diff --git a/chicagoland.pandemicresponsecommons.org/etlMapping.yaml b/chicagoland.pandemicresponsecommons.org/etlMapping.yaml index 80333622e6..103621f078 100644 --- a/chicagoland.pandemicresponsecommons.org/etlMapping.yaml +++ b/chicagoland.pandemicresponsecommons.org/etlMapping.yaml @@ -1,5 +1,5 @@ mappings: - - name: covid19 + - name: covid19_location doc_type: location type: aggregator root: summary_location diff --git a/chicagoland.pandemicresponsecommons.org/manifest.json b/chicagoland.pandemicresponsecommons.org/manifest.json index 69b9134130..6ea80d2952 100644 --- a/chicagoland.pandemicresponsecommons.org/manifest.json +++ b/chicagoland.pandemicresponsecommons.org/manifest.json @@ -4,32 +4,32 @@ "That's all I have to say" ], "versions": { - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.03", - "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.03", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.03", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.10", + "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.10", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.10", "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", "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", "covid19-bayes": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/covid19-bayes:5.1.4", "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.03", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.03", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.03", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.03", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.33.1", - "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.03", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.10", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.10", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.10", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.10", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.35.0", + "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.10", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.03", - "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.03", - "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.03", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.03", + "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.10", + "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.10", + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.10", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.10", "ambassador": "quay.io/datawire/ambassador:1.4.2", - "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.03", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.03", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.03", + "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.10", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.10", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.10", "auspice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-auspice:v2.25.gen3.2.15", - "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.03", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.03" + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.10", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.10" }, "global": { "environment": "covid19-prod", @@ -130,7 +130,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.03" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.10" } }, "sower": [ @@ -139,7 +139,7 @@ "action": "export", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.03", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.10", "pull_policy": "Always", "env": [ { @@ -214,7 +214,7 @@ "guppy": { "indices": [ { - "index": "covid19", + "index": "covid19_location", "type": "location" }, { @@ -237,4 +237,4 @@ "config_index": "covid19_array-config", "auth_filter_field": "auth_resource_path" } -} +} \ No newline at end of file diff --git a/chicagoland.pandemicresponsecommons.org/portal/gitops.json b/chicagoland.pandemicresponsecommons.org/portal/gitops.json index 781371be3f..febeae38b1 100644 --- a/chicagoland.pandemicresponsecommons.org/portal/gitops.json +++ b/chicagoland.pandemicresponsecommons.org/portal/gitops.json @@ -77,6 +77,12 @@ "icon": "dictionary", "tooltip": "The Data Dictionary serves to inform the data model and is updated as new data is ingested." }, + { + "name": "Discovery", + "link": "/discovery", + "icon": "query", + "tooltip": "Discovery page where one can take a detailed look at publications." + }, { "name": "Profile", "link": "/identity", @@ -142,10 +148,13 @@ }, "featureFlags": { "explorer": true, + "discovery": true, "analysis": true, "explorerPublic": true, "explorerHideEmptyFilterSection": true, - "explorerFilterValuesToHide": ["no data"] + "explorerFilterValuesToHide": [ + "no data" + ] }, "analysisTools": [], "explorerConfig": [ @@ -204,7 +213,9 @@ "manifestMapping": { "referenceIdFieldInResourceIndex": "code" }, - "accessibleFieldCheckList": ["project_id"], + "accessibleFieldCheckList": [ + "project_id" + ], "accessibleValidationField": "project_id" } }, @@ -390,7 +401,8 @@ "field": "study_doi", "name": "Study DOI" }, - { "field": "pO2_saturation", + { + "field": "pO2_saturation", "name": "pO2 Saturation (percent)" }, { @@ -409,7 +421,9 @@ "manifestMapping": { "referenceIdFieldInResourceIndex": "_subject_id" }, - "accessibleFieldCheckList": ["project_id"], + "accessibleFieldCheckList": [ + "project_id" + ], "accessibleValidationField": "project_id" } }, @@ -507,11 +521,13 @@ "field": "project_investigator_affiliation", "name": "Source" }, - { "field": "title", + { + "field": "title", "name": "Intervention Name" }, - { "field": "nct_number", - "name": "NCT Number" + { + "field": "nct_number", + "name": "NCT Number" }, { "field": "project_date_collected", @@ -521,7 +537,9 @@ "manifestMapping": { "referenceIdFieldInResourceIndex": "project_id" }, - "accessibleFieldCheckList": ["project_id"], + "accessibleFieldCheckList": [ + "project_id" + ], "accessibleValidationField": "project_id" } }, @@ -709,7 +727,9 @@ "referenceIdFieldInDataIndex": "object_id" }, "downloadAccessor": "object_id", - "accessibleFieldCheckList": ["project_id"], + "accessibleFieldCheckList": [ + "project_id" + ], "accessibleValidationField": "project_id" } }, @@ -1000,7 +1020,7 @@ "field": "med_hhinc", "name": "Median Household Income (USD)" }, - { + { "field": "population_density", "name": "Population Density (residents per square mile)" }, @@ -1041,7 +1061,9 @@ "manifestMapping": { "referenceIdFieldInResourceIndex": "project_id" }, - "accessibleFieldCheckList": ["project_id"], + "accessibleFieldCheckList": [ + "project_id" + ], "accessibleValidationField": "project_id" } } @@ -1207,7 +1229,6 @@ ] } } - }, { "title": "Age Demographics in Illinois", @@ -1271,7 +1292,348 @@ } } }, + "discoveryConfig": { + "features": { + "advSearchFilters": { + "enabled": true, + "field": "advSearchFilters", + "displayName": "Filters", + "filters": [ + { + "key": "Sample Type" + }, + { + "key": "Immune status" + }, + { + "key": "Race/Ethnicity" + }, + { + "key": "Gender" + }, + { + "key": "Age" + }, + { + "key": "Available Data" + } + ] + }, + "guidType": "covid_sample_discovery_metadata", + "pageTitle": { + "enabled": false + }, + "tagsInDescription": { + "enabled": true + }, + "tagsColumn": { + "enabled": false, + "text": "Publication Discovery" + }, + "exportToWorkspace": { + "enabled": false, + "manifestFieldName": "__manifest", + "downloadManifestButtonText": "Download", + "enableDownloadManifest": false, + "downloadZipButtonText": "Download Zip", + "enableDownloadZip": false, + "enableFillRequestForm": true, + "fillRequestFormDisplayText": "Request Information", + "fillRequestFormURL": "https://pandemicresponsecommons.org/access-for-samples", + "externalWebsiteName": "Pandemic Response Commons Website", + "externalWebsiteURL": "https://pandemicresponsecommons.org", + "fillRequestFormCheckField": "_medical_sample_id", + "documentationLinks": { + "gen3Client": "https://gen3.org/resources/user/gen3-client/", + "gen3Workspaces": "https://gen3.org/resources/user/analyze-data/" + }, + "verifyExternalLogins": true + }, + "search": { + "tagSearchDropdown": { + "enabled": true, + "collapsibleButtonText": "Sample Filters" + }, + "searchBar": { + "enabled": true + } + }, + "authorization": { + "enabled": true, + "columnTooltip": "Filter by data access", + "supportedValues": { + "accessible": { + "enabled": true, + "menuText": "Available" + }, + "unaccessible": { + "enabled": false, + "menuText": "Not Accessible" + }, + "waiting": { + "enabled": true, + "menuText": "Waiting" + }, + "notAvailable": { + "enabled": true, + "menuText": "Not Available" + } + } + } + }, + "aggregations": [ + { + "name": "Samples", + "field": "_medical_sample_id", + "type": "count" + } + ], + "tagSelector": { + "title": "Tags by category" + }, + "studyColumns": [ + { + "name": "Sample Type", + "field": "sample_type", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "SARS-CoV-2 Infection Status", + "field": "SARS_CoV2_Infection_Status", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "SARS_CoV-2 Vaccination Status", + "field": "CoVID_Vaccination_Status", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Immune status", + "field": "Immune_Status", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Age", + "field": "demographics__age", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Gender", + "field": "demographics__gender", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Race/Ethnicity", + "field": "demographics__race_enthnicity", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Available Data", + "field": "Available_Data", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + } + ], + "studyPreviewField": { + "name": "Abstract", + "field": "abstract", + "contentType": "string", + "includeName": true, + "includeIfNotAvailable": false + }, + "studyPageFields": { + "showAllAvailableFields": false, + "header": { + "field": "title" + }, + "fieldsToShow": [ + { + "groupName": "Publication Identifiers", + "includeName": false, + "fields": [ + { + "name": "Sample ID", + "field": "_medical_sample_id", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Sample Type", + "field": "sample_type", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Demographics Age", + "field": "demographics__age", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Demographics Gender", + "field": "demographics__gender", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Demographics_race", + "field": "demographics__race", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Demographics_ethnicity", + "field": "demographics__ethnicity", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "SARS CoV2 Infection Status", + "field": "SARS_CoV2_Infection_Status", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "CoVID Vaccination Status_status", + "field": "CoVID_Vaccination_Status__status", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "CoVID Vaccination Status_antigen", + "field": "CoVID_Vaccination_Status__antigen", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "CoVID Vaccination Status_manufacturer", + "field": "CoVID_Vaccination_Status__manufacturer", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Immune Status", + "field": "Immune_Status", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Available Data", + "field": "Available_Data", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Data Availability Date", + "field": "data_availability_date", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Description of Data Available", + "field": "data_description", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Condition", + "field": "condition", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Websites", + "field": "websites", + "contentType": "string", + "includeIfNotAvailable": false + } + ] + }, + { + "fields": [ + { + "name": "Abstract", + "field": "abstract", + "contentType": "paragraphs", + "includeName": false, + "includeIfNotAvailable": false + } + ] + } + ] + }, + "minimalFieldMapping": { + "tagsListFieldName": "tags", + "authzField": "auth_resource_path", + "uid": "_medical_sample_id" + }, + "tagCategories": [ + { + "name": "Sample Type", + "field": "Sample Type", + "color": "#532565", + "display": true + }, + { + "name": "SARS-CoV2 Infection Status", + "field": "SARS-CoV2 Infection Status", + "color": "#981f32", + "display": true + }, + { + "name": "SARS_CoV-2 Vaccination Status", + "field": "SARS_CoV-2 Vaccination Status", + "color": "#532565", + "display": true + }, + { + "name": "Immune Status", + "field": "Immune Status", + "color": "#bf362e", + "display": true + }, + { + "name": "Age", + "field": "Age", + "color": "#982568", + "display": true + }, + { + "name": "Gender", + "field": "Gender", + "color": "#982568", + "display": true + }, + { + "name": "Race/Ethnicity", + "field": "Race/Ethnicity", + "color": "#982568", + "display": true + }, + { + "name": "Available Data", + "field": "Available Data", + "color": "#982568", + "display": true + } + ] + }, "connectSrcCSPWhitelist": [ "https://covd-map-occ-prc-prod.s3.amazonaws.com" ] -} +} \ No newline at end of file