aliquot - props: - - name: project_id - - name: submitter_id - - name: aliquot_container - - name: clinical_or_contrived - - name: preservation_method - - name: storage_temperature - - name: aliquot_volume - - name: methanol_added - - name: hours_to_freezer_lower - - name: hours_to_freezer_lower_other - - name: hours_to_freezer_upper - - name: hours_to_freezer_upper_other - - name: aliquot_quantity - - name: contrivance_method - flatten_props: - - path: analytes - props: - - name: analyte_isolation_method - - name: analyte_type - - name: cell_type - - name: cell_identifier - - name: frame_identifier - - name: run_identifier - - name: days_to_assay - sorted_by: updated_datetime, desc - - name: jenkins-blood.planx-pla.net_read_group - doc_type: read_group - type: aggregator - root: read_group - props: - - name: project_id - - name: submitter_id - - name: instrument_model - - name: is_paired_end - - name: library_preparation_kit_name - - name: library_preparation_kit_vendor - - name: library_preparation_kit_version - - name: library_strategy - - name: platform - - name: read_group_name - - name: read_length_lower - - name: read_length_upper - - name: barcoding_applied - - name: target_capture_kit_name - - name: library_name - - name: library_selection - - name: sequencing_center - - name: library_strand - - name: flow_cell_barcode - - name: adapter_sequence - - name: library_preparation_kit_catalog_number - - name: cycles - - name: jenkins-blood.planx-pla.net_medical_history - doc_type: medical_history - type: aggregator - root: case - props: - - name: project_id - - name: submitter_id - flatten_props: - - path: comorbidities - props: - - name: comorbidity - - name: days_to_comorbidity - sorted_by: updated_datetime, desc - - path: diagnoses - props: - - name: age_at_diagnosis - - name: best_overall_response - - name: classification_of_tumor - - name: days_to_best_overall_response - - name: days_to_diagnosis - - name: morphology - - name: primary_diagnosis - - name: prior_treatment - - name: tissue_or_organ_of_origin - - name: tumor_grade - - name: ajcc_clinical_stage - - name: overall_survival - - name: progression_free_survival - - name: ajcc_pathologic_stage - - name: method_of_diagnosis - - name: ajcc_pathologic_n - - name: ajcc_pathologic_t - - name: ajcc_pathologic_m - sorted_by: updated_datetime, desc - - path: diagnostic_tests - props: - - name: analyte_name - - name: days_to_test - - name: test_result - - name: test_sample_composition - - name: test_type - - name: test_units - - name: test_value - sorted_by: updated_datetime, desc - - path: followups - props: - - name: days_to_followup - - name: time_from_alcohol - - name: time_from_biopsy - - name: time_from_exercise - - name: time_from_food - - name: time_from_physical_trauma - - name: time_from_recreational_drugs - - name: time_from_tobacco - - name: time_from_treatment - sorted_by: updated_datetime, desc - - path: treatments - props: - - name: therapeutic_agents - - name: treatment_intent_type - - name: treatment_type - - name: days_to_treatment_start - - name: regimen_or_line_of_therapy - - name: days_to_treatment_end - - name: treatment_class - - name: dosage - - name: dosage_units - sorted_by: updated_datetime, desc - - name: jenkins-blood.planx-pla.net_publication - doc_type: publication - type: aggregator - root: publication - props: - - name: project_id - - name: accession_id - - name: title - - name: abstract - - name: authors - - name: author_affiliations - - name: journal - - name: publication_url - - name: data_availability_date - - name: data_description - - name: sponsors - - name: study_codes - - name: condition - - name: study_type - - name: websites + - name: data_category + src: data_category + fn: set + - name: file_count + src: _file_id + fn: count + parent_props: + - path: projects[project_code:code] + - path: projects[project_name:name] + - path: projects[project_dbgap_phs:dbgap_phs] + - path: projects[project_dbgap_consent_text:dbgap_consent_text] + - path: projects[project_short_name:short_name] + - path: projects[project_dbgap_accession_number:dbgap_accession_number] - name: jenkins-blood.planx-pla.net_file doc_type: file type: collector root: None category: data_file props: + - name: project_id - name: submitter_id - name: object_id - name: md5sum @@ -341,11 +112,53 @@ mappings: - name: file_size - name: data_format - name: data_type - - name: data_category - name: state + - name: data_category + - name: analyte_type + - name: sequencing_assay + - name: source_node injecting_props: - case: + subject: props: - - name: _case_id + - name: _subject_id src: id - - name: project_id + fn: set + - name: subject_submitter_id + src: submitter_id + fn: set + - name: anvil_project_id + src: anvil_project_id + fn: set + - name: sex + src: sex + fn: set + - name: age_value + src: age_value + fn: set + - name: ancestry + src: ancestry + fn: set + - name: disease_description + src: disease_description + fn: set + - name: phenotype_present + src: phenotype_present + fn: set + - name: phenotype_absent + src: phenotype_absent + fn: set + - name: disease_id + src: disease_id + fn: set + - name: solve_state + src: solve_state + fn: set + - name: congenital_status + src: congenital_status + fn: set + - name: age_of_onset + src: age_of_onset + fn: set + - name: phenotype_group + src: phenotype_group + fn: set diff --git a/jenkins-blood.planx-pla.net/manifest.json b/jenkins-blood.planx-pla.net/manifest.json index 1ed364ef9..5c189c89b 100644 --- a/jenkins-blood.planx-pla.net/manifest.json +++ b/jenkins-blood.planx-pla.net/manifest.json @@ -277,7 +277,7 @@ "environment": "qaplanetv1", "hostname": "jenkins-blood.planx-pla.net", "revproxy_arn": "arn:aws:acm:us-east-1:707767160287:certificate/c676c81c-9546-4e9a-9a72-725dd3912bc8", - "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/bpadictionary/master/schema.json", + "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/anvil/master/schema.json", "portal_app": "gitops", "kube_bucket": "kube-qaplanetv1-gen3", "logs_bucket": "logs-qaplanetv1-gen3", @@ -298,7 +298,7 @@ "guppy": { "indices": [ { - "index": "jenkins_subject_alias", + "index": "jenkins_subject_new_alias", "type": "subject" }, { diff --git a/jenkins-blood.planx-pla.net/portal/gitops.json b/jenkins-blood.planx-pla.net/portal/gitops.json index d92a1d1be..a83685657 100644 --- a/jenkins-blood.planx-pla.net/portal/gitops.json +++ b/jenkins-blood.planx-pla.net/portal/gitops.json @@ -2,37 +2,9 @@ "gaTrackingId": "UA-119127212-2", "argoTemplate": "gwas-template", "graphql": { - "boardCounts": [{ - "graphql": "_study_count", - "name": "Study", - "plural": "Studies" - }, - { - "graphql": "_case_count", - "name": "Case", - "plural": "Cases" - }, - { - "graphql": "_aliquot_count", - "name": "Aliquot", - "plural": "Aliquots" - } + "boardCounts": [ ], - "chartCounts": [{ - "graphql": "_study_count", - "name": "Study", - "plural": "Studies" - }, - { - "graphql": "_case_count", - "name": "Case", - "plural": "Cases" - }, - { - "graphql": "_aliquot_count", - "name": "Aliquot", - "plural": "Aliquots" - } + "chartCounts": [ ], "projectDetails": "boardCounts" }, @@ -75,16 +47,8 @@ "link": "/submission" }, "homepageChartNodes": [{ - "node": "study", - "name": "Studies" - }, - { - "node": "case", - "name": "Cases" - }, - { - "node": "aliquot", - "name": "Aliquots" + "node": "subject", + "name": "Subjects" } ], "buttons": [{ @@ -589,22 +553,19 @@ }, "studyViewerConfig": [ { - "dataType": "clinical_trials", + "dataType": "subject", "title": "Studies", - "titleField": "title", - "rowAccessor": "cmc_unique_id", + "titleField": "project_id", + "rowAccessor": "submitter_id", "listItemConfig": { - "blockFields": ["brief_summary"], - "tableFields": ["data_availability_date", "data_available", "creator", "nct_number", "condition", "category", "clinical_trial_website", "publications"] + "blockFields": ["project_id"], + "tableFields": ["data_type"] }, "fieldMapping": [ - { "field": "brief_summary", "name": "Brief Study Description" }, - { "field": "description", "name": "Detailed Description"}, - { "field": "creator", "name": "Sponsor"}, { "field": "category", "name": "Study Type"}, - { "field": "clinical_trial_website", "name": "Websites"}, - { "field": "nct_number", "name": "NCT Number"}, - { "field": "publications", "name": "Study Publications"} + { "field": "project_id", "name": "Project_ID"}, + { "field": "data_type", "name": "Data_Type"}, + { "field": "condition", "name": "Condition"} ], "openMode": "close-all", "buttons": [ @@ -619,34 +580,20 @@ }] } ], - "explorerConfig": [{ - "tabTitle": "Studies", + "dataExplorerConfig": { "charts": { "project_id": { "chartType": "count", "title": "Projects" - }, - "study_setup": { - "chartType": "bar", - "title": "Study Setup" - }, - "study_objective": { - "chartType": "bar", - "title": "Study Objective" - }, - "study_design": { - "chartType": "bar", - "title": "Study Design" } }, "filters": { "tabs": [{ - "title": "Studies", + "title": "Project", "fields": [ "project_id", - "study_setup", - "study_objective", - "study_design" + "data_type", + "data_format" ] }] }, @@ -654,149 +601,15 @@ "enabled": true, "fields": [ "project_id", - "submitter_id", - "study_description", - "data_description", - "study_setup", - "study_objective", - "study_design", - "associated_study", - "_cases_count", - "_biospecimens_count", - "_samples_count", - "_aliquots_count", - "_analytes_count", - "_immunoassays_count", - "_pcr_assays_count", - "_pcr_assay_files_count", - "_read_groups_count", - "_cell_images_count", - "_mass_cytometry_assays_count", - "_mass_cytometry_images_count", - "_slide_images_count", - "_submitted_unaligned_reads_files_count", - "_submitted_aligned_reads_files_count", - "_submitted_somatic_mutations_count", - "_submitted_methylations_count" + "data_format" ] }, - "buttons": [{ - "enabled": true, - "type": "data", - "title": "Download Studies", - "leftIcon": "user", - "rightIcon": "download", - "fileName": "studies.json" - }, + "buttons": [ { - "enabled": false, - "type": "manifest", - "title": "Download Manifest", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "manifest.json" - }, - { - "enabled": true, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" - }, - { - "enabled": true, - "type": "export-to-pfb", - "title": "Export to PFB", - "leftIcon": "datafile", - "rightIcon": "download" - } - ], - "guppyConfig": { - "dataType": "study", - "nodeCountTitle": "Studies", - "fieldMapping": [], - "manifestMapping": { - "resourceIndexType": "file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "_case_id", - "referenceIdFieldInDataIndex": "_case_id" - }, - "accessibleFieldCheckList": ["project_id"], - "accessibleValidationField": "project_id" - } - }, - { - "tabTitle": "Cases", - "charts": { - "project_id": { - "chartType": "count", - "title": "Projects" - }, - "gender": { - "chartType": "pie", - "title": "Gender" - }, - "race": { - "chartType": "bar", - "title": "Race" - }, - "ethnicity": { - "chartType": "bar", - "title": "Ethnicity" - } - }, - "filters": { - "tabs": [{ - "title": "Cases", - "fields": [ - "project_id", - "index_date", - "lost_to_followup", - "gender", - "days_to_birth", - "race", - "ethnicity" - ] - }] - }, - "table": { - "enabled": true, - "fields": [ - "project_id", - "submitter_id", - "index_date", - "lost_to_followup", - "gender", - "days_to_birth", - "race", - "ethnicity", - "data_format", - "data_type", - "_biospecimens_count", - "_samples_count", - "_aliquots_count", - "_analytes_count", - "_immunoassays_count", - "_pcr_assays_count", - "_pcr_assay_files_count", - "_read_groups_count", - "_cell_images_count", - "_mass_cytometry_assays_count", - "_mass_cytometry_images_count", - "_slide_images_count", - "_submitted_unaligned_reads_files_count", - "_submitted_aligned_reads_files_count", - "_submitted_somatic_mutations_count", - "_submitted_methylations_count" - ] - }, - "buttons": [{ "enabled": true, - "type": "data-tsv", - "title": "Download Case Metadata", - "leftIcon": "user", - "rightIcon": "download", - "fileName": "BloodPAC_cases.tsv" + "type": "export", + "title": "Export All to Terra", + "rightIcon": "external-link" }, { "enabled": false, @@ -819,580 +632,23 @@ "title": "Export to PFB", "leftIcon": "datafile", "rightIcon": "download" - } - ], - "guppyConfig": { - "dataType": "case", - "nodeCountTitle": "Cases", - "fieldMapping": [], - "manifestMapping": { - "resourceIndexType": "file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "case_id", - "referenceIdFieldInDataIndex": "case_id" - }, - "accessibleFieldCheckList": ["project_id"], - "accessibleValidationField": "project_id" - } - }, - { - "tabTitle": "Biospecimens", - "charts": { - "project_id": { - "chartType": "count", - "title": "Projects" - }, - "biospecimen_anatomic_site": { - "chartType": "bar", - "title": "Anatomic Site" - }, - "biospecimen_type": { - "chartType": "pie", - "title": "Biospecimen Type" - }, - "blood_tube_type": { - "chartType": "bar", - "title": "Blood Tube Type" - } - }, - "filters": { - "tabs": [{ - "title": "Biospecimens", - "fields": [ - "project_id", - "biospecimen_anatomic_site", - "biospecimen_type", - "blood_tube_type", - "days_to_collection", - "days_to_procurement", - "method_of_procurement", - "procured_or_purchased", - "tissue_type", - "disease_type", - "shipping_temperature", - "tumor_code", - "tumor_morphology", - "days_to_collection_other", - "days_to_procurement_other", - "biospecimen_volume", - "blood_draw_method", - "clinical_site", - "primary_site", - "tumor_descriptor", - "procurement_temperature", - "metastatic_bone", - "metastatic_visceral", - "metastatic_lymph_node", - "biospecimen_weight" - ] - }, - { - "title": "Samples", - "fields": [ - "composition", - "hours_to_fractionation_lower", - "hours_to_fractionation_upper", - "blood_fractionation_method", - "sample_volume", - "storage_agitation", - "storage_agitation_hours" - ] - } - ] - }, - "table": { - "enabled": true, - "fields": [ - "project_id", - "submitter_id", - "biospecimen_anatomic_site", - "biospecimen_type", - "blood_tube_type", - "days_to_collection", - "days_to_procurement", - "method_of_procurement", - "procured_or_purchased", - "tissue_type", - "disease_type", - "shipping_temperature", - "tumor_code", - "tumor_morphology", - "days_to_collection_other", - "days_to_procurement_other", - "biospecimen_volume", - "blood_draw_method", - "clinical_site", - "primary_site", - "tumor_descriptor", - "procurement_temperature", - "metastatic_bone", - "metastatic_visceral", - "metastatic_lymph_node", - "biospecimen_weight", - "composition", - "hours_to_fractionation_lower", - "hours_to_fractionation_upper", - "blood_fractionation_method", - "sample_volume", - "storage_agitation", - "storage_agitation_hours" - ] - }, - "buttons": [{ - "enabled": true, - "type": "data-tsv", - "title": "Download Biospecimen Metadata", - "leftIcon": "user", - "rightIcon": "download", - "fileName": "BloodPAC_biospecimens.tsv" - }, - { - "enabled": false, - "type": "manifest", - "title": "Download Manifest", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "manifest.json" - }, - { - "enabled": true, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" - } - ], - "guppyConfig": { - "dataType": "biospecimen", - "nodeCountTitle": "Biospecimens", - "fieldMapping": [], - "manifestMapping": { - "resourceIndexType": "file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "case_id", - "referenceIdFieldInDataIndex": "case_id" - }, - "accessibleFieldCheckList": ["project_id"], - "accessibleValidationField": "project_id" - } - }, - { - "tabTitle": "Aliquots", - "charts": { - "aliquot_container": { - "chartType": "bar", - "title": "Aliquot Container" - }, - "clinical_or_contrived": { - "chartType": "pie", - "title": "Clinical vs. Contrived" - }, - "analyte_type": { - "chartType": "bar", - "title": "Analyte Type" - } - }, - "filters": { - "tabs": [{ - "title": "Aliquots", - "fields": [ - "project_id", - "aliquot_container", - "clinical_or_contrived", - "preservation_method", - "storage_temperature", - "aliquot_volume", - "methanol_added", - "hours_to_freezer_lower", - "hours_to_freezer_lower_other", - "hours_to_freezer_upper", - "hours_to_freezer_upper_other", - "aliquot_quantity", - "contrivance_method" - ] - }, - { - "title": "Analytes", - "fields": [ - "analyte_isolation_method", - "analyte_type", - "cell_type", - "cell_identifier", - "frame_identifier", - "run_identifier", - "days_to_assay" - ] - } - ] - }, - "table": { - "enabled": true, - "fields": [ - "project_id", - "submitter_id", - "aliquot_container", - "clinical_or_contrived", - "preservation_method", - "storage_temperature", - "aliquot_volume", - "methanol_added", - "hours_to_freezer_lower", - "hours_to_freezer_lower_other", - "hours_to_freezer_upper", - "hours_to_freezer_upper_other", - "aliquot_quantity", - "contrivance_method", - "analyte_isolation_method", - "analyte_type", - "cell_type", - "cell_identifier", - "frame_identifier", - "run_identifier", - "days_to_assay" - ] - }, - "buttons": [{ - "enabled": true, - "type": "data-tsv", - "title": "Download Aliquot Metadata", - "leftIcon": "user", - "rightIcon": "download", - "fileName": "aliquots.tsv" - }, - { - "enabled": false, - "type": "manifest", - "title": "Download Manifest", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "manifest.json" - }, - { - "enabled": true, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" - } - ], - "guppyConfig": { - "dataType": "aliquot", - "nodeCountTitle": "Aliquots", - "fieldMapping": [], - "manifestMapping": { - "resourceIndexType": "file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "case_id", - "referenceIdFieldInDataIndex": "case_id" - }, - "accessibleFieldCheckList": ["project_id"], - "accessibleValidationField": "project_id" - } - }, - { - "tabTitle": "Read Groups", - "charts": { - "instrument_model": { - "chartType": "bar", - "title": "Instrument Model" - }, - "library_preparation_kit_name": { - "chartType": "bar", - "title": "Library Prep Kit" - }, - "library_strategy": { - "chartType": "bar", - "title": "Library Strategy" - }, - "platform": { - "chartType": "bar", - "title": "Platform" - } - }, - "filters": { - "tabs": [{ - "title": "Read Groups", - "fields": [ - "project_id", - "instrument_model", - "is_paired_end", - "library_preparation_kit_name", - "library_preparation_kit_vendor", - "library_preparation_kit_version", - "library_strategy", - "platform", - "read_group_name", - "read_length_lower", - "read_length_upper", - "barcoding_applied", - "target_capture_kit_name", - "library_name", - "library_selection", - "sequencing_center", - "library_strand", - "flow_cell_barcode", - "adapter_sequence", - "library_preparation_kit_catalog_number", - "cycles" - ] - }] - }, - "table": { - "enabled": true, - "fields": [ - "project_id", - "submitter_id", - "instrument_model", - "is_paired_end", - "library_preparation_kit_name", - "library_preparation_kit_vendor", - "library_preparation_kit_version", - "library_strategy", - "platform", - "read_group_name", - "read_length_lower", - "read_length_upper", - "barcoding_applied", - "target_capture_kit_name", - "library_name", - "library_selection", - "sequencing_center", - "library_strand", - "flow_cell_barcode", - "adapter_sequence", - "library_preparation_kit_catalog_number", - "cycles" - ] - }, - "buttons": [{ - "enabled": true, - "type": "data-tsv", - "title": "Download Read Group Metadata", - "leftIcon": "user", - "rightIcon": "download", - "fileName": "BloodPAC_read_groups.tsv" - }, - { - "enabled": false, - "type": "manifest", - "title": "Download Manifest", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "manifest.json" - }, - { - "enabled": true, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" - } - ], - "guppyConfig": { - "dataType": "read_group", - "nodeCountTitle": "Read Groups", - "fieldMapping": [], - "manifestMapping": { - "resourceIndexType": "file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "case_id", - "referenceIdFieldInDataIndex": "case_id" - }, - "accessibleFieldCheckList": ["project_id"], - "accessibleValidationField": "project_id" - } - }, - { - "tabTitle": "Medical History", - "charts": { - "primary_diagnosis": { - "chartType": "bar", - "title": "Primary Diagnoses" - }, - "comorbidity": { - "chartType": "bar", - "title": "Comorbidities" - }, - "analyte_name": { - "chartType": "bar", - "title": "Diagnostic Tests" - }, - "therapeutic_agents": { - "chartType": "bar", - "title": "Treatments" - } - }, - "filters": { - "tabs": [{ - "title": "Projects", - "fields": [ - "project_id" - ] - }, - { - "title": "Comorbidities", - "fields": [ - "comorbidity", - "days_to_comorbidity" - ] - }, - { - "title": "Diagnoses", - "fields": [ - "age_at_diagnosis", - "best_overall_response", - "classification_of_tumor", - "days_to_best_overall_response", - "days_to_diagnosis", - "morphology", - "primary_diagnosis", - "prior_treatment", - "tissue_or_organ_of_origin", - "tumor_grade", - "ajcc_clinical_stage", - "overall_survival", - "progression_free_survival", - "ajcc_pathologic_stage", - "method_of_diagnosis", - "ajcc_pathologic_n", - "ajcc_pathologic_t", - "ajcc_pathologic_m" - ] - }, - { - "title": "Diagnostic Tests", - "fields": [ - "analyte_name", - "days_to_test", - "test_result", - "test_sample_composition", - "test_type", - "test_units", - "test_value" - ] - }, - { - "title": "Followups", - "fields": [ - "days_to_followup", - "time_from_alcohol", - "time_from_biopsy", - "time_from_exercise", - "time_from_food", - "time_from_physical_trauma", - "time_from_recreational_drugs", - "time_from_tobacco", - "time_from_treatment" - ] - }, - { - "title": "Treatments", - "fields": [ - "therapeutic_agents", - "treatment_intent_type", - "treatment_type", - "days_to_treatment_start", - "regimen_or_line_of_therapy", - "days_to_treatment_end", - "treatment_class", - "dosage", - "dosage_units" - ] - } - ] - }, - "table": { - "enabled": true, - "fields": [ - "project_id", - "submitter_id", - "comorbidity", - "days_to_comorbidity", - "age_at_diagnosis", - "best_overall_response", - "classification_of_tumor", - "days_to_best_overall_response", - "days_to_diagnosis", - "morphology", - "primary_diagnosis", - "prior_treatment", - "tissue_or_organ_of_origin", - "tumor_grade", - "ajcc_clinical_stage", - "overall_survival", - "progression_free_survival", - "ajcc_pathologic_stage", - "method_of_diagnosis", - "ajcc_pathologic_n", - "ajcc_pathologic_t", - "ajcc_pathologic_m", - "analyte_name", - "days_to_test", - "test_result", - "test_sample_composition", - "test_type", - "test_units", - "test_value", - "days_to_followup", - "time_from_alcohol", - "time_from_biopsy", - "time_from_exercise", - "time_from_food", - "time_from_physical_trauma", - "time_from_recreational_drugs", - "time_from_tobacco", - "time_from_treatment", - "therapeutic_agents", - "treatment_intent_type", - "treatment_type", - "days_to_treatment_start", - "regimen_or_line_of_therapy", - "days_to_treatment_end", - "treatment_class", - "dosage", - "dosage_units" - ] - }, - "buttons": [{ - "enabled": true, - "type": "data-tsv", - "title": "Download Medical History", - "leftIcon": "user", - "rightIcon": "download", - "fileName": "medical_history.tsv" - }, - { - "enabled": false, - "type": "manifest", - "title": "Download Manifest", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "manifest.json" - }, - { - "enabled": true, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" } ], "guppyConfig": { - "dataType": "medical_history", - "nodeCountTitle": "Medical History", + "dataType": "subject", + "nodeCountTitle": "Subjects", "fieldMapping": [], "manifestMapping": { "resourceIndexType": "file", "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "case_id", - "referenceIdFieldInDataIndex": "case_id" + "referenceIdFieldInResourceIndex": "_subject_id", + "referenceIdFieldInDataIndex": "_subject_id" }, "accessibleFieldCheckList": ["project_id"], "accessibleValidationField": "project_id" } }, - { - "tabTitle": "Files", + "fileExplorerConfig": { "charts": { "data_type": { "chartType": "stackedBar", @@ -1404,14 +660,20 @@ } }, "filters": { - "tabs": [{ - "title": "File", - "fields": [ - "project_id", - "data_type", - "data_format" - ] - }] + "tabs": [ + { + "title": "File", + "fields": [ + "project_id", + "data_category", + "data_type", + "data_format" + ], + "searchFields": [ + "file_name" + ] + } + ] }, "table": { "enabled": true, @@ -1419,27 +681,35 @@ "project_id", "file_name", "file_size", - "object_id" - ] + "object_id" ] }, "guppyConfig": { "dataType": "file", - "fieldMapping": [{ - "field": "object_id", - "name": "GUID" - }], + "fieldMapping": [ + { + "field": "object_id", + "name": "GUID" + }, + { + "field": "programs_name", + "name": "Program" + } + ], "nodeCountTitle": "Files", "manifestMapping": { - "resourceIndexType": "case", - "resourceIdField": "case_id", + "resourceIndexType": "subject", + "resourceIdField": "_subject_id", "referenceIdFieldInResourceIndex": "object_id", "referenceIdFieldInDataIndex": "object_id" }, - "accessibleFieldCheckList": ["project_id"], + "accessibleFieldCheckList": [ + "project_id" + ], "accessibleValidationField": "project_id", "downloadAccessor": "object_id" }, - "buttons": [{ + "buttons": [ + { "enabled": true, "type": "file-manifest", "title": "Download Manifest", @@ -1454,9 +724,35 @@ "title": "Export to Workspace", "leftIcon": "datafile", "rightIcon": "download" + }, + { + "enabled": true, + "type": "export-files-to-pfb", + "title": "Export All to PFB", + "rightIcon": "external-link" + }, + { + "enabled": true, + "type": "export-files", + "title": "Export All to Terra", + "rightIcon": "external-link" + }, + { + "enabled": true, + "type": "export-files-to-seven-bridges", + "title": "Export All to Seven Bridges", + "rightIcon": "external-link" } ], + "terraExportURL": "https://terra.biodatacatalyst.nhlbi.nih.gov/#import-data", + "terraTemplate": [ + "bdc", + "gen3" + ], + "sevenBridgesExportURL": "https://platform.sb.biodatacatalyst.nhlbi.nih.gov/import/windmill", + "enableLimitedFilePFBExport": { + "sourceNodeField": "source_node" + }, "dropdowns": {} } - ] } diff --git a/jenkins-brain.planx-pla.net/etlMapping.yaml b/jenkins-brain.planx-pla.net/etlMapping.yaml index cacdef457..59fb89402 100644 --- a/jenkins-brain.planx-pla.net/etlMapping.yaml +++ b/jenkins-brain.planx-pla.net/etlMapping.yaml @@ -1,183 +1,82 @@ mappings: - - name: jenkins-brain.planx-pla.net_case - doc_type: case + - name: jenkins-brain.planx-pla.net_subject + doc_type: subject type: aggregator - root: case + root: subject props: - name: submitter_id - name: project_id - - name: gender - - name: ethnicity - - name: race - - name: age_at_enrollment - - name: experimental_group + - name: sex + - name: age_value + - name: ancestry + - name: disease_description + - name: phenotype_present + - name: phenotype_absent + - name: disease_id + - name: solve_state + - name: congenital_status + - name: age_of_onset + - name: phenotype_group + - name: anvil_project_id +# flatten_props: aggregated_props: - - name: education_years - path: demographics - src: education_years - fn: max - - name: age_at_onset - path: diagnoses - src: age_at_onset - fn: min - - name: mds_updrs - value_mappings: - - uploaded: MDS-UPDRS - - md5summed: MDS-UPDRS - - validating: MDS-UPDRS - - validated: MDS-UPDRS - - released: MDS-UPDRS - path: mds_unified_pd_ratings - src: state - fn: set - - name: unified_parkinsons_disease_ratings - value_mappings: - - uploaded: UPDRS - - md5summed: UPDRS - - validating: UPDRS - - validated: UPDRS - - released: UPDRS - path: unified_parkinsons_disease_ratings - src: state - fn: set - - name: hopkins_verbal_learning_tests - value_mappings: - - uploaded: HVLT-R - - md5summed: HVLT-R - - validating: HVLT-R - - validated: HVLT-R - - released: HVLT-R - path: hopkins_verbal_learning_tests - src: state + - name: sample_provider + path: samples + src: sample_provider fn: set - - name: scales_for_outcomes_in_pds - value_mappings: - - uploaded: Scales for Outcomes in Parkinson’s Disease - Autonomic - - md5summed: Scales for Outcomes in Parkinson’s Disease - Autonomic - - validating: Scales for Outcomes in Parkinson’s Disease - Autonomic - - validated: Scales for Outcomes in Parkinson’s Disease - Autonomic - - released: Scales for Outcomes in Parkinson’s Disease - Autonomic - path: scales_for_outcomes_in_pds - src: state + - name: tissue_affected_status + path: samples + src: tissue_affected_status fn: set - - name: modified_schwab_england_scales - value_mappings: - - uploaded: Modified Schwab - - md5summed: Modified Schwab - - validating: Modified Schwab - - validated: Modified Schwab - - released: Modified Schwab - path: modified_schwab_england_scales - src: state + - name: tissue_type + path: samples + src: tissue_type fn: set - - name: baseline_dyspnea_indexes - value_mappings: - - uploaded: BDI - - md5summed: BDI - - validating: BDI - - validated: BDI - - released: BDI - path: baseline_dyspnea_indexes - src: state + - name: sample_type + path: samples + src: sample_type fn: set - - name: hamilton_depression_ratings - value_mappings: - - uploaded: Hamilton - - md5summed: Hamilton - - validating: Hamilton - - validated: Hamilton - - released: Hamilton - path: hamilton_depression_ratings - src: state + - name: original_material_type + path: samples + src: original_material_type fn: set - - name: state_trait_anxiety_inventories - value_mappings: - - uploaded: Anxiety – State-Trait Anxiety Inventory (STAI) - - md5summed: Anxiety – State-Trait Anxiety Inventory (STAI) - - validating: Anxiety – State-Trait Anxiety Inventory (STAI) - - validated: Anxiety – State-Trait Anxiety Inventory (STAI) - - released: Anxiety – State-Trait Anxiety Inventory (STAI) - path: state_trait_anxiety_inventories - src: state + - name: exome_capture_platform + path: samples.sequencings + src: exome_capture_platform fn: set - - name: upenn_smell_tests - value_mappings: - - uploaded: UPSIT - - md5summed: UPSIT - - validating: UPSIT - - validated: UPSIT - - released: UPSIT - path: upenn_smell_tests - src: state + - name: library_prep_kit_method + path: samples.sequencings + src: library_prep_kit_method fn: set - - name: geriatric_depression_scales - value_mappings: - - uploaded: Geriatric Depression Scale Short Form Questionnaire - - md5summed: Geriatric Depression Scale Short Form Questionnaire - - validating: Geriatric Depression Scale Short Form Questionnaire - - validated: Geriatric Depression Scale Short Form Questionnaire - - released: Geriatric Depression Scale Short Form Questionnaire - path: geriatric_depression_scales - src: state + - name: capture_region_bed_file + path: samples.sequencings + src: capture_region_bed_file fn: set - - name: montreal_cognitive_functional_tests - value_mappings: - - uploaded: MOCA - - md5summed: MOCA - - validating: MOCA - - validated: MOCA - - released: MOCA - path: montreal_cognitive_functional_tests - src: state + - name: reference_genome_build + path: samples.sequencings + src: reference_genome_build fn: set - - name: mini_mental_status_exams - value_mappings: - - uploaded: MMSE - - md5summed: MMSE - - validating: MMSE - - validated: MMSE - - released: MMSE - path: mini_mental_status_exams - src: state + - name: sequencing_assay + path: samples.sequencings + src: sequencing_assay fn: set - - name: rem_sleep_behaviors - value_mappings: - - uploaded: REM Sleep Behavior Disorder Questionnaire - - md5summed: REM Sleep Behavior Disorder Questionnaire - - validating: REM Sleep Behavior Disorder Questionnaire - - validated: REM Sleep Behavior Disorder Questionnaire - - released: REM Sleep Behavior Disorder Questionnaire - path: rem_sleep_behaviors - src: state + - name: alignment_method + path: samples.sequencings + src: alignment_method fn: set - - name: epworth_sleepiness_scales - value_mappings: - - uploaded: Epworth Sleepiness Scale - - md5summed: Epworth Sleepiness Scale - - validating: Epworth Sleepiness Scale - - validated: Epworth Sleepiness Scale - - released: Epworth Sleepiness Scale - path: epworth_sleepiness_scales - src: state + - name: data_processing_pipeline + path: samples.sequencings + src: data_processing_pipeline fn: set - name: _samples_count path: samples fn: count - - name: _aliquots_count - path: samples.aliquots - fn: count - - name: _read_group_count - path: samples.aliquots.read_groups - fn: count - - name: _submitted_expression_arrays_count - path: samples.aliquots.submitted_expression_array_files - fn: count - - name: _submitted_unaligned_reads_count - path: samples.aliquots.read_groups.submitted_unaligned_reads_files + - name: _sequencings_count + path: samples.sequencings fn: count joining_props: - index: file - join_on: _case_id + join_on: _subject_id props: - name: data_format src: data_format @@ -185,12 +84,27 @@ mappings: - name: data_type src: data_type fn: set + - name: data_category + src: data_category + fn: set + - name: file_count + src: _file_id + fn: count + parent_props: + - path: projects[project_code:code] + - path: projects[project_name:name] + - path: projects[project_dbgap_phs:dbgap_phs] + - path: projects[project_dbgap_consent_text:dbgap_consent_text] + - path: projects[project_short_name:short_name] + - path: projects[project_dbgap_accession_number:dbgap_accession_number] - name: jenkins-brain.planx-pla.net_file doc_type: file type: collector root: None category: data_file props: + - name: project_id + - name: submitter_id - name: object_id - name: md5sum - name: file_name @@ -198,11 +112,52 @@ mappings: - name: data_format - name: data_type - name: state + - name: data_category + - name: analyte_type + - name: sequencing_assay + - name: source_node injecting_props: - case: + subject: props: - - name: _case_id + - name: _subject_id src: id fn: set - - name: project_id + - name: subject_submitter_id + src: submitter_id + fn: set + - name: anvil_project_id + src: anvil_project_id + fn: set + - name: sex + src: sex + fn: set + - name: age_value + src: age_value + fn: set + - name: ancestry + src: ancestry + fn: set + - name: disease_description + src: disease_description + fn: set + - name: phenotype_present + src: phenotype_present + fn: set + - name: phenotype_absent + src: phenotype_absent + fn: set + - name: disease_id + src: disease_id + fn: set + - name: solve_state + src: solve_state + fn: set + - name: congenital_status + src: congenital_status + fn: set + - name: age_of_onset + src: age_of_onset fn: set + - name: phenotype_group + src: phenotype_group + fn: set \ No newline at end of file diff --git a/jenkins-brain.planx-pla.net/manifest.json b/jenkins-brain.planx-pla.net/manifest.json index 96af36156..4f8a60fd0 100644 --- a/jenkins-brain.planx-pla.net/manifest.json +++ b/jenkins-brain.planx-pla.net/manifest.json @@ -274,7 +274,7 @@ "environment": "qaplanetv1", "hostname": "jenkins-brain.planx-pla.net", "revproxy_arn": "arn:aws:acm:us-east-1:707767160287:certificate/c676c81c-9546-4e9a-9a72-725dd3912bc8", - "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/bhcdictionary/master/schema.json", + "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/anvil/master/schema.json", "portal_app": "gitops", "kube_bucket": "kube-qaplanetv1-gen3", "logs_bucket": "logs-qaplanetv1-gen3", @@ -295,7 +295,7 @@ "guppy": { "indices": [ { - "index": "jenkins_subject_alias", + "index": "jenkins_subject_new_alias", "type": "subject" }, { diff --git a/jenkins-brain.planx-pla.net/portal/gitops.json b/jenkins-brain.planx-pla.net/portal/gitops.json index 41fa210b7..c2ab68a15 100644 --- a/jenkins-brain.planx-pla.net/portal/gitops.json +++ b/jenkins-brain.planx-pla.net/portal/gitops.json @@ -3,31 +3,8 @@ "argoTemplate": "gwas-template", "graphql": { "boardCounts": [ - { - "graphql": "_case_count", - "name": "Case", - "plural": "Cases" - }, - { - "graphql": "_study_count", - "name": "Study", - "plural": "Studies" - }, - { - "graphql": "_visit_count", - "name": "Visit", - "plural": "Visits" - } ], "chartCounts": [ - { - "graphql": "_case_count", - "name": "Case" - }, - { - "graphql": "_study_count", - "name": "Study" - } ], "projectDetails": "boardCounts" }, @@ -566,22 +543,19 @@ }, "studyViewerConfig": [ { - "dataType": "clinical_trials", + "dataType": "subject", "title": "Studies", - "titleField": "title", - "rowAccessor": "cmc_unique_id", + "titleField": "project_id", + "rowAccessor": "submitter_id", "listItemConfig": { - "blockFields": ["brief_summary"], - "tableFields": ["data_availability_date", "data_available", "creator", "nct_number", "condition", "category", "clinical_trial_website", "publications"] + "blockFields": ["project_id"], + "tableFields": ["data_type"] }, "fieldMapping": [ - { "field": "brief_summary", "name": "Brief Study Description" }, - { "field": "description", "name": "Detailed Description"}, - { "field": "creator", "name": "Sponsor"}, { "field": "category", "name": "Study Type"}, - { "field": "clinical_trial_website", "name": "Websites"}, - { "field": "nct_number", "name": "NCT Number"}, - { "field": "publications", "name": "Study Publications"} + { "field": "project_id", "name": "Project_ID"}, + { "field": "data_type", "name": "Data_Type"}, + { "field": "condition", "name": "Condition"} ], "openMode": "close-all", "buttons": [ @@ -601,61 +575,16 @@ "project_id": { "chartType": "count", "title": "Projects" - }, - "node_id": { - "chartType": "count", - "title": "Cases" - }, - "gender": { - "chartType": "pie", - "title": "Gender" - }, - "race": { - "chartType": "bar", - "title": "Race" - }, - "ethnicity": { - "chartType": "bar", - "title": "Ethnicity" } }, "filters": { "tabs": [ { - "title": "Study Selection", + "title": "Project", "fields": [ - "project_id" - ] - }, - { - "title": "Demographics", - "fields": [ - "gender", - "race", - "ethnicity", - "veteran_status", - "age_at_enrollment", - "age_at_onset", - "education_years" - ] - }, - { - "title": "Assessment", - "fields": [ - "unified_parkinsons_disease_ratings", - "mds_updrs", - "hopkins_verbal_learning_tests", - "scales_for_outcomes_in_pds", - "modified_schwab_england_scales", - "baseline_dyspnea_indexes", - "hamilton_depression_ratings", - "state_trait_anxiety_inventories", - "upenn_smell_tests", - "geriatric_depression_scales", - "montreal_cognitive_functional_tests", - "mini_mental_status_exams", - "rem_sleep_behaviors", - "epworth_sleepiness_scales" + "project_id", + "data_type", + "data_format" ] } ] @@ -664,44 +593,23 @@ "enabled": true, "fields": [ "project_id", - "submitter_id", - "gender", - "race", - "ethnicity", - "age_at_enrollment", - "age_at_onset", - "education_years" + "data_format" ] }, "guppyConfig": { - "dataType": "case", - "nodeCountTitle": "Cases", + "dataType": "subject", + "nodeCountTitle": "Subjects", "fieldMapping": [ - {"field": "unified_parkinsons_disease_ratings", "name": "UPDRS"}, - {"field": "mds_updrs", "name": "MDS-UPDRS"}, - {"field": "hopkins_verbal_learning_tests", "name": "HVLT-R"}, - {"field": "scales_for_outcomes_in_pds", "name": "Scales for Outcomes in Parkinson’s Disease – Autonomic"}, - {"field": "modified_schwab_england_scales", "name": "Modified Schwab"}, - {"field": "baseline_dyspnea_indexes", "name": "BDI"}, - {"field": "hamilton_depression_ratings", "name": "Hamilton"}, - {"field": "state_trait_anxiety_inventories", "name": "Anxiety – State-Trait Anxiety Inventory (STAI)"}, - {"field": "upenn_smell_tests", "name": "UPSIT"}, - {"field": "geriatric_depression_scales", "name": "Geriatric Depression Scale Short Form Questionnaire"}, - {"field": "montreal_cognitive_functional_tests", "name": "MOCA"}, - {"field": "mini_mental_status_exams", "name": "MMSE"}, - {"field": "rem_sleep_behaviors", "name": "REM Sleep Behavior Disorder Questionnaire"}, - {"field": "epworth_sleepiness_scales", "name": "Epworth Sleepiness Scale"}, - {"field": "_aliquots_count", "name": "Aliquots Count"}, - {"field": "_read_group_count", "name": "Read Groups Count"}, - {"field": "_samples_count", "name": "Samples Count"}, - {"field": "_submitted_expression_arrays_count", "name": "Submitted Expression Arrays Count"}, - {"field": "_submitted_unaligned_reads_count", "name": "Submitted Unaligned Reads Count"} + { + "field": "_subject_id", + "name": "Subject ID" + } ], "manifestMapping": { "resourceIndexType": "file", "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "_case_id", - "referenceIdFieldInDataIndex": "_case_id" + "referenceIdFieldInResourceIndex": "_subject_id", + "referenceIdFieldInDataIndex": "_subject_id" }, "accessibleFieldCheckList": ["project_id"], "accessibleValidationField": "project_id" @@ -756,6 +664,7 @@ "title": "File", "fields": [ "project_id", + "data_category", "data_type", "data_format" ] @@ -774,12 +683,13 @@ "guppyConfig": { "dataType": "file", "fieldMapping": [ - { "field": "object_id", "name": "GUID" } + { "field": "object_id", "name": "GUID" }, + { "field": "programs_name", "name": "Program" } ], "nodeCountTitle": "Files", "manifestMapping": { - "resourceIndexType": "case", - "resourceIdField": "case_id", + "resourceIndexType": "subject", + "resourceIdField": "_subject_id", "referenceIdFieldInResourceIndex": "object_id", "referenceIdFieldInDataIndex": "object_id" }, diff --git a/jenkins-dcp.planx-pla.net/etlMapping.yaml b/jenkins-dcp.planx-pla.net/etlMapping.yaml index a93d19f07..2abad9ea8 100644 --- a/jenkins-dcp.planx-pla.net/etlMapping.yaml +++ b/jenkins-dcp.planx-pla.net/etlMapping.yaml @@ -6,115 +6,74 @@ mappings: props: - name: submitter_id - name: project_id - - name: consent_codes - - name: geographic_site - flatten_props: - - path: demographics - props: - - name: age_at_index - - name: hispanic_subgroup - - name: subcohort - - name: weight_baseline - - name: bmi_baseline - - name: height_baseline - - path: medical_histories - props: - - name: diabetes - - name: hypertension - - name: cerebrovascular_disease - - name: chronic_respiratory_disease - - name: coronary_artery_disease - - name: asthma - - name: cabg_presence - - name: copd - - name: emphysema - - name: heart_failure - - name: myocardial_infarction - - name: stroke - - name: cac_score - - name: cac_volume - - name: carotid_plaque - - name: carotid_stenosis - - name: cimt_1 - - name: cimt_2 - - name: vte_case_status - - name: vte_followup_start_age - - name: vte_prior_history - - path: blood_pressure_test - props: - - name: bp_systolic - - name: bp_diastolic - sorted_by: updated_datetime, desc - - path: medication_records - props: - - name: hypertension_meds - - name: antihypertensive_meds - - name: fasting_lipids - - name: lipid_lowering_medication - - path: lab_results - props: - - name: lymphocyte_ncnc_bld - - name: mch_entmass_rbc - - name: mcv_entvol_rbc - - name: mchc_mcnc_rbc - - name: monocyte_ncnc_bld - - name: neutrophil_ncnc_bld - - name: pmv_entvol_bld - - name: rbc_ncnc_bld - - name: rdw_ratio_rbc - - name: hemoglobin_mcnc_bld - - name: platelet_ncnc_bld - - name: hematocrit_vfr_bld - - name: wbc_ncnc_bld - - name: basophil_ncnc_bld - - name: eosinophil_ncnc_bld - - name: unit_triglycerides - - name: hdl - - name: ldl - - name: triglycerides - - name: total_cholesterol + - name: sex + - name: age_value + - name: ancestry + - name: disease_description + - name: phenotype_present + - name: phenotype_absent + - name: disease_id + - name: solve_state + - name: congenital_status + - name: age_of_onset + - name: phenotype_group + - name: anvil_project_id +# flatten_props: aggregated_props: - - name: annotated_sex - path: demographics - src: annotated_sex + - name: sample_provider + path: samples + src: sample_provider + fn: set + - name: tissue_affected_status + path: samples + src: tissue_affected_status + fn: set + - name: tissue_type + path: samples + src: tissue_type + fn: set + - name: sample_type + path: samples + src: sample_type + fn: set + - name: original_material_type + path: samples + src: original_material_type + fn: set + - name: exome_capture_platform + path: samples.sequencings + src: exome_capture_platform + fn: set + - name: library_prep_kit_method + path: samples.sequencings + src: library_prep_kit_method + fn: set + - name: capture_region_bed_file + path: samples.sequencings + src: capture_region_bed_file fn: set - - name: race - path: demographics - src: race + - name: reference_genome_build + path: samples.sequencings + src: reference_genome_build fn: set - - name: ethnicity - path: demographics - src: ethnicity + - name: sequencing_assay + path: samples.sequencings + src: sequencing_assay + fn: set + - name: alignment_method + path: samples.sequencings + src: alignment_method + fn: set + - name: data_processing_pipeline + path: samples.sequencings + src: data_processing_pipeline fn: set - name: _samples_count path: samples fn: count - - name: _aliquots_count - path: samples.aliquots - fn: count - - name: _read_groups_count - path: samples.aliquots.read_groups - fn: count - - name: _submitted_unaligned_reads_files_count - path: samples.aliquots.read_groups.submitted_unaligned_reads_files - fn: count - - name: _submitted_aligned_reads_files_count - path: samples.aliquots.read_groups.submitted_aligned_reads_files + - name: _sequencings_count + path: samples.sequencings fn: count - - name: _simple_germline_variations_count - path: samples.aliquots.read_groups.simple_germline_variations - fn: count - - name: current_smoker_baseline - path: exposures - src: current_smoker_baseline - fn: set - - name: ever_smoker_baseline - path: exposures - src: ever_smoker_baseline - fn: set - parent_props: - - path: studies[studies_submitter_id:submitter_id].projects[code] - - path: studies[studies_submitter_id:submitter_id].projects[code].programs[programs_name:name] joining_props: - index: file join_on: _subject_id @@ -125,25 +84,37 @@ mappings: - name: data_type src: data_type fn: set + - name: data_category + src: data_category + fn: set - name: file_count src: _file_id fn: count + parent_props: + - path: projects[project_code:code] + - path: projects[project_name:name] + - path: projects[project_dbgap_phs:dbgap_phs] + - path: projects[project_dbgap_consent_text:dbgap_consent_text] + - path: projects[project_short_name:short_name] + - path: projects[project_dbgap_accession_number:dbgap_accession_number] - name: jenkins-dcp.planx-pla.net_file doc_type: file type: collector root: None category: data_file props: + - name: project_id + - name: submitter_id - name: object_id - name: md5sum - name: file_name - name: file_size - - name: data_category - name: data_format - name: data_type - name: state - - name: callset - - name: bucket_path + - name: data_category + - name: analyte_type + - name: sequencing_assay - name: source_node injecting_props: subject: @@ -151,9 +122,42 @@ mappings: - name: _subject_id src: id fn: set - - name: project_id - program: - props: - - name: programs_name - src: name + - name: subject_submitter_id + src: submitter_id + fn: set + - name: anvil_project_id + src: anvil_project_id + fn: set + - name: sex + src: sex + fn: set + - name: age_value + src: age_value + fn: set + - name: ancestry + src: ancestry + fn: set + - name: disease_description + src: disease_description + fn: set + - name: phenotype_present + src: phenotype_present + fn: set + - name: phenotype_absent + src: phenotype_absent + fn: set + - name: disease_id + src: disease_id + fn: set + - name: solve_state + src: solve_state + fn: set + - name: congenital_status + src: congenital_status + fn: set + - name: age_of_onset + src: age_of_onset fn: set + - name: phenotype_group + src: phenotype_group + fn: set \ No newline at end of file diff --git a/jenkins-dcp.planx-pla.net/manifest.json b/jenkins-dcp.planx-pla.net/manifest.json index 9cccac2f2..838b40828 100644 --- a/jenkins-dcp.planx-pla.net/manifest.json +++ b/jenkins-dcp.planx-pla.net/manifest.json @@ -270,7 +270,7 @@ "environment": "qaplanetv1", "hostname": "jenkins-dcp.planx-pla.net", "revproxy_arn": "arn:aws:acm:us-east-1:707767160287:certificate/c676c81c-9546-4e9a-9a72-725dd3912bc8", - "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/gtexdictionary/master/schema.json", + "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/anvil/master/schema.json", "portal_app": "gitops", "kube_bucket": "kube-qaplanetv1-gen3", "logs_bucket": "logs-qaplanetv1-gen3", @@ -291,7 +291,7 @@ "guppy": { "indices": [ { - "index": "jenkins_subject_alias", + "index": "jenkins_subject_new_alias", "type": "subject" }, { diff --git a/jenkins-dcp.planx-pla.net/portal/gitops.json b/jenkins-dcp.planx-pla.net/portal/gitops.json index 6f585b54c..6c2a745db 100644 --- a/jenkins-dcp.planx-pla.net/portal/gitops.json +++ b/jenkins-dcp.planx-pla.net/portal/gitops.json @@ -55,10 +55,6 @@ { "node": "subject", "name": "Subjects" - }, - { - "node": "study", - "name": "Studies" } ] }, @@ -575,16 +571,14 @@ "titleField": "project_id", "rowAccessor": "submitter_id", "listItemConfig": { - "blockFields": ["breed"], - "tableFields": ["data_type", "auth_resource_path", "disease_type"] + "blockFields": ["project_id"], + "tableFields": ["data_type"] }, "fieldMapping": [ - { "field": "breed", "name": "Breed" }, + { "field": "category", "name": "Category" }, { "field": "project_id", "name": "Project_ID"}, - { "field": "submitter_id", "name": "Submitter_ID"}, { "field": "data_type", "name": "Data_Type"}, - { "field": "auth_resource_path", "name": "Resource Path"}, - { "field": "disease_type", "name": "Disease"} + { "field": "condition", "name": "Condition"} ], "openMode": "close-all", "buttons": [ @@ -605,88 +599,60 @@ "chartType": "count", "title": "Projects" }, - "_subject_id": { - "chartType": "count", - "title": "Subjects" - }, - "annotated_sex": { + "sex": { "chartType": "pie", - "title": "Annotated Sex" + "title": "Sex" }, - "race": { + "ancestry": { "chartType": "bar", - "title": "Race" - }, - "fileCounts": false + "title": "Ancestry" + } }, "filters": { "tabs": [ { "title": "Project", "fields": [ - "programs_name", "project_id", - "consent_codes", - "studies_submitter_id", - "geographic_site", + "anvil_project_id", "data_type", "data_format" ] }, { "title": "Subject", - "searchFields": [ - "submitter_id" - ], + "fields":[ + "sex", + "ancestry", + "age_value", + "disease_description", + "phenotype_present", + "phenotype_absent", + "disease_id", + "solve_state", + "congenital_status", + "age_of_onset", + "phenotype_group" + ] + }, { + "title": "Sample", "fields": [ - "annotated_sex", - "race", - "ethnicity", - "hispanic_subgroup", - "subcohort", - "weight_baseline", - "bmi_baseline", - "height_baseline", - "current_smoker_baseline", - "ever_smoker_baseline" + "tissue_type", + "sample_type", + "original_material_type", + "sample_provider", + "tissue_affected_status" ] - }, - { - "title": "Harmonized Variables", + }, { + "title": "Sequencing", "fields": [ - "total_cholesterol", - "hdl", - "ldl", - "triglycerides", - "fasting_lipids", - "lipid_lowering_medication", - "cac_score", - "cac_volume", - "carotid_plaque", - "carotid_stenosis", - "cimt_1", - "cimt_2", - "bp_diastolic", - "bp_systolic", - "antihypertensive_meds", - "vte_case_status", - "vte_followup_start_age", - "vte_prior_history", - "basophil_ncnc_bld", - "eosinophil_ncnc_bld", - "hematocrit_vfr_bld", - "hemoglobin_mcnc_bld", - "lymphocyte_ncnc_bld", - "mch_entmass_rbc", - "mchc_mcnc_rbc", - "mcv_entvol_rbc", - "monocyte_ncnc_bld", - "neutrophil_ncnc_bld", - "platelet_ncnc_bld", - "pmv_entvol_bld", - "rbc_ncnc_bld", - "rdw_ratio_rbc", - "wbc_ncnc_bld" + "sequencing_assay", + "reference_genome_build", + "library_prep_kit_method", + "exome_capture_platform", + "capture_region_bed_file", + "alignment_method", + "data_processing_pipeline" ] } ] @@ -695,13 +661,13 @@ "enabled": true, "fields": [ "project_id", - "data_format", - "race", - "annotated_sex", - "ethnicity", - "bp_diastolic", - "hdl", - "ldl" + "anvil_project_id", + "ancestry", + "sex", + "age_value", + "phenotype_group", + "_samples_count", + "_sequencings_count" ] }, "dropdowns": { @@ -742,154 +708,11 @@ "nodeCountTitle": "Subjects", "fileCountField": "file_count", "fieldMapping": [ - { - "field": "_subject_id", - "name": "Subject ID" - }, - { - "field": "consent_codes", - "name": "data use restriction" - }, - { - "field": "cac_score", - "name": "CAC Score" - }, - { - "field": "cac_volume", - "name": "CAC Volume" - }, - { - "field": "cimt_1", - "name": "CIMT 1" - }, - { - "field": "cimt_2", - "name": "CIMT 2" - }, - { - "field": "vte_case_status", - "name": "VTE Case Status" - }, - { - "field": "vte_followup_start_age", - "name": "VTE Followup Start Age" - }, - { - "field": "vte_prior_history", - "name": "VTE Prior History" - }, - { - "field": "bp_diastolic", - "name": "BP Diastolic" - }, - { - "field": "bp_systolic", - "name": "BP Systolic" - }, - { - "field": "basophil_ncnc_bld", - "name": "Basophils Number Concentration Bld" - }, - { - "field": "eosinophil_ncnc_bld", - "name": "Eosinophils Number Concentration Bld" - }, - { - "field": "hdl", - "name": "HDL" - }, - { - "field": "hematocrit_vfr_bld", - "name": "Hematocrit Fraction of Volume Bld" - }, - { - "field": "hemoglobin_mcnc_bld", - "name": "Hemoglobin Mass Concentration Bld" - }, - { - "field": "ldl", - "name": "LDL" - }, - { - "field": "lymphocyte_ncnc_bld", - "name": "Lymphocytes Number Concentration Bld" - }, - { - "field": "mch_entmass_rbc", - "name": "MCH Average Mass Rbc" - }, - { - "field": "mchc_mcnc_rbc", - "name": "MCHC Mass Concentration Rbc" - }, - { - "field": "mcv_entvol_rbc", - "name": "MCV Average Volume Rbc" - }, - { - "field": "monocyte_ncnc_bld", - "name": "Monocytes Number Concentration Bld" - }, - { - "field": "neutrophil_ncnc_bld", - "name": "Neutrophils Number Concentration Bld" - }, - { - "field": "platelet_ncnc_bld", - "name": "Platelets Number Concentration Bld" - }, - { - "field": "pmv_entvol_bld", - "name": "PMV Mean Volume Bld" - }, - { - "field": "rbc_ncnc_bld", - "name": "Red Blood Cells Number Concentration Bld" - }, - { - "field": "rdw_ratio_rbc", - "name": "Red Cell Distribution Width Ratio Rbc" - }, - { - "field": "wbc_ncnc_bld", - "name": "White Blood Cells Number Concentration Bld" - }, - { - "field": "bmi_baseline", - "name": "BMI Baseline" - }, - { - "field": "current_smoker_baseline", - "name": "Current Smoker Baseline" - }, - { - "field": "ever_smoker_baseline", - "name": "Ever Smoker Baseline" - }, - { - "field": "geographic_site", - "name": "Geographic Site" - }, - { - "field": "height_baseline", - "name": "Height Baseline" - }, - { - "field": "total_cholesterol", - "name": "Total Cholesterol" - }, - { - "field": "triglycerides", - "name": "Triglycerides" - }, - { - "field": "studies_submitter_id", - "name": "Study" - }, - { - "field": "programs_name", - "name": "Program" - } + { "field": "disease_id", "name": "Disease ID" }, + { "field": "age_of_onset", "name": "Age of Onset" }, + { "field": "project_dbgap_accession_number", "name": "Project dbGaP Accession Number" }, + { "field": "project_dbgap_consent_text", "name":"Project dbGaP Consent Text"}, + { "field": "project_dbgap_phs", "name":"Project dbGaP Phs"} ], "manifestMapping": { "resourceIndexType": "file", @@ -926,13 +749,10 @@ { "title": "File", "fields": [ - "programs_name", "project_id", "data_category", "data_type", - "data_format", - "callset", - "bucket_path" + "data_format" ], "searchFields": [ "file_name" @@ -946,9 +766,7 @@ "project_id", "file_name", "file_size", - "object_id", - "callset" - ] + "object_id" ] }, "guppyConfig": { "dataType": "file", diff --git a/jenkins-genomel.planx-pla.net/etlMapping.yaml b/jenkins-genomel.planx-pla.net/etlMapping.yaml index a3a08106b..9160a71ee 100644 --- a/jenkins-genomel.planx-pla.net/etlMapping.yaml +++ b/jenkins-genomel.planx-pla.net/etlMapping.yaml @@ -1,40 +1,163 @@ mappings: - - name: jenkins-genomel.planx-pla.net_case - doc_type: case + - name: jenkins-genomel.planx-pla.net_subject + doc_type: subject type: aggregator - root: case + root: subject props: - - name: project_id - name: submitter_id - flatten_props: - - path: demographics - props: - - name: gender - - name: race - - name: ethnicity - - name: year_of_birth + - name: project_id + - name: sex + - name: age_value + - name: ancestry + - name: disease_description + - name: phenotype_present + - name: phenotype_absent + - name: disease_id + - name: solve_state + - name: congenital_status + - name: age_of_onset + - name: phenotype_group + - name: anvil_project_id +# flatten_props: aggregated_props: + - name: sample_provider + path: samples + src: sample_provider + fn: set + - name: tissue_affected_status + path: samples + src: tissue_affected_status + fn: set + - name: tissue_type + path: samples + src: tissue_type + fn: set + - name: sample_type + path: samples + src: sample_type + fn: set + - name: original_material_type + path: samples + src: original_material_type + fn: set + - name: exome_capture_platform + path: samples.sequencings + src: exome_capture_platform + fn: set + - name: library_prep_kit_method + path: samples.sequencings + src: library_prep_kit_method + fn: set + - name: capture_region_bed_file + path: samples.sequencings + src: capture_region_bed_file + fn: set + - name: reference_genome_build + path: samples.sequencings + src: reference_genome_build + fn: set + - name: sequencing_assay + path: samples.sequencings + src: sequencing_assay + fn: set + - name: alignment_method + path: samples.sequencings + src: alignment_method + fn: set + - name: data_processing_pipeline + path: samples.sequencings + src: data_processing_pipeline + fn: set - name: _samples_count path: samples fn: count - - name: _aliquots_count - path: samples.aliquots + - name: _sequencings_count + path: samples.sequencings fn: count + joining_props: + - index: file + join_on: _subject_id + props: + - name: data_format + src: data_format + fn: set + - name: data_type + src: data_type + fn: set + - name: data_category + src: data_category + fn: set + - name: file_count + src: _file_id + fn: count + parent_props: + - path: projects[project_code:code] + - path: projects[project_name:name] + - path: projects[project_dbgap_phs:dbgap_phs] + - path: projects[project_dbgap_consent_text:dbgap_consent_text] + - path: projects[project_short_name:short_name] + - path: projects[project_dbgap_accession_number:dbgap_accession_number] - name: jenkins-genomel.planx-pla.net_file doc_type: file type: collector root: None category: data_file props: + - name: project_id + - name: submitter_id - name: object_id - name: md5sum - name: file_name - name: file_size + - name: data_format + - name: data_type - name: state + - name: data_category + - name: analyte_type + - name: sequencing_assay + - name: source_node injecting_props: - case: + subject: props: - - name: case_id + - name: _subject_id src: id - - name: project_id - + fn: set + - name: subject_submitter_id + src: submitter_id + fn: set + - name: anvil_project_id + src: anvil_project_id + fn: set + - name: sex + src: sex + fn: set + - name: age_value + src: age_value + fn: set + - name: ancestry + src: ancestry + fn: set + - name: disease_description + src: disease_description + fn: set + - name: phenotype_present + src: phenotype_present + fn: set + - name: phenotype_absent + src: phenotype_absent + fn: set + - name: disease_id + src: disease_id + fn: set + - name: solve_state + src: solve_state + fn: set + - name: congenital_status + src: congenital_status + fn: set + - name: age_of_onset + src: age_of_onset + fn: set + - name: phenotype_group + src: phenotype_group + fn: set \ No newline at end of file diff --git a/jenkins-genomel.planx-pla.net/manifest.json b/jenkins-genomel.planx-pla.net/manifest.json index 3dab215f1..0de2496de 100644 --- a/jenkins-genomel.planx-pla.net/manifest.json +++ b/jenkins-genomel.planx-pla.net/manifest.json @@ -278,7 +278,7 @@ "environment": "qaplanetv1", "hostname": "jenkins-genomel.planx-pla.net", "revproxy_arn": "arn:aws:acm:us-east-1:707767160287:certificate/c676c81c-9546-4e9a-9a72-725dd3912bc8", - "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/genomel-dictionary/master/schema.json", + "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/anvil/master/schema.json", "portal_app": "gitops", "kube_bucket": "kube-qaplanetv1-gen3", "logs_bucket": "logs-qaplanetv1-gen3", @@ -299,7 +299,7 @@ "guppy": { "indices": [ { - "index": "jenkins_subject_alias", + "index": "jenkins_subject_new_alias", "type": "subject" }, { diff --git a/jenkins-genomel.planx-pla.net/portal/gitops.json b/jenkins-genomel.planx-pla.net/portal/gitops.json index 865e57a38..47706697e 100644 --- a/jenkins-genomel.planx-pla.net/portal/gitops.json +++ b/jenkins-genomel.planx-pla.net/portal/gitops.json @@ -3,31 +3,8 @@ "argoTemplate": "gwas-template", "graphql": { "boardCounts": [ - { - "graphql": "_case_count", - "name": "Case", - "plural": "Cases" - }, - { - "graphql": "_sample_count", - "name": "Sample", - "plural": "Samples" - }, - { - "graphql": "_family_count", - "name": "Family", - "plural": "Families" - } ], "chartCounts": [ - { - "graphql": "_case_count", - "name": "Case" - }, - { - "graphql": "_sample_count", - "name": "Sample" - } ], "projectDetails": "boardCounts" }, @@ -498,22 +475,16 @@ }, "studyViewerConfig": [ { - "dataType": "clinical_trials", + "dataType": "subject", "title": "Studies", - "titleField": "title", - "rowAccessor": "cmc_unique_id", + "titleField": "project_id", + "rowAccessor": "submitter_id", "listItemConfig": { - "blockFields": ["brief_summary"], - "tableFields": ["data_availability_date", "data_available", "creator", "nct_number", "condition", "category", "clinical_trial_website", "publications"] + "blockFields": ["project_id"], + "tableFields": ["data_type"] }, "fieldMapping": [ - { "field": "brief_summary", "name": "Brief Study Description" }, - { "field": "description", "name": "Detailed Description"}, - { "field": "creator", "name": "Sponsor"}, - { "field": "category", "name": "Study Type"}, - { "field": "clinical_trial_website", "name": "Websites"}, - { "field": "nct_number", "name": "NCT Number"}, - { "field": "publications", "name": "Study Publications"} + ], "openMode": "close-all", "buttons": [ @@ -530,12 +501,20 @@ ], "useArboristUI": true, "dataExplorerConfig": { + "charts": { + "project_id": { + "chartType": "count", + "title": "Projects" + } + }, "filters": { "tabs": [ { - "title": "Cases", + "title": "Project", "fields": [ - "project_id" + "project_id", + "data_type", + "data_format" ] } ] @@ -544,22 +523,28 @@ "enabled": true, "fields": [ "project_id", - "ethnicity", - "gender", - "submitter_id" + "data_format" ] }, "guppyConfig": { - "dataType": "case", - "nodeCountTitle": "Cases", + "dataType": "subject", + "nodeCountTitle": "Subjects", "fieldMapping": [ + { + "field": "_subject_id", + "name": "Subject ID" + } ], "manifestMapping": { "resourceIndexType": "file", "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "case_id", - "referenceIdFieldInDataIndex": "case_id" - } + "referenceIdFieldInResourceIndex": "_subject_id", + "referenceIdFieldInDataIndex": "_subject_id" + }, + "accessibleFieldCheckList": [ + "project_id" + ], + "accessibleValidationField": "project_id" }, "buttons": [ { @@ -597,6 +582,9 @@ "project_id", "data_type", "data_format" + ], + "searchFields": [ + "file_name" ] } ] @@ -613,12 +601,19 @@ "guppyConfig": { "dataType": "file", "fieldMapping": [ - { "field": "object_id", "name": "GUID" } + { + "field": "object_id", + "name": "GUID" + }, + { + "field": "programs_name", + "name": "Program" + } ], "nodeCountTitle": "Files", "manifestMapping": { - "resourceIndexType": "case", - "resourceIdField": "case_id", + "resourceIndexType": "subject", + "resourceIdField": "_subject_id", "referenceIdFieldInResourceIndex": "object_id", "referenceIdFieldInDataIndex": "object_id" }, diff --git a/jenkins-niaid.planx-pla.net/etlMapping.yaml b/jenkins-niaid.planx-pla.net/etlMapping.yaml index 9b3d75e26..b2f08f641 100644 --- a/jenkins-niaid.planx-pla.net/etlMapping.yaml +++ b/jenkins-niaid.planx-pla.net/etlMapping.yaml @@ -1,56 +1,163 @@ mappings: - - name: jenkins-niaid.planx-pla.net_clinical_trials - doc_type: clinical_trials + - name: jenkins-niaid.planx-pla.net_subject + doc_type: subject type: aggregator - root: core_metadata_collection + root: subject props: - - name: creator - - name: nct_number - - name: condition - - name: category - - name: study_design_allocation - - name: study_design_intervention_model - - name: study_design_masking - - name: study_design_primary_purpose - - name: responsible_party - - name: study_start_date - - name: study_completion_date - - name: data_available - - name: data_availability_date - - name: data_available_for_request - - name: clinical_trial_website - - name: publications - - name: brief_summary - - name: description - - name: title - - name: project_id - - name: cmc_unique_id - src: submitter_id - - name: jenkins-niaid.planx-pla.net_ctfile - doc_type: ctfile - type: aggregator - root: clinical_trial_file - props: - - name: object_id - - name: md5sum - - name: file_name - - name: file_size - - name: data_format - - name: data_type + - name: submitter_id - name: project_id + - name: sex + - name: age_value + - name: ancestry + - name: disease_description + - name: phenotype_present + - name: phenotype_absent + - name: disease_id + - name: solve_state + - name: congenital_status + - name: age_of_onset + - name: phenotype_group + - name: anvil_project_id +# flatten_props: + aggregated_props: + - name: sample_provider + path: samples + src: sample_provider + fn: set + - name: tissue_affected_status + path: samples + src: tissue_affected_status + fn: set + - name: tissue_type + path: samples + src: tissue_type + fn: set + - name: sample_type + path: samples + src: sample_type + fn: set + - name: original_material_type + path: samples + src: original_material_type + fn: set + - name: exome_capture_platform + path: samples.sequencings + src: exome_capture_platform + fn: set + - name: library_prep_kit_method + path: samples.sequencings + src: library_prep_kit_method + fn: set + - name: capture_region_bed_file + path: samples.sequencings + src: capture_region_bed_file + fn: set + - name: reference_genome_build + path: samples.sequencings + src: reference_genome_build + fn: set + - name: sequencing_assay + path: samples.sequencings + src: sequencing_assay + fn: set + - name: alignment_method + path: samples.sequencings + src: alignment_method + fn: set + - name: data_processing_pipeline + path: samples.sequencings + src: data_processing_pipeline + fn: set + - name: _samples_count + path: samples + fn: count + - name: _sequencings_count + path: samples.sequencings + fn: count + joining_props: + - index: file + join_on: _subject_id + props: + - name: data_format + src: data_format + fn: set + - name: data_type + src: data_type + fn: set + - name: data_category + src: data_category + fn: set + - name: file_count + src: _file_id + fn: count parent_props: - - path: core_metadata_collections[cmc_unique_id:submitter_id] - - name: jenkins-niaid.planx-pla.net_oafile - doc_type: oafile - type: aggregator - root: open_access_doc + - path: projects[project_code:code] + - path: projects[project_name:name] + - path: projects[project_dbgap_phs:dbgap_phs] + - path: projects[project_dbgap_consent_text:dbgap_consent_text] + - path: projects[project_short_name:short_name] + - path: projects[project_dbgap_accession_number:dbgap_accession_number] + - name: jenkins-niaid.planx-pla.net_file + doc_type: file + type: collector + root: None + category: data_file props: + - name: project_id + - name: submitter_id + - name: object_id - name: md5sum - name: file_name - name: file_size - name: data_format - name: data_type - - name: doc_url - - name: project_id - parent_props: - - path: core_metadata_collections[cmc_unique_id:submitter_id] + - name: state + - name: data_category + - name: analyte_type + - name: sequencing_assay + - name: source_node + injecting_props: + subject: + props: + - name: _subject_id + src: id + fn: set + - name: subject_submitter_id + src: submitter_id + fn: set + - name: anvil_project_id + src: anvil_project_id + fn: set + - name: sex + src: sex + fn: set + - name: age_value + src: age_value + fn: set + - name: ancestry + src: ancestry + fn: set + - name: disease_description + src: disease_description + fn: set + - name: phenotype_present + src: phenotype_present + fn: set + - name: phenotype_absent + src: phenotype_absent + fn: set + - name: disease_id + src: disease_id + fn: set + - name: solve_state + src: solve_state + fn: set + - name: congenital_status + src: congenital_status + fn: set + - name: age_of_onset + src: age_of_onset + fn: set + - name: phenotype_group + src: phenotype_group + fn: set \ No newline at end of file diff --git a/jenkins-niaid.planx-pla.net/manifest.json b/jenkins-niaid.planx-pla.net/manifest.json index a6ca0514e..65beffb21 100644 --- a/jenkins-niaid.planx-pla.net/manifest.json +++ b/jenkins-niaid.planx-pla.net/manifest.json @@ -280,7 +280,7 @@ "environment": "qaplanetv1", "hostname": "jenkins-niaid.planx-pla.net", "revproxy_arn": "arn:aws:acm:us-east-1:707767160287:certificate/c676c81c-9546-4e9a-9a72-725dd3912bc8", - "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/niaid-clinical-trials-dictionary/master/schema.json", + "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/anvil/master/schema.json", "portal_app": "gitops", "kube_bucket": "kube-qaplanetv1-gen3", "logs_bucket": "logs-qaplanetv1-gen3", @@ -301,7 +301,7 @@ "guppy": { "indices": [ { - "index": "jenkins_subject_alias", + "index": "jenkins_subject_new_alias", "type": "subject" }, { diff --git a/jenkins-niaid.planx-pla.net/portal/gitops.json b/jenkins-niaid.planx-pla.net/portal/gitops.json index 0a5866657..a45c6453c 100644 --- a/jenkins-niaid.planx-pla.net/portal/gitops.json +++ b/jenkins-niaid.planx-pla.net/portal/gitops.json @@ -494,22 +494,19 @@ }, "studyViewerConfig": [ { - "dataType": "clinical_trials", + "dataType": "subject", "title": "Studies", - "titleField": "title", - "rowAccessor": "cmc_unique_id", + "titleField": "project_id", + "rowAccessor": "submitter_id", "listItemConfig": { - "blockFields": ["brief_summary"], - "tableFields": ["data_availability_date", "data_available", "creator", "nct_number", "condition", "category", "clinical_trial_website", "publications"] + "blockFields": ["project_id"], + "tableFields": ["data_type"] }, "fieldMapping": [ - { "field": "brief_summary", "name": "Brief Study Description" }, - { "field": "description", "name": "Detailed Description"}, - { "field": "creator", "name": "Sponsor"}, { "field": "category", "name": "Study Type"}, - { "field": "clinical_trial_website", "name": "Websites"}, - { "field": "nct_number", "name": "NCT Number"}, - { "field": "publications", "name": "Study Publications"} + { "field": "project_id", "name": "Project_ID"}, + { "field": "data_type", "name": "Data_Type"}, + { "field": "condition", "name": "Condition"} ], "openMode": "close-all", "buttons": [ @@ -527,13 +524,18 @@ ], "useArboristUI": true, "dataExplorerConfig": { + "charts": { + "project_id": { + "chartType": "count", + "title": "Projects" + } + }, "filters": { "tabs": [ { "title": "Files", "fields": [ "project_id", - "file_size", "data_format", "data_type" ] @@ -544,22 +546,33 @@ "enabled": true, "fields": [ "project_id", - "file_name", - "file_size", "data_format" ] }, + "dropdowns": { + "download": { + "title": "Download" + } + }, "guppyConfig": { - "dataType": "ctfile", - "nodeCountTitle": "Files", + "dataType": "subject", + "nodeCountTitle": "Subjects", "fieldMapping": [ + { + "field": "_subject_id", + "name": "Subject ID" + } ], "manifestMapping": { - "resourceIndexType": "ctfile", + "resourceIndexType": "file", "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "project_id", - "referenceIdFieldInDataIndex": "project_id" - } + "referenceIdFieldInResourceIndex": "_subject_id", + "referenceIdFieldInDataIndex": "_subject_id" + }, + "accessibleFieldCheckList": [ + "project_id" + ], + "accessibleValidationField": "project_id" }, "buttons": [ { @@ -578,89 +591,102 @@ } ] }, - "arrangerConfig": { + "fileExplorerConfig": { "charts": { - "project_id": { - "chartType": "count", - "title": "Projects" - }, - "submitter_id": { - "chartType": "count", - "title": "Subjects" + "data_type": { + "chartType": "stackedBar", + "title": "File Type" }, - "gender": { - "chartType": "pie", - "title": "Gender" - }, - "race": { - "chartType": "bar", - "title": "Race" - }, - "ethnicity": { - "chartType": "bar", - "title": "Ethnicity" + "data_format": { + "chartType": "stackedBar", + "title": "File Format" } }, "filters": { "tabs": [ { - "title": "Subject", - "fields":[ - "project_id", - "gender", - "race", - "ethnicity", - "vital_status", - "frstdthd" - ] - }, { - "title": "Diagnosis", + "title": "File", "fields": [ - "arthxbase", - "bshbvstat", - "bshcvstat", - "cd4nadir", - "status", - "virus_type", - "virus_subtype" + "project_id", + "data_category", + "data_type", + "data_format" + ], + "searchFields": [ + "file_name" ] } ] }, - "manifestMapping": { - "resourceIndexType": "file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "subject_id", - "referenceIdFieldInDataIndex": "node_id" - }, "table": { - "buttons": [ + "enabled": true, + "fields": [ + "project_id", + "file_name", + "file_size", + "object_id" ] + }, + "guppyConfig": { + "dataType": "file", + "fieldMapping": [ { - "enabled": true, - "type": "data", - "title": "Download Clinical", - "leftIcon": "user", - "rightIcon": "download", - "fileName": "clinical.json" + "field": "object_id", + "name": "GUID" }, { - "enabled": true, - "type": "manifest", - "title": "Download Manifest", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "manifest.json" - },{ - "enabled": false, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" - } - ] + "field": "programs_name", + "name": "Program" + } + ], + "nodeCountTitle": "Files", + "manifestMapping": { + "resourceIndexType": "subject", + "resourceIdField": "_subject_id", + "referenceIdFieldInResourceIndex": "object_id", + "referenceIdFieldInDataIndex": "object_id" + }, + "accessibleFieldCheckList": [ + "project_id" + ], + "accessibleValidationField": "project_id", + "downloadAccessor": "object_id" }, - "projectId": "search", - "graphqlField": "subject", - "index": "" + "buttons": [ + { + "enabled": true, + "type": "file-manifest", + "title": "Download Manifest", + "leftIcon": "datafile", + "rightIcon": "download", + "fileName": "file-manifest.json", + "dropdownId": "download" + }, + { + "enabled": true, + "type": "export-files-to-workspace", + "title": "Export to Workspace", + "leftIcon": "datafile", + "rightIcon": "download" + }, + { + "enabled": true, + "type": "export-files-to-pfb", + "title": "Export All to PFB", + "rightIcon": "external-link" + }, + { + "enabled": true, + "type": "export-files", + "title": "Export All to Terra", + "rightIcon": "external-link" + }, + { + "enabled": true, + "type": "export-files-to-seven-bridges", + "title": "Export All to Seven Bridges", + "rightIcon": "external-link" + } + ], + "dropdowns": {} } } diff --git a/jenkins-perf.planx-pla.net/manifest.json b/jenkins-perf.planx-pla.net/manifest.json index cddbe602a..c50348946 100644 --- a/jenkins-perf.planx-pla.net/manifest.json +++ b/jenkins-perf.planx-pla.net/manifest.json @@ -7,21 +7,21 @@ "autodeploy": "yes" }, "versions": { - "arborist": "quay.io/cdis/arborist:2024.06", + "arborist": "quay.io/cdis/arborist:integration202407", "aws-es-proxy": "quay.io/cdis/aws-es-proxy:v1.3.1", - "fence": "quay.io/cdis/fence:2024.06", + "fence": "quay.io/cdis/fence:integration202407", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "indexd": "quay.io/cdis/indexd:2024.06", - "peregrine": "quay.io/cdis/peregrine:2024.06", - "portal": "quay.io/cdis/data-portal:2024.06", - "revproxy": "quay.io/cdis/nginx:2024.06", - "sheepdog": "quay.io/cdis/sheepdog:2024.06", - "manifestservice": "quay.io/cdis/manifestservice:2024.06", - "wts": "quay.io/cdis/workspace-token-service:2024.06", - "sower": "quay.io/cdis/sower:2024.06", - "hatchery": "quay.io/cdis/hatchery:2024.06", - "metadata": "quay.io/cdis/metadata-service:2024.06", - "dashboard": "quay.io/cdis/gen3-statics:2024.06" + "indexd": "quay.io/cdis/indexd:integration202407", + "peregrine": "quay.io/cdis/peregrine:integration202407", + "portal": "quay.io/cdis/data-portal:integration202407", + "revproxy": "quay.io/cdis/nginx:integration202407", + "sheepdog": "quay.io/cdis/sheepdog:integration202407", + "manifestservice": "quay.io/cdis/manifestservice:integration202407", + "wts": "quay.io/cdis/workspace-token-service:integration202407", + "sower": "quay.io/cdis/sower:integration202407", + "hatchery": "quay.io/cdis/hatchery:integration202407", + "metadata": "quay.io/cdis/metadata-service:integration202407", + "dashboard": "quay.io/cdis/gen3-statics:integration202407" }, "arborist": { "deployment_version": "2" @@ -45,7 +45,7 @@ "name": "pelican-export", "container": { "name": "job-task", - "image": "quay.io/cdis/pelican:2024.06", + "image": "quay.io/cdis/pelican:integration202407", "pull_policy": "always", "env": [] }, diff --git a/jenkins-perf.planx-pla.net/manifests/hatchery/hatchery.json b/jenkins-perf.planx-pla.net/manifests/hatchery/hatchery.json index 3b4dd05f1..01929ba62 100644 --- a/jenkins-perf.planx-pla.net/manifests/hatchery/hatchery.json +++ b/jenkins-perf.planx-pla.net/manifests/hatchery/hatchery.json @@ -5,7 +5,7 @@ "sidecar": { "cpu-limit": "1.0", "memory-limit": "256Mi", - "image": "quay.io/cdis/gen3fuse-sidecar:2024.06", + "image": "quay.io/cdis/gen3fuse-sidecar:integration202407", "env": { "NAMESPACE": "jenkins-perf", "HOSTNAME": "jenkins-perf.planx-pla.net" diff --git a/qa-brh.planx-pla.net/manifest.json b/qa-brh.planx-pla.net/manifest.json index 76fc538f0..c8e164859 100644 --- a/qa-brh.planx-pla.net/manifest.json +++ b/qa-brh.planx-pla.net/manifest.json @@ -13,7 +13,7 @@ "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.05", "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.05", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.05", + "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:master", "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.05", "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:0.2.0", "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.05", @@ -92,4 +92,4 @@ "targetCpu": 40 } } -} \ No newline at end of file +} diff --git a/qa-covid19.planx-pla.net/manifest.json b/qa-covid19.planx-pla.net/manifest.json index a96c223e3..2d879a701 100644 --- a/qa-covid19.planx-pla.net/manifest.json +++ b/qa-covid19.planx-pla.net/manifest.json @@ -5,31 +5,31 @@ ], "versions": { "ambassador": "quay.io/datawire/ambassador:1.4.2", - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.04", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.04", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.06", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.06", "auspice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-auspice:v2.25.gen3.2.15", "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", - "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.04", + "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.06", "covid19-bayes": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/covid19-bayes:5.1.4", "covid19-etl": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/covid19-etl:5.2.4", "covid19-notebook-etl": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/covid19-notebook-etl:5.1.6", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.04", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.04", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.06", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.06", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.04", - "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.04", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.04", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.04", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.04", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.04", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.04", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.04", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.04", - "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.04", - "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.04", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.04", - "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.04", - "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.04" + "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.06", + "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.06", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.06", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.06", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.06", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.06", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.06", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.06", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.06", + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.06", + "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.06", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.06", + "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.06", + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.06" }, "global": { "environment": "qa-covid19", @@ -65,7 +65,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.04" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.06" } }, "sower": [ @@ -74,7 +74,7 @@ "action": "export", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.04", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.06", "pull_policy": "Always", "env": [ { @@ -151,7 +151,7 @@ "serviceAccountName": "jobs-qa-covid19-planx-pla-net", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2024.04", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2024.06", "pull_policy": "Always", "env": [ { @@ -191,7 +191,7 @@ "serviceAccountName": "jobs-qa-covid19-planx-pla-net", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2024.04", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2024.06", "pull_policy": "Always", "env": [ { diff --git a/qa-covid19.planx-pla.net/manifests/hatchery/hatchery.json b/qa-covid19.planx-pla.net/manifests/hatchery/hatchery.json index 4eaed0ad1..223ac5795 100644 --- a/qa-covid19.planx-pla.net/manifests/hatchery/hatchery.json +++ b/qa-covid19.planx-pla.net/manifests/hatchery/hatchery.json @@ -5,7 +5,7 @@ "sidecar": { "cpu-limit": "1.0", "memory-limit": "256Mi", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2024.04", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2024.06", "env": { "NAMESPACE": "qa-covid19", "HOSTNAME": "qa-covid19.planx-pla.net" diff --git a/qa-heal.planx-pla.net/manifest.json b/qa-heal.planx-pla.net/manifest.json index f4bc646bb..d6a965d34 100644 --- a/qa-heal.planx-pla.net/manifest.json +++ b/qa-heal.planx-pla.net/manifest.json @@ -11,7 +11,7 @@ "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.06", "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.06", "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", - "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:0.4.0", + "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:0.5.0", "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.06", "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.06", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", @@ -19,7 +19,7 @@ "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.06", "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.06", "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:0.2.3", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.06", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:0.5.1", "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.06", "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.06", "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:feat_cde-submission", diff --git a/qa-heal.planx-pla.net/portal/gitops.json b/qa-heal.planx-pla.net/portal/gitops.json index 7cde4613b..5f617b573 100644 --- a/qa-heal.planx-pla.net/portal/gitops.json +++ b/qa-heal.planx-pla.net/portal/gitops.json @@ -160,6 +160,8 @@ "exportToWorkspace": { "enabled": true, "manifestFieldName": "__manifest", + "enableExportFullMetadata": true, + "excludedMetadataFields": ["authz", "registration_authz", "registrant_username", "advSearchFilters", "__accessible", "commons_name", "commons_url", "commons", "frontend_uid"], "enableDownloadManifest": true, "enableDownloadZip": true, "downloadZipButtonText": "Download Zip", @@ -465,23 +467,23 @@ }, { "name": "Common Data Elements", - "color": "#dabeca", + "color": "#532565", "display": false }, { "name": "Other", - "color": "#dbb9b3", + "color": "#982568", "display": false }, { "name": "Commons", "displayName": "Data Resources", - "color": "#eecdcb", + "color": "#981f32", "display": false }, { "name": "Data Repository", - "color": "#f5d8c3", + "color": "#bf362e", "display": true } ] @@ -566,16 +568,58 @@ "studyRegistrationValidationField": "is_registered", "studyRegistrationAccessCheckField": "registration_authz", "studyRegistrationFormDisclaimerField": "Information provided on this page will be used for correspondence regarding your request and may be shared with the NIH and/or the HEAL Data Stewards", - "clinicalTrialFields": ["NCTId", "OfficialTitle", "BriefTitle", "Acronym", "StudyType", "OverallStatus", "StartDate", "StartDateType", "CompletionDate", "CompletionDateType", "IsFDARegulatedDrug", "IsFDARegulatedDevice", "IsPPSD", "BriefSummary", "DetailedDescription", "Condition", "DesignAllocation", "DesignPrimaryPurpose", "Phase", "DesignInterventionModel", "EnrollmentCount", "EnrollmentType", "DesignObservationalModel", "InterventionType", "PrimaryOutcomeMeasure", "SecondaryOutcomeMeasure", "OtherOutcomeMeasure", "Gender", "GenderBased", "MaximumAge", "MinimumAge", "IPDSharing", "IPDSharingTimeFrame", "IPDSharingAccessCriteria", "IPDSharingURL", "SeeAlsoLinkURL", "AvailIPDURL", "AvailIPDId", "AvailIPDComment"], + "clinicalTrialFields": [ + "NCTId", + "OfficialTitle", + "BriefTitle", + "Acronym", + "StudyType", + "OverallStatus", + "StartDate", + "StartDateType", + "CompletionDate", + "CompletionDateType", + "IsFDARegulatedDrug", + "IsFDARegulatedDevice", + "IsPPSD", + "BriefSummary", + "DetailedDescription", + "Condition", + "DesignAllocation", + "DesignPrimaryPurpose", + "Phase", + "DesignInterventionModel", + "EnrollmentCount", + "EnrollmentType", + "DesignObservationalModel", + "InterventionType", + "PrimaryOutcomeMeasure", + "SecondaryOutcomeMeasure", + "OtherOutcomeMeasure", + "Gender", + "GenderBased", + "MaximumAge", + "MinimumAge", + "IPDSharing", + "IPDSharingTimeFrame", + "IPDSharingAccessCriteria", + "IPDSharingURL", + "SeeAlsoLinkURL", + "AvailIPDURL", + "AvailIPDId", + "AvailIPDComment", + "PatientRegistry", + "DesignTimePerspective" + ], "dataDictionarySubmissionBucket": "", "dataDictionarySubmissionDisclaimerField": "All submitted data dictionaries will be openly accessible to all users.", "cdeSubmissionDisclaimerField": "All submitted CDEs will be openly accessible to all users.", "variableMetadataField": "variable_level_metadata" }, - "workspaceRegistrationConfig" : { + "workspaceRegistrationConfig": { "workspacePolicyId": "workspace_strides_integrated", "workspaceInfoMessage": "The HEAL workspace provides a standardized computational environment for accessing and analyzing data from HEAL studies. Please fill out this form to request access to the workspace and start computing!", - "successRedirect" : { + "successRedirect": { "link": "/discovery", "text": "Go to Discovery Page" } diff --git a/qa-jcoin.planx-pla.net/manifest.json b/qa-jcoin.planx-pla.net/manifest.json index 59f3b8d68..37a0d221f 100644 --- a/qa-jcoin.planx-pla.net/manifest.json +++ b/qa-jcoin.planx-pla.net/manifest.json @@ -4,26 +4,26 @@ "That's all I have to say." ], "versions": { - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.05", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.06", "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.05", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.05", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.05", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.05", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.05", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.05", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.05", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.05", - "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.05", - "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.05", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.06", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.06", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.06", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.06", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.06", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.06", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.06", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.06", + "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.06", + "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.06", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.05", - "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.05", - "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.05", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.05", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.05", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.05", - "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.05", + "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.06", + "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.06", + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.06", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.06", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.06", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.06", + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.06", "ambassador": "quay.io/datawire/ambassador:1.4.2" }, "guppy": { @@ -75,7 +75,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.05" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.06" } }, "sower": [ @@ -86,7 +86,7 @@ "serviceAccountName": "jobs-qa-jcoin-planx-pla-net", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-manifest-ingestion:2024.05", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-manifest-ingestion:2024.06", "pull_policy": "Always", "env": [ { @@ -126,7 +126,7 @@ "serviceAccountName": "jobs-qa-jcoin-planx-pla-net", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/get-dbgap-metadata:2024.05", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/get-dbgap-metadata:2024.06", "pull_policy": "Always", "env": [], "volumeMounts": [ @@ -157,7 +157,7 @@ "serviceAccountName": "jobs-qa-jcoin-planx-pla-net", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2024.05", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2024.06", "pull_policy": "Always", "env": [ { @@ -198,7 +198,7 @@ "serviceAccountName": "jobs-qa-jcoin-planx-pla-net", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cdis/manifest-merging:2024.05", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cdis/manifest-merging:2024.06", "pull_policy": "Always", "env": [ { @@ -239,7 +239,7 @@ "serviceAccountName": "jobs-qa-jcoin-planx-pla-net", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2024.05", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2024.06", "pull_policy": "Always", "env": [ { diff --git a/qa-jcoin.planx-pla.net/manifests/hatchery/hatchery.json b/qa-jcoin.planx-pla.net/manifests/hatchery/hatchery.json index 5bafad405..0eaa54de7 100644 --- a/qa-jcoin.planx-pla.net/manifests/hatchery/hatchery.json +++ b/qa-jcoin.planx-pla.net/manifests/hatchery/hatchery.json @@ -5,7 +5,7 @@ "sidecar": { "cpu-limit": "1.0", "memory-limit": "256Mi", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2024.05", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2024.06", "env": { "NAMESPACE": "qa-jcoin", "HOSTNAME": "qa-jcoin.planx-pla.net" diff --git a/qa-kidsfirst.planx-pla.net/manifest.json b/qa-kidsfirst.planx-pla.net/manifest.json index 5122cc738..1582c38f9 100644 --- a/qa-kidsfirst.planx-pla.net/manifest.json +++ b/qa-kidsfirst.planx-pla.net/manifest.json @@ -7,16 +7,16 @@ "autodeploy": "yes" }, "versions": { - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.04", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.04", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.04", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.04", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.04", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.04", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.04", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.04", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.04", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.04", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.06", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.06", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.06", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.06", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.06", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.06", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.06", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.06", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.06", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.06", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0" }, "arborist": { diff --git a/qa-mickey.planx-pla.net/portal/gitops-sponsors/login-logo.png b/qa-mickey.planx-pla.net/portal/gitops-sponsors/login-logo.png new file mode 100644 index 000000000..98398e69f Binary files /dev/null and b/qa-mickey.planx-pla.net/portal/gitops-sponsors/login-logo.png differ diff --git a/qa-mickey.planx-pla.net/portal/gitops.css b/qa-mickey.planx-pla.net/portal/gitops.css index 545059b87..fe7a78d17 100644 --- a/qa-mickey.planx-pla.net/portal/gitops.css +++ b/qa-mickey.planx-pla.net/portal/gitops.css @@ -9,3 +9,50 @@ .footer__version-area { width: 600px; } + +.login-page .login-page__central-content { + flex-flow: row wrap; + justify-content: center; +} + +.login-page .login-page__central-content > div { + flex-basis: 100%; +} + +.login-page .login-page__central-content > div.login-page__entries { + flex-basis: auto; +} + +.login-page .login-page__title { + display: block; + background-image: url(/custom/sponsors/gitops-sponsors/login-logo.png); + background-size: contain; + background-repeat: no-repeat; + background-position-x: center; + height: 59px; + overflow: hidden; + text-indent: -9999px; + margin-bottom: 20px; +} + +.login-page .login-page__sub-title { + font-size: 24px; +} + +.login-page .login-page__separator { + display: none; +} + +.login-page .body-typo { + margin-top: 16px; +} + + +.login-page .login-page__entries { + width: 200px; + margin: 40px auto; +} + +.login-page .login-page__entry-button { + width: 200px; +} diff --git a/qa-mickey.planx-pla.net/portal/gitops.json b/qa-mickey.planx-pla.net/portal/gitops.json index ce875ab77..eb375c216 100644 --- a/qa-mickey.planx-pla.net/portal/gitops.json +++ b/qa-mickey.planx-pla.net/portal/gitops.json @@ -1,6 +1,6 @@ { "gaTrackingId": "UA-119127212-3", - "argoTemplate": "gwas-template-new-arborist-resource", + "argoTemplate": "gwas-template-new-arborist-resource-team-projects", "graphql": { "boardCounts": [], "chartCounts": [], @@ -44,7 +44,7 @@ "items": [ { "link": "https://qa-mickey.planx-pla.net/dashboard/Public/documentation/index.html", - "name": "Help and Guidance" + "name": "VADC Documentation" }, { "link": "support@datacommons.io", @@ -54,7 +54,7 @@ "useProfileDropdown": false }, "login": { - "title": "VA Data Commons", + "title": "U.S. Department of Veterans Affairs Data Commons", "subTitle": "search, compare, and analyze data", "text": "The VA Data Commons supports the research and analysis of US military Veteran medical and genomic data and aims to accelerate scientific discovery and development of therapies, diagnostic tests, and other technologies for improving the lives of Veterans and beyond.", "contact": "If you have any questions about access or the registration process, please contact ", diff --git a/qa-niaid.planx-pla.net/manifest.json b/qa-niaid.planx-pla.net/manifest.json index 2db66429b..b277fa974 100644 --- a/qa-niaid.planx-pla.net/manifest.json +++ b/qa-niaid.planx-pla.net/manifest.json @@ -7,28 +7,28 @@ "autodeploy": "yes" }, "versions": { - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.05", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.05", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.06", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.06", "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.05", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.05", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.05", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.05", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.05", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.05", - "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.05", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.05", - "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.05", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.06", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.06", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.06", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.06", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.06", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.06", + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.06", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.06", + "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.06", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.05", - "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2024.05", - "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.05", - "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.05", + "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.06", + "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2024.06", + "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.06", + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.06", "ambassador": "quay.io/datawire/ambassador:1.4.2", - "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.05", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.05", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.05", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.05" + "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.06", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.06", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.06", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.06" }, "arborist": { "deployment_version": "2" @@ -38,7 +38,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.05" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.06" } }, "global": { @@ -89,7 +89,7 @@ "action": "export", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.05", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.06", "pull_policy": "Always", "env": [ { diff --git a/qa-niaid.planx-pla.net/manifests/hatchery/hatchery.json b/qa-niaid.planx-pla.net/manifests/hatchery/hatchery.json index 8daea7cf7..86f975c87 100644 --- a/qa-niaid.planx-pla.net/manifests/hatchery/hatchery.json +++ b/qa-niaid.planx-pla.net/manifests/hatchery/hatchery.json @@ -5,7 +5,7 @@ "sidecar": { "cpu-limit": "1.0", "memory-limit": "256Mi", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2024.05", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2024.06", "env": { "NAMESPACE": "qa-niaid", "HOSTNAME": "qa-niaid.planx-pla.net"