From bc99d8c87238903b7c2bc5e1d374afef84edcd2a Mon Sep 17 00:00:00 2001 From: Urvi Sheth Date: Mon, 27 Jul 2026 15:32:03 -0500 Subject: [PATCH] PR to turn off services related to logging, explorer and dashboard --- .../values/portal/gitops.json | 1546 +---------------- .../values/values.yaml | 934 +++++----- 2 files changed, 472 insertions(+), 2008 deletions(-) diff --git a/covid19prod/chicagoland.pandemicresponsecommons.org/values/portal/gitops.json b/covid19prod/chicagoland.pandemicresponsecommons.org/values/portal/gitops.json index 6855928b9..b701c3065 100644 --- a/covid19prod/chicagoland.pandemicresponsecommons.org/values/portal/gitops.json +++ b/covid19prod/chicagoland.pandemicresponsecommons.org/values/portal/gitops.json @@ -6,51 +6,8 @@ "grafanaFaroEnable": true, "grafanaFaroNamespace": "covid19prod" }, - "graphql": { - "boardCounts": [ - { - "graphql": "_summary_location_count", - "name": "Location", - "plural": "Locations" - }, - { - "graphql": "_subject_count", - "name": "Subject", - "plural": "Subjects" - } - ], - "chartCounts": [ - { - "graphql": "_subject_count", - "name": "Subject" - }, - { - "graphql": "_study_count", - "name": "Study" - } - ], - "projectDetails": "boardCounts" - }, "components": { "appName": "Chicagoland COVID-19 Commons", - "index": { - "introduction": { - "heading": "Chicagoland COVID-19 Commons", - "text": "The Chicagoland COVID-19 Commons supports the management, analysis and sharing of COVID-19 data", - "link": "/submission" - }, - "buttons": [], - "homepageChartNodes": [ - { - "node": "summary_location", - "name": "Locations" - }, - { - "node": "subject", - "name": "Subjects" - } - ] - }, "systemUse": { "systemUseTitle": "Data Use Agreement for Academic and Institutional Users", "systemUseText": [ @@ -68,36 +25,12 @@ }, "navigation": { "items": [ - { - "name": "Notebook Browser", - "link": "/resource-browser", - "icon": "query", - "tooltip": "The notebooks pull data from various external sources to generate and output useful tables, charts, graphs, and models." - }, - { - "name": "Exploration", - "link": "/explorer", - "icon": "exploration", - "tooltip": "The Exploration Page enables discovery of the data at the subject level and features a cohort builder." - }, { "name": "Workspace", "link": "/workspace", "icon": "workspace", "tooltip": "The Workspace provides a secure cloud environment featuring Jupyter Notebooks and RStudio." }, - { - "name": "Dictionary", - "link": "/DD", - "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", @@ -115,11 +48,6 @@ "link": "https://pandemicresponsecommons.org/chicagoland-covid-19-commons/", "name": "About" }, - { - "icon": "upload", - "link": "/submission", - "name": "Submit Data" - }, { "link": "https://uc-cdis.github.io/platform-citation/prc-cite/", "name": "Cite" @@ -162,1024 +90,16 @@ ] }, "featureFlags": { - 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The animations will allow you to see how testing data has changed over time.", - "link": "/dashboard/Public/notebooks/CTP_testing.html", - "imageUrl": "/dashboard/Public/notebooks/CTP_testing.png" - }, - { - "title": "nCoV-2019 Data Visualization", - "description": "In this notebook, we are performing some visual analysis on the individual COVID-19 case reports that provide aggregated data on demographic data, geographic location and symptoms. Please note that the data is available from Jan 3, 2020 to April 30, 2020. All results shown in this notebook are for demonstration purposes and should not be considered scientifically rigorous.", - "link": "/dashboard/Public/notebooks/nCoV-2019_data_analysis.html", - "imageUrl": "/dashboard/Public/notebooks/nCoV-2019_data_analysis.png" - }, - { - "title": "Demo: Exploring clinical data from multiple commons", - "description": "In this notebook, we obtain the clinical data for multiple projects from the Chicagoland Pandemic Response Commons and the NCI Genomic Data Commons (GDC) and visualize some of the clinical attributes. This notebook is for demonstration purposes only and not biologically meaningful.", - "link": "/dashboard/Public/notebooks/TCGA_COAD_COVID.html", - "imageUrl": "/dashboard/Public/notebooks/TCGA_COAD_COVID.png" - }, - { - "title": "Visualize Statistical Summary Reports from Partnering Healthcare Providers", - "description": "This notebook provides an example on how to visualize the status of COVID-19 and general patients information at multiple regional healthcare providers using the demo Statistical Summary Report data from 03/10/2020 to 11/10/2020.", - "link": "/dashboard/Public/notebooks/SSR_notebook.html", - "imageUrl": "/dashboard/Public/notebooks/SSR_notebook.png" - }, - { - "title": "COVID-19 X-ray images classification", - "description": "This notebook replicates the DarkCovidNet model and performes transfer learning with the GoogLeNet model to classify radiological images as indicative of either 'COVID-19', 'Normal' or 'Pneumonia' to assist in the diagnosis of COVID-19.", - "link": "/dashboard/Public/notebooks/CNN_XRAY_CF.html", - "imageUrl": "/dashboard/Public/notebooks/CNN_XRAY_CF.png" - }, - { - "title": "Google Mobility Data Visualization", - "description": "In this notebook, we demonstrate how to query the google mobility data using the BigQuery API client python library, and visualize the mobility changes over time across the United States since February 2020.", - "link": "/dashboard/Public/notebooks/google_mobility.html", - "imageUrl": "/dashboard/Public/notebooks/google_mobility.png" - }, - { - "title": "COVID-19 Data Visualization in Illinois", - "description": "This notebook provides a snapshot of publicly available data related to COVID-19 in Illinois from the Illinois Department of Public Health, Google and Johns Hopkins CSSE. Graphics illustrate the demographics, administered vaccine doses, google mobility data and forecasted COVID-19 cases in Illinois.", - "link": "/dashboard/Public/notebooks/IL_tab_charts.html", - "imageUrl": "/dashboard/Public/notebooks/IL_tab_charts.png" - }, - { - "title": "3D Coronavirus SARS-CoV-2 Protein Visualization", - "description": "This notebook provides an example to manipulate coronavirus SARS-CoV-2 DNA sequence, amino acid sequence and use visualization tools to present the three-dimensional (3D) structure of SARS-CoV-2 protein structures interactively.", - "link": "/dashboard/Public/notebooks/3D_Protein_Vis.html", - "imageUrl": "/dashboard/Public/notebooks/3D_Protein_Vis.png" - }, - { - "title": "Data Visualization of COVID-19 Vaccinations, Cases, and Deaths in Illinois", - "description": "This notebook is a snapshot of publically available data and has data visualizations of administed vaccine doses, daily new cases, and daily deaths related to COVID-19.", - "link": "/dashboard/Public/notebooks/covid19_datavis_il.html", - "imageUrl": "/dashboard/Public/notebooks/covid19_datavis_il.png" - }, - { - "title": "Percentage of ICU bed availability prediction in the state of Illinois", - "description": "Since the COVID-19 breakout, the healthcare system in Illinois is under tremendous pressure to satisfy the increased need for COVID-19 treatment. The Delta variant of the coronavirus has been spreading rapidly throughout the US and the world. This variant is highly transmissible and more virulent. It's critical to prepare sufficient medical supplies to meet patients needs, such as ICU beds and ventilators. In this notebook, we construct an Hierarchical Bayesian Binomial Regression model, a Univariate/Multivariate LSTM model and a Univariate/Multivariate CNN-LSTM model forecasting the percentage of ICU bed availability for the next 14 days.", - "link": "/dashboard/Public/notebooks/Percentage_ICU_prediction.html", - "imageUrl": "/dashboard/Public/notebooks/Percentage_ICU_prediction.png" - } - ] - }, "workspacePageTitle": "Welcome to the Gen3 Workspace", "workspacePageDescription": "
What is a Gen3 Workspace?
Gen3 workspaces are secure data analysis environments in the cloud that can access data from one or more data resources, including Gen3 Data Commons.
What can I do with a Gen3 Workspace?
By default Gen3 Workspaces include Jupyter notebooks and RStudio but can be configured to host virtually any application, including analysis workflows, data processing pipelines, or data visualization apps.
How do I get started with Gen3 Workspaces?
Click on any of the images below to start analyzing data!
", "useArboristUI": true, @@ -1192,462 +112,6 @@ "service": "jupyterhub" } }, - "covid19DashboardConfig": { - "dataUrl": "https://opendata.datacommons.io/", - "chartsConfig": { - "illinois": [ - [ - { - "title": "Daily Reported Administered Vaccine Doses in Illinois", - "description": "The source of the data used to compile this chart is retrieved on a daily basis from the Illinois Department of Public Health. This chart depicts the daily reported administered vaccine doses in Illinois.", - "type": "image", - "path": "charts_data/IL_tab_charts_daily_vaccine.svg" - }, - { - "title": "Cumulative Reported Administered Vaccine Doses in Illinois ", - "description": "The source of the data used to compile this chart is retrieved on a daily basis from the Illinois Department of Public Health. This chart depicts the cumulative reported administered vaccine doses in Illinois.", - "type": "image", - "path": "charts_data/IL_tab_charts_cumulative_vaccine.svg" - }, - { - "title": "10 IL Counties With The Highest Administered Vaccine Doses As Of The Most Recent Date", - "description": "The source of the data used to compile this chart is retrieved on a daily basis from the Illinois Department of Public Health. This chart depicts the 10 counties with the highest administered vaccine doses as of the most recent date.", - "type": "image", - "path": "charts_data/IL_tab_charts_vaccine_by_county_top10.svg" - }, - { - "title": "10 IL Counties With The Lowest Administered Vaccine Doses As Of The Most Recent Date", - "description": "The source of the data used to compile this chart is retrieved on a daily basis from the Illinois Department of Public Health. This chart depicts the 10 counties with the lowest administered vaccine doses as of the most recent date.", - "type": "image", - "path": "charts_data/IL_tab_charts_vaccine_by_county_bottom10.svg" - }, - { - "title": "Total Deaths per 10,000 in Chicago", - "description": "The source of the data used to compile this chart is the Cook County Data Portal.", - "xTitle": "", - "yTitle": "", - "type": "barChart", - "layout": "vertical", - "maxItems": 15, - "barColor": "#421C52", - "guppyConfig": { - "dataType": "location", - "xAxisProp": "community_area", - "yAxisProp": "deaths_per_10000", - "filters": { - "AND": [ - { - "=": { - "project_id": "open-CHI-NBHD" - } - } - ] - } - } - }, - { - "title": "Age Demographics in Illinois", - "description": "The source of the data used to compile this chart is retrieved on a daily basis from the Illinois Department of Public Health. This chart depicts the total number of confirmed cases to date by age groups and by race in Illinois.", - "type": "image", - "path": "charts_data/IL_tab_charts_age_demographic.svg" - }, - { - "title": "Race Demographics in Illinois", - "description": "The source of the data used to compile this chart is retrieved on a daily basis from the Illinois Department of Public Health. This chart depicts the total number of confirmed cases to date by race in Illinois.", - "type": "image", - "path": "charts_data/IL_tab_charts_race_demographic.svg" - }, - { - "title": "Gender Demographics in Illinois", - "description": "The source of the data used to compile this chart is retrieved on a daily basis from the Illinois Department of Public Health. This chart depicts the total number of confirmed cases to date by gender in Illinois.", - "type": "image", - "path": "charts_data/IL_tab_charts_gender_demographic.svg" - }, - { - "title": "COVID-19 Google Mobility Data Visualization in Illinois In The Past 3 Months", - "description": "The source of the data used to compile this chart is retrieved on a daily basis from the COVID-19 Community Mobility Reports by Google. This chart shows how visits to places, such as grocery stores and parks, are changing in Illinois in the past 3 months.\nGoogle LLC \"Google COVID-19 Community Mobility Reports\". https://www.google.com/covid19/mobility/ Accessed: Today", - "type": "image", - "path": "charts_data/IL_tab_charts_IL_mobility.svg" - } - ], - [ - { - "title": "Cook County Daily New Cases and Forecast", - "description": "Here we plot daily case counts over time in Cook county, where the red line is reported cases and the grey shaded area depicts the inferred posterior predicted cases. Forecasts (blue shaded area) show how new case numbers would have developed (95% Bayesian credible intervals).", - "type": "image", - "path": "generative_bayes_model/17031/cases.svg" - }, - { - "title": "Cook County Estimated Reproduction Rate (Rt)", - "description": "Here we plot estimated Rt over time in Cook county. We use a generative logic (primary infection, infection delay and onset delay) to explain how an initial pool of infected cases spreads the COVID-19 at each time-point, according to the time-varying reproduction factor. Shaded areas indicate 95% Bayesian credible intervals.", - "type": "image", - "path": "generative_bayes_model/17031/rt.svg" - }, - { - "title": "Using 4-phase Logistic Model And Data From Past 180 Days to Obtain Cumulative Cases Forecasts For Future 60 Days in Illinois", - "description": "The source of the data used to compile this chart is retrieved on a daily basis from the COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University. This chart depicts the future 60 days forecasts for cumulative COVID-19 cases using 4-phase logistic model and data from past 180 days. R square values pertain to the fits of model (olive dash line) to the previous 180 days of observed data (pink dots).", - "type": "image", - "path": "charts_data/IL_tab_charts_cumulative_logistic_last180days.svg" - }, - { - "title": "Using 4-phase Logistic Model And Data From Past 360 Days to Obtain Cumulative Cases Forecasts For Future 120 Days in Illinois", - "description": "The source of the data used to compile this chart is retrieved on a daily basis from the COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University. This chart depicts the future 120 days forecasts for cumulative COVID-19 cases using 4-phase logistic model and data from past 360 days. R square values pertain to the fits of model (olive dash line) to the previous 360 days of observed data (pink dots).", - "type": "image", - "path": "charts_data/IL_tab_charts_cumulative_logistic_last360.svg" - } - ] - ], - "simulations": { - "imgCases": { - "description": "Here we plot daily case counts over time in Cook county, where the red line is reported cases and the grey shaded area depicts the inferred posterior predicted cases. Forecasts (blue shaded area) show how new case numbers would have developed (95% Bayesian credible intervals)." - }, - "imgRt": { - "description": "Here we plot estimated Rt over time in Cook county. We use a generative logic (primary infection, infection delay and onset delay) to explain how an initial pool of infected cases spreads the COVID-19 at each time-point, according to the time-varying reproduction factor. Shaded areas indicate 95% Bayesian credible intervals." - } - } - } - }, - "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", - 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}, - { - "name": "Available Data", - "field": "Available Data", - "color": "#982568", - "display": true - } - ] - }, "connectSrcCSPWhitelist": [ "https://covd-map-occ-prc-prod.s3.amazonaws.com" ] diff --git a/covid19prod/chicagoland.pandemicresponsecommons.org/values/values.yaml b/covid19prod/chicagoland.pandemicresponsecommons.org/values/values.yaml index f7bb17595..df3aae9fc 100644 --- a/covid19prod/chicagoland.pandemicresponsecommons.org/values/values.yaml +++ b/covid19prod/chicagoland.pandemicresponsecommons.org/values/values.yaml @@ -7,427 +7,427 @@ arborist: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist tag: '2026.07' audit: - replicaCount: 2 - enabled: true - externalSecrets: - auditG3auto: covid19prod-audit-g3auto - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service - tag: '2026.07' - serviceAccount: - annotations: - eks.amazonaws.com/role-arn: arn:aws:iam::236714345101:role/covid19prod--covid19prod-helm--audit-sqs-receiver + # replicaCount: 2 + enabled: false + # externalSecrets: + # auditG3auto: covid19prod-audit-g3auto + # image: + # repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service + # tag: '2026.07' + # serviceAccount: + # annotations: + # eks.amazonaws.com/role-arn: arn:aws:iam::236714345101:role/covid19prod--covid19prod-helm--audit-sqs-receiver auspice: - 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- name: date - - name: deaths - - name: deaths_per_10000 - - name: estimated_full_mech_ventilators_per_100000 - - name: estimated_full_mech_pediatric_ventilators - - name: estimated_full_mech_pediatric_ventilators_per_100000 - - name: icu_beds - - name: icu_bed_occupancy_rate - - name: icu_in_use_beds_non_covid - - name: icu_in_use_beds_covid - - name: icu_open_beds - - name: lastUpdateEt - - name: licensed_all_beds - - name: licensed_all_beds_per_1000 - - name: licensed_all_beds_per_1000_gtr_20 - - name: licensed_all_beds_per_1000_gtr_65 - - name: negative - - name: recovered - - name: region_icu_avail - - name: region_icu_capacity - - name: region_vents_available - - name: region_vents_capacity - - name: state_icu_capacity - - name: staffed_all_beds_per_1000 - - name: staffed_all_beds_per_1000_gtr_20 - - name: staffed_all_beds_per_1000_gtr_65 - - name: staffed_icu_beds_per_1000 - - name: staffed_icu_beds_per_1000_gtr_20 - - name: staffed_icu_beds_per_1000_gtr_65 - - name: state_total_beds - - name: testing - - name: ventilator_capacity - - name: ventilator_in_use_non_covid - - name: ventilator_in_use_covid - - name: total_in_use_beds_non_covid - - name: total_in_use_beds_covid - - name: totalTestsViral - - name: provider_subtype - - name: detailed_specialty - - name: new_cases - - name: new_deaths - - name: positive_rate - - name: vaccine_administered_count - - name: vaccine_persons_fully_vaccinated_pct - - name: vaccine_total_delivered_vaccine_doses - - name: vaccine_community_reported_inventory - - name: vaccine_reported_inventory - sorted_by: updated_datetime, desc - - path: summary_socio_demographics - props: - - name: population - - name: population_gtr_65 - - name: population_density - - name: share_asian - - name: share_black - - name: share_hisp - - name: share_white - - name: college_degree - - name: graduate_degree - - name: completed_high_school - - name: employment - - name: job_density - - name: extreme_poverty - - name: jail - - name: hhinc_mean - - name: med_hhinc - - name: gdp_per_capita - - name: life_expectancy - - name: grocery_and_pharmacy_percent_change_from_baseline - - name: parks_percent_change_from_baseline - - name: retail_and_recreation_percent_change_from_baseline - - name: transit_stations_percent_change_from_baseline - - name: workplaces_percent_change_from_baseline - - name: handwashing_facilities - - name: stringency_index - sorted_by: updated_datetime, desc - name: covid19 - parent_props: - - path: projects[project_code:code,project_name:name,project_url:url,project_investigator_affiliation:investigator_affiliation,project_date_collected:date_collected] - props: - - name: submitter_id - - name: project_id - - name: country_region - value_mappings: - - US: United States - - Korea, South: South Korea - - Taiwan*: Taiwan - - name: community_area - - name: province_state - value_mappings: - - AL: Alabama - - AK: Alaska - - AS: American Samoa - - AZ: Arizona - - AR: Arkansas - - CA: California - - CO: Colorado - - CT: Connecticut - - DE: Delaware - - DC: District of Columbia - - FL: Florida - - GA: Georgia - - GU: Guam - - HI: Hawaii - - ID: Idaho - - IL: Illinois - - IN: Indiana - - IA: Iowa - - KS: Kansas - - KY: Kentucky - - LA: Louisiana - - ME: Maine - - MD: Maryland - - MA: Massachusetts - - MI: Michigan - - MN: Minnesota - - MS: Mississippi - - MO: Missouri - - MT: Montana - - NE: Nebraska - - NV: Nevada - - NH: New Hampshire - - NJ: New Jersey - - NM: New Mexico - - NY: New York - - NC: North Carolina - - ND: North Dakota - - MP: Northern Mariana Islands - - OH: Ohio - - OK: Oklahoma - - OR: Oregon - - PA: Pennsylvania - - PR: Puerto Rico - - RI: Rhode Island - - SC: South Carolina - - SD: South Dakota - - TN: Tennessee - - TX: Texas - - VI: US Virgin Islands - - UT: Utah - - VT: Vermont - - VA: Virginia - - WA: Washington - - WV: West Virginia - - WI: Wisconsin - - WY: Wyoming - - name: county - - name: latitude - - name: longitude - - name: FIPS - - name: iso2 - - name: iso3 - - name: reporting_org - - name: state_hospital_region - - name: state_region_description - root: summary_location - type: aggregator - - aggregated_props: - - fn: set - name: image_location - path: imaging_files - src: image_location - doc_type: subject - flatten_props: - - path: demographics - props: - - name: gender - - name: age - - name: race - - name: ethnicity - - name: age_decade - - name: year_of_birth - - name: country_region - - name: province_state - - name: city - - path: observations - props: - - name: treatment_status - - name: isolation_status - - name: icu_status - - name: hospitalized_status - - name: needed_supplemental_O2 - - name: condition - - name: symptoms - - name: reporting_date - - name: reporting_source - - name: date_onset_symptoms - - name: exposure - - name: released_date - - name: hospital - - name: pneumonia_type - - name: ventilator_status - sorted_by: updated_datetime, desc - - path: follow_ups - props: - - name: extubated - value_mappings: - - Y: 'True' - - N: 'False' - - name: pO2_saturation - - name: leukocyte_count - - name: neutrophil_count - - name: lymphocyte_count - - name: view - sorted_by: updated_datetime, desc - name: covid19_subject - parent_props: - - path: projects[project_code:code,project_name:name,project_url:url,project_data_description:data_description,project_investigator_affiliation:investigator_affiliation,project_availability_type:availability_type,project_date_collected:date_collected] - - path: studies[study_doi:study_doi] - props: - - name: project_id - - name: vital_status - - name: covid_19_status - - name: date_confirmation - - name: travel_history_location - - name: infected_by - root: subject - type: aggregator - - doc_type: clinical_trials - name: covid19_clinical_trials - parent_props: - - path: projects[project_code:code,project_name:name,project_url:url,project_data_description:data_description,project_investigator_affiliation:investigator_affiliation,project_availability_type:availability_type,project_date_collected:date_collected] - props: - - name: project_id - - name: completed_clinical_trials - - name: description - - name: development_stage - - name: fda_regulated_drug_product - - name: focus - - name: inprogress_clinical_trials - - name: location - - name: nct_number - - name: phase - - name: sponsor - - name: technology - - name: title - root: clinical_trials - type: aggregator - - category: genomic_data_file - doc_type: genomic_file - injecting_props: - project: - props: - - fn: set - name: project_code - src: code - - fn: set - name: project_name - src: name - - fn: set - name: project_url - src: url - - fn: set - name: project_data_description - src: data_description - - fn: set - name: project_investigator_affiliation - src: investigator_affiliation - - fn: set - name: project_availability_type - src: availability_type - - fn: set - name: project_date_collected - src: date_collected - sample: - props: - - fn: set - name: location - src: location - - fn: set - name: continent - src: continent - - fn: set - name: country_region - src: country_region - - fn: set - name: province_state - src: province_state - - fn: set - name: county - src: county - - fn: set - name: zipcode - src: zipcode - - fn: set - name: host - src: host - - fn: set - name: organism - src: organism - - fn: set - name: sample_type - src: sample_type - - fn: set - name: isolation_source - src: isolation_source - - fn: set - name: isolate - src: isolate - - fn: set - name: collection_date - src: collection_date - - fn: set - name: originating_lab - src: originating_lab - - fn: set - name: submitting_lab - src: submitting_lab - - fn: set - name: submitting_lab_PI - src: submitting_lab_PI - study: - props: - - fn: set - name: journal - src: journal - - fn: set - name: pmid - src: pmid - name: covid19_genomic_file - props: - - name: object_id - - name: md5sum - - name: file_name - - name: file_size - - name: data_format - - name: data_type - - name: state - - name: accession - - name: genbank_accession - - name: sra_accession - - name: assay_type - - name: center_name - - name: nextstrain_clade - - name: submitter_id - root: None - type: collector - - doc_type: dataset - name: covid19_dataset - parent_props: - - path: programs[program_name:name] - props: - - name: code - - name: name - - name: url - - name: data_description - - name: investigator_affiliation - - name: availability_type - - name: date_collected - - name: disclaimer - root: project - type: aggregator - image: - tube: - tag: '2026.07' - spark: - tag: '2026.07' + # replicaCount: 2 + # dashboardConfig: + # bucket: dashboard-236714345101-covid19-prod-gen3 + # prefix: chicagoland.pandemicresponsecommons.org + enabled: false + # image: + # repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics + # tag: '2026.07' + # serviceAccount: + # annotations: + # eks.amazonaws.com/role-arn: arn:aws:iam::236714345101:role/covid19prod--covid19prod-helm--dashboard-access +# etl: +# esEndpoint: elasticsearch +# etlMapping: +# mappings: +# - doc_type: location +# flatten_props: +# - path: summary_clinicals +# props: +# - name: all_bed_occupancy_rate +# - name: confirmed +# - name: date +# - name: deaths +# - name: deaths_per_10000 +# - name: estimated_full_mech_ventilators_per_100000 +# - name: estimated_full_mech_pediatric_ventilators +# - name: estimated_full_mech_pediatric_ventilators_per_100000 +# - name: icu_beds +# - name: icu_bed_occupancy_rate +# - name: icu_in_use_beds_non_covid +# - name: icu_in_use_beds_covid +# - name: icu_open_beds +# - name: lastUpdateEt +# - name: licensed_all_beds +# - name: licensed_all_beds_per_1000 +# - name: licensed_all_beds_per_1000_gtr_20 +# - name: licensed_all_beds_per_1000_gtr_65 +# - name: negative +# - name: recovered +# - name: region_icu_avail +# - name: region_icu_capacity +# - name: region_vents_available +# - name: region_vents_capacity +# - name: state_icu_capacity +# - name: staffed_all_beds_per_1000 +# - name: staffed_all_beds_per_1000_gtr_20 +# - name: staffed_all_beds_per_1000_gtr_65 +# - name: staffed_icu_beds_per_1000 +# - name: staffed_icu_beds_per_1000_gtr_20 +# - name: staffed_icu_beds_per_1000_gtr_65 +# - name: state_total_beds +# - name: testing +# - name: ventilator_capacity +# - name: ventilator_in_use_non_covid +# - name: ventilator_in_use_covid +# - name: total_in_use_beds_non_covid +# - name: total_in_use_beds_covid +# - name: totalTestsViral +# - name: provider_subtype +# - name: detailed_specialty +# - name: new_cases +# - name: new_deaths +# - name: positive_rate +# - name: vaccine_administered_count +# - name: vaccine_persons_fully_vaccinated_pct +# - name: vaccine_total_delivered_vaccine_doses +# - name: vaccine_community_reported_inventory +# - name: vaccine_reported_inventory +# sorted_by: updated_datetime, desc +# - path: summary_socio_demographics +# props: +# - name: population +# - name: population_gtr_65 +# - name: population_density +# - name: share_asian +# - name: share_black +# - name: share_hisp +# - name: share_white +# - name: college_degree +# - name: graduate_degree +# - name: completed_high_school +# - name: employment +# - name: job_density +# - name: extreme_poverty +# - name: jail +# - name: hhinc_mean +# - name: med_hhinc +# - name: gdp_per_capita +# - name: life_expectancy +# - name: grocery_and_pharmacy_percent_change_from_baseline +# - name: parks_percent_change_from_baseline +# - name: retail_and_recreation_percent_change_from_baseline +# - name: transit_stations_percent_change_from_baseline +# - name: workplaces_percent_change_from_baseline +# - name: handwashing_facilities +# - name: stringency_index +# sorted_by: updated_datetime, desc +# name: covid19 +# parent_props: +# - path: projects[project_code:code,project_name:name,project_url:url,project_investigator_affiliation:investigator_affiliation,project_date_collected:date_collected] +# props: +# - name: submitter_id +# - name: project_id +# - name: country_region +# value_mappings: +# - US: United States +# - Korea, South: South Korea +# - Taiwan*: Taiwan +# - name: community_area +# - name: province_state +# value_mappings: +# - AL: Alabama +# - AK: Alaska +# - AS: American Samoa +# - AZ: Arizona +# - AR: Arkansas +# - CA: California +# - CO: Colorado +# - CT: Connecticut +# - DE: Delaware +# - DC: District of Columbia +# - FL: Florida +# - GA: Georgia +# - GU: Guam +# - HI: Hawaii +# - ID: Idaho +# - IL: Illinois +# - IN: Indiana +# - IA: Iowa +# - KS: Kansas +# - KY: Kentucky +# - LA: Louisiana +# - ME: Maine +# - MD: Maryland +# - MA: Massachusetts +# - MI: Michigan +# - MN: Minnesota +# - MS: Mississippi +# - MO: Missouri +# - MT: Montana +# - NE: Nebraska +# - NV: Nevada +# - NH: New Hampshire +# - NJ: New Jersey +# - NM: New Mexico +# - NY: New York +# - NC: North Carolina +# - ND: North Dakota +# - MP: Northern Mariana Islands +# - OH: Ohio +# - OK: Oklahoma +# - OR: Oregon +# - PA: Pennsylvania +# - PR: Puerto Rico +# - RI: Rhode Island +# - SC: South Carolina +# - SD: South Dakota +# - TN: Tennessee +# - TX: Texas +# - VI: US Virgin Islands +# - UT: Utah +# - VT: Vermont +# - VA: Virginia +# - WA: Washington +# - WV: West Virginia +# - WI: Wisconsin +# - WY: Wyoming +# - name: county +# - name: latitude +# - name: longitude +# - name: FIPS +# - name: iso2 +# - name: iso3 +# - name: reporting_org +# - name: state_hospital_region +# - name: state_region_description +# root: summary_location +# type: aggregator +# - aggregated_props: +# - fn: set +# name: image_location +# path: imaging_files +# src: image_location +# doc_type: subject +# flatten_props: +# - path: demographics +# props: +# - name: gender +# - name: age +# - name: race +# - name: ethnicity +# - name: age_decade +# - name: year_of_birth +# - name: country_region +# - name: province_state +# - name: city +# - path: observations +# props: +# - name: treatment_status +# - name: isolation_status +# - name: icu_status +# - name: hospitalized_status +# - name: needed_supplemental_O2 +# - name: condition +# - name: symptoms +# - name: reporting_date +# - name: reporting_source +# - name: date_onset_symptoms +# - name: exposure +# - name: released_date +# - name: hospital +# - name: pneumonia_type +# - name: ventilator_status +# sorted_by: updated_datetime, desc +# - path: follow_ups +# props: +# - name: extubated +# value_mappings: +# - Y: 'True' +# - N: 'False' +# - name: pO2_saturation +# - name: leukocyte_count +# - name: neutrophil_count +# - name: lymphocyte_count +# - name: view +# sorted_by: updated_datetime, desc +# name: covid19_subject +# parent_props: +# - path: projects[project_code:code,project_name:name,project_url:url,project_data_description:data_description,project_investigator_affiliation:investigator_affiliation,project_availability_type:availability_type,project_date_collected:date_collected] +# - path: studies[study_doi:study_doi] +# props: +# - name: project_id +# - name: vital_status +# - name: covid_19_status +# - name: date_confirmation +# - name: travel_history_location +# - name: infected_by +# root: subject +# type: aggregator +# - doc_type: clinical_trials +# name: covid19_clinical_trials +# parent_props: +# - path: projects[project_code:code,project_name:name,project_url:url,project_data_description:data_description,project_investigator_affiliation:investigator_affiliation,project_availability_type:availability_type,project_date_collected:date_collected] +# props: +# - name: project_id +# - name: completed_clinical_trials +# - name: description +# - name: development_stage +# - name: fda_regulated_drug_product +# - name: focus +# - name: inprogress_clinical_trials +# - name: location +# - name: nct_number +# - name: phase +# - name: sponsor +# - name: technology +# - name: title +# root: clinical_trials +# type: aggregator +# - category: genomic_data_file +# doc_type: genomic_file +# injecting_props: +# project: +# props: +# - fn: set +# name: project_code +# src: code +# - fn: set +# name: project_name +# src: name +# - fn: set +# name: project_url +# src: url +# - fn: set +# name: project_data_description +# src: data_description +# - fn: set +# name: project_investigator_affiliation +# src: investigator_affiliation +# - fn: set +# name: project_availability_type +# src: availability_type +# - fn: set +# name: project_date_collected +# src: date_collected +# sample: +# props: +# - fn: set +# name: location +# src: location +# - fn: set +# name: continent +# src: continent +# - fn: set +# name: country_region +# src: country_region +# - fn: set +# name: province_state +# src: province_state +# - fn: set +# name: county +# src: county +# - fn: set +# name: zipcode +# src: zipcode +# - fn: set +# name: host +# src: host +# - fn: set +# name: organism +# src: organism +# - fn: set +# name: sample_type +# src: sample_type +# - fn: set +# name: isolation_source +# src: isolation_source +# - fn: set +# name: isolate +# src: isolate +# - fn: set +# name: collection_date +# src: collection_date +# - fn: set +# name: originating_lab +# src: originating_lab +# - fn: set +# name: submitting_lab +# src: submitting_lab +# - fn: set +# name: submitting_lab_PI +# src: submitting_lab_PI +# study: +# props: +# - fn: set +# name: journal +# src: journal +# - fn: set +# name: pmid +# src: pmid +# name: covid19_genomic_file +# props: +# - name: object_id +# - name: md5sum +# - name: file_name +# - name: file_size +# - name: data_format +# - name: data_type +# - name: state +# - name: accession +# - name: genbank_accession +# - name: sra_accession +# - name: assay_type +# - name: center_name +# - name: nextstrain_clade +# - name: submitter_id +# root: None +# type: collector +# - doc_type: dataset +# name: covid19_dataset +# parent_props: +# - path: programs[program_name:name] +# props: +# - name: code +# - name: name +# - name: url +# - name: data_description +# - name: investigator_affiliation +# - name: availability_type +# - name: date_collected +# - name: disclaimer +# root: project +# type: aggregator +# image: +# tube: +# tag: '2026.07' +# spark: +# tag: '2026.07' fence: - replicaCount: 2 + replicaCount: 1 usersync: usersync: true userYamlS3Path: s3://cdis-gen3-users/covid19/user.yaml @@ -443,10 +443,10 @@ fence: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence tag: '2026.07' fluentd: - enabled: true - image: - repository: fluent/fluentd-kubernetes-daemonset - tag: v1.15.3-debian-cloudwatch-1.0 + enabled: false + # image: + # repository: fluent/fluentd-kubernetes-daemonset + # tag: v1.15.3-debian-cloudwatch-1.0 global: pdb: true aws: @@ -483,27 +483,27 @@ global: dbCreate: false revproxyArn: arn:aws:acm:us-east-1:236714345101:certificate/e5edf56f-4003-4ee3-9ecd-162aaf19c058 guppy: - replicaCount: 2 - authFilterField: auth_resource_path - configIndex: covid19_array-config - enabled: true - esEndpoint: http://elasticsearch:9200 - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy - tag: '2026.07' - indices: - - index: covid19 - type: location - - index: covid19_genomic_file - type: genomic_file - - index: covid19_subject - type: subject - - index: covid19_clinical_trials - type: clinical_trials - - index: covid19_dataset - type: dataset + # replicaCount: 2 + # authFilterField: auth_resource_path + # configIndex: covid19_array-config + enabled: false + # esEndpoint: http://elasticsearch:9200 + # image: + # repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy + # tag: '2026.07' + # indices: + # - index: covid19 + # type: location + # - index: covid19_genomic_file + # type: genomic_file + # - index: covid19_subject + # type: subject + # - index: covid19_clinical_trials + # type: clinical_trials + # - index: covid19_dataset + # type: dataset hatchery: - replicaCount: 2 + replicaCount: 1 enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery @@ -626,35 +626,35 @@ indexd: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd tag: '2026.07' manifestservice: - replicaCount: 2 - enabled: true - externalSecrets: - manifestserviceG3auto: covid19prod-manifestservice-g3auto - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice - tag: '2026.07' - serviceAccount: - annotations: - eks.amazonaws.com/role-arn: arn:aws:iam::236714345101:role/covid19prod--covid19prod-helm--manifest-service-sa + # replicaCount: 2 + enabled: false + # externalSecrets: + # manifestserviceG3auto: covid19prod-manifestservice-g3auto + # image: + # repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice + # tag: '2026.07' + # serviceAccount: + # annotations: + # eks.amazonaws.com/role-arn: arn:aws:iam::236714345101:role/covid19prod--covid19prod-helm--manifest-service-sa metadata: - replicaCount: 2 - enabled: true - esEndpoint: http://elasticsearch:9200 - externalSecrets: - metadataG3auto: covid19prod-metadata-g3auto - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service - tag: '2026.07' + # replicaCount: 1 + enabled: false + # esEndpoint: http://elasticsearch:9200 + # externalSecrets: + # metadataG3auto: covid19prod-metadata-g3auto + # image: + # repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service + # tag: '2026.07' mutatingWebhook: enabled: false peregrine: - replicaCount: 2 - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine - tag: '2026.07' + # replicaCount: 2 + # enabled: false + # image: + # repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine + # tag: '2026.07' portal: - replicaCount: 2 + replicaCount: 1 enabled: true resources: requests: @@ -670,7 +670,7 @@ portal: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal tag: '2026.07' revproxy: - replicaCount: 2 + replicaCount: 1 enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx @@ -679,13 +679,13 @@ revproxy: aws: group: covid19prod sheepdog: - replicaCount: 2 - enabled: true + # replicaCount: 2 + enabled: false image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog tag: '2026.07' sower: - replicaCount: 2 + replicaCount: 1 enabled: true externalSecrets: createK8sPelicanServiceSecret: true @@ -751,12 +751,12 @@ sower: secret: secretName: pelicanservice-g3auto spark: - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark - tag: '2026.05' + enabled: false + # image: + # repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark + # tag: '2026.05' ssjdispatcher: - replicaCount: 2 + replicaCount: 1 enabled: true externalSecrets: credsFile: covid19prod-ssjdispatcher-creds @@ -770,7 +770,7 @@ tube: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube tag: '2026.05' wts: - replicaCount: 2 + replicaCount: 1 enabled: true externalSecrets: createWtsOidcClientSecret: false