From 2bcaacfb764b4c87e2ed411fc4b84d3f4e209ace Mon Sep 17 00:00:00 2001 From: matthewpeterkort Date: Fri, 10 Feb 2023 09:09:44 -0800 Subject: [PATCH 1/2] updated gitops from staging --- examples/Secrets/gitops.json | 262 ++++++++++++++++++----------------- 1 file changed, 135 insertions(+), 127 deletions(-) diff --git a/examples/Secrets/gitops.json b/examples/Secrets/gitops.json index e192df1f..96739a13 100644 --- a/examples/Secrets/gitops.json +++ b/examples/Secrets/gitops.json @@ -15,118 +15,87 @@ "explorerConfig":[ { - - "tabTitle": "File", + "tabTitle": "Patient", "charts": { - "data_type": { + "project_id": { "chartType": "stackedBar", - "title": "File Type" + "title": "project_id" }, - "data_format": { + "us_core_race": { "chartType": "stackedBar", - "title": "File Format" + "title": "us_core_race" }, - "patient_gender": { + "us_core_ethnicity": { "chartType": "stackedBar", - "title": "Gender" + "title": "us_core_ethnicity" }, - "patient_maritalStatus_coding_0_display": { + "gender": { "chartType": "stackedBar", - "title": "Marital Status" + "title": "gender" }, - "patient_ombCategory": { + "maritalStatus": { "chartType": "stackedBar", - "title": "OMB Category" + "title": "maritalStatus" } }, "filters": { "tabs": [ - { - "title": "File", - "fields": [ - "project_id", - "file_category", - "data_type", - "data_format" - ] - }, { "title": "Patient", "fields": [ "project_id", - "patient_id", - "patient_gender", - "patient_disability_adjusted_life_years", - "patient_ombCategory", - "patient_ombCategory_detail", - "patient_us_core_birthsex", - "patient_quality_adjusted_life_years" + "us_core_race", + "us_core_ethnicity", + "gender", + "maritalStatus", + "quality_adjusted_life_years_valueDecimal", + "disability_adjusted_life_years_valueDecimal" ] } - ] }, "table": { "enabled": true, "fields": [ + "id", "project_id", - "patient_id", - "patient_gender", - "patient_disability_adjusted_life_years", - "patient_ombCategory", - "patient_ombCategory_detail", - "patient_us_core_birthsex", - "patient_quality_adjusted_life_years", - "file_category", - "file_name", - "file_size", - "object_id" + "us_core_race", + "us_core_ethnicity", + "gender", + "maritalStatus", + "quality_adjusted_life_years_valueDecimal", + "disability_adjusted_life_years_valueDecimal" ] }, "dropdowns": {}, "guppyConfig": { - "dataType": "file", - "fieldMapping": [ - { "field": "object_id", "name": "Download ID" }, - { "field": "patient_gender", "name": "Gender" }, - { "field": "patient_disability_adjusted_life_years", "name": "Disability Adjusted Life Years" }, - { "field": "patient_quality_adjusted_life_years", "name": "Quality Adjusted Life Years" }, - { "field": "patient_ombCategory", "name": "OMB Category" }, - { "field": "patient_ombCategory_detail", "name": "OMB Category Detail" }, - { "field": "patient_us_core_birthsex", "name": "Birth Sex" }, - { "field": "file_category", "name": "Category" }, - { "field": "file_name", "name": "Name" }, - { "field": "data_type", "name": "Type" }, - { "field": "data_format", "name": "Format" } + "dataType": "patient", + "fieldMapping": [ + { "field": "quality_adjusted_life_years_valueDecimal", "name": "quality_adjusted_life_years" }, + { "field": "disability_adjusted_life_years_valueDecimal", "name": "disability_adjusted_life_years" } ], - "nodeCountTitle": "Files", + "nodeCountTitle": "Patients", "manifestMapping": { "resourceIndexType": "Patient", - "resourceIdField": "_patient_id", - "referenceIdFieldInResourceIndex": "object_id", - "referenceIdFieldInDataIndex": "object_id" + "resourceIdField": "id", + "referenceIdFieldInResourceIndex": "id", + "referenceIdFieldInDataIndex": "id" }, "accessibleFieldCheckList": ["project_id"], - "accessibleValidationField": "project_id", - "downloadAccessor": "object_id" + "accessibleValidationField": "project_id" } }, - { "tabTitle": "Observation", "charts": { - "category": { - "chartType": "stackedBar", - "title": "Category" - }, - "encounter_type": { + "project_id": { "chartType": "stackedBar", - "title": "Encounter Type" + "title": "Project" }, - "code_display": { + "category": { "chartType": "stackedBar", - "title": "Code" + "title": "Category" } }, "filters": { @@ -134,16 +103,83 @@ { "title": "Observation", "fields": [ + "project_id", "category", - "code_display" + "code" ] - }, + } + ] + }, + "table": { + "enabled": true, + "fields": [ + "patient_id", + "project_id", + "category", + "code", + "bodySite", + "effectiveDateTime", + "valueBoolean", + "valueCodeableConcept", + "valueDateTime", + "valueInteger", + "valueQuantity", + "valueRange", + "valueRatio", + "valueSampledData", + "valueString", + "diastolic_blood_pressure", + "systolic_blood_pressure", + "conclusion_string", + "evidence_level", + "evidence_level_coding", + "gene_studied_id", + "gene_studied_id_coding", + "genomic_reference_sequence_id", + "genomic_reference_sequence_id_coding", + "interpretation", + "observation_interpretation", + "predicted_phenotype", + "predicted_phenotype_coding" + ] + }, + "dropdowns": {}, + "guppyConfig": { + "dataType": "observation", + "fieldMapping": [], + "nodeCountTitle": "Observations", + "manifestMapping": { + "resourceIndexType": "Patient", + "resourceIdField": "_patient_id", + "referenceIdFieldInResourceIndex": "object_id", + "referenceIdFieldInDataIndex": "object_id" + }, + "accessibleFieldCheckList": ["project_id"], + "accessibleValidationField": "project_id" + } + }, + + { + + "tabTitle": "File", + "charts": { + "data_type": { + "chartType": "stackedBar", + "title": "File Type" + }, + "data_format": { + "chartType": "stackedBar", + "title": "File Format" + } + }, + "filters": { + "tabs": [ { - "title": "Encounter", + "title": "File", "fields": [ - "patient_id", - "encounter_type", - "encounter_start" + "project_id", + "data_type", + "data_format" ] } ] @@ -151,37 +187,33 @@ "table": { "enabled": true, "fields": [ + "project_id", "patient_id", - "category", - "code_display", - "valueQuantity_value", - "valueQuantity_unit", - "valueCodeableConcept_coding_0_display", - "component_0_code_coding_0_display", - "component_0_valueQuantity_value", - "component_0_valueQuantity_unit", - "component_1_code_coding_0_display", - "component_1_valueQuantity_value", - "component_1_valueQuantity_unit" + "object_id", + "author", + "content_url", + "category_coding", + "category_coding_display", + "date", + "data_type", + "data_format", + "file_name", + "file_size", + "id", + "status", + "type_coding" ] }, "dropdowns": {}, "guppyConfig": { - "dataType": "case", - "fieldMapping": [ - { "field": "category", "name": "Category" }, - { "field": "code_display", "name": "Code" }, - { "field": "valueQuantity_value", "name": "Quantity Value" }, - { "field": "valueQuantity_unit", "name": "Quantity Unit" }, - { "field": "valueCodeableConcept_coding_0_display", "name": "Coding" }, - { "field": "component_0_code_coding_0_display", "name": "Component" }, - { "field": "component_0_valueQuantity_value", "name": "Component Value" }, - { "field": "component_0_valueQuantity_unit", "name": "Component Unit" }, - { "field": "component_1_code_coding_0_display", "name": "Component" }, - { "field": "component_1_valueQuantity_value", "name": "Component Value" }, - { "field": "component_1_valueQuantity_unit", "name": "Component Unit" } + "dataType": "file", + "fieldMapping": [ + { "field": "object_id", "name": "Download ID" }, + { "field": "file_name", "name": "Name" }, + { "field": "data_type", "name": "Type" }, + { "field": "data_format", "name": "Format" } ], - "nodeCountTitle": "Observations", + "nodeCountTitle": "Files", "manifestMapping": { "resourceIndexType": "Patient", "resourceIdField": "_patient_id", @@ -193,7 +225,6 @@ "downloadAccessor": "object_id" } } - ], @@ -429,8 +460,7 @@ "index": { "introduction": { "heading": "Open Access Data Commons", - "text": "The Open Access Data Commons supports the management, analysis and sharing of data for the research community with the aim of accelerating discovery and development of diagnostics, treatment and prevention of diseases.", - "link": "/submission" + "text": "The Open Access Data Commons supports the management, analysis and sharing of data for the research community with the aim of accelerating discovery and development of diagnostics, treatment and prevention of diseases." }, "buttons": [ { @@ -460,15 +490,9 @@ "body": "Discover study descriptions and other metadata stored on the Data Commons", "link": "/discovery", "label": "Discover Study Metadata" - }, - { - "name": "Analyze Data", - "icon": "data-analyze", - "body": "Perform analysis on the Open Access Data Commons data using Jupyter Notebooks.", - "link": "/workspace", - "label": "Run analysis" } ] + }, "navigation": { "items": [ @@ -499,19 +523,6 @@ "name": "Query", "tooltip": "Query the databases using GraphiQL." }, - { - "name": "Notebook Browser", - "link": "/resource-browser", - "icon": "analysis", - "tooltip": "Learn how to use Jupyter Notebooks to explore and visualize data available by running a tutorial notebook, or use one of these examples as a launching point for your own custom analysis." - }, - { - "icon": "workspace", - "link": "#hostname#workspace/", - "color": "#a2a2a2", - "name": "Workspace", - "tooltip": "Gen3 workspaces are secure data analysis environments in the cloud that can access data from one or more data resources." - }, { "icon": "profile", "link": "/identity", @@ -523,11 +534,6 @@ }, "topBar": { "items": [ - { - "icon": "upload", - "link": "/submission", - "name": "Submit Data" - }, { "link": "https://gen3.org/resources/user", "name": "Documentation" @@ -602,4 +608,6 @@ ], "projectDetails": "boardCounts" } + } + From ec69395bb3a642a7e41f9ff980c818b5b2cc6d48 Mon Sep 17 00:00:00 2001 From: matthewpeterkort Date: Mon, 13 Feb 2023 09:07:04 -0800 Subject: [PATCH 2/2] further gitops changes --- examples/Secrets/gitops.json | 38 +++++++----------------------------- 1 file changed, 7 insertions(+), 31 deletions(-) diff --git a/examples/Secrets/gitops.json b/examples/Secrets/gitops.json index 96739a13..6d158df2 100644 --- a/examples/Secrets/gitops.json +++ b/examples/Secrets/gitops.json @@ -456,11 +456,11 @@ }, "components": { - "appName": "The Open Access Data Commons Portal", + "appName": "ACED", "index": { "introduction": { - "heading": "Open Access Data Commons", - "text": "The Open Access Data Commons supports the management, analysis and sharing of data for the research community with the aim of accelerating discovery and development of diagnostics, treatment and prevention of diseases." + "heading": "ACED", + "text": "We are uniting world leading researchers to tackle the biggest challenges in early detection, an important area of unmet clinical need. Scientists in the Alliance are working together at the forefront of technological innovation to translate research into realistic ways to improve cancer diagnosis, which can be implemented into health systems and meaningfully benefit people with cancer." }, "buttons": [ { @@ -470,20 +470,6 @@ "link": "/DD", "label": "Explore Data Model" }, - { - "name": "Explore Data", - "icon": "data-explore", - "body": "Search and download subsets of data from the Open Access Data Commons using intuitive navigation tools.", - "link": "/explorer", - "label": "Explore data" - }, - { - "name": "Query Data", - "icon": "data-access", - "body": "Search and download subsets of data from the Open Access Data Commons using GraphQL queries.", - "link": "/query", - "label": "Query data" - }, { "name": "Discover Study Metadata", "icon": "data-explore", @@ -535,30 +521,20 @@ "topBar": { "items": [ { - "link": "https://gen3.org/resources/user", - "name": "Documentation" + "link": "https://www.cancerresearchuk.org/funding-for-researchers/research-opportunities-in-early-detection-and-diagnosis/international-alliance-for-cancer-early-detection", + "name": "ACED" } ] }, "login": { - "title": "Open Access Data Commons", + "title": "ACED", "subTitle": "Explore, Analyze, and Share Data", - "text": "The Open Access Data Commons is a scalable cloud-based platform for computational discovery designed for the health community.", + "text": "We are uniting world leading researchers to tackle the biggest challenges in early detection, an important area of unmet clinical need. Scientists in the Alliance are working together at the forefront of technological innovation to translate research into realistic ways to improve cancer diagnosis, which can be implemented into health systems and meaningfully benefit people with cancer.", "contact": "If you have any questions about access or the registration process, please contact ", "email": "support@datacommons.io", "image": "/../../../../custom/sponsors/gitops-sponsors/gene_bgy" }, "footerLogos": [ - { - "src": "/src/img/gen3.png", - "href": "https://ctds.uchicago.edu/gen3", - "alt": "Gen3 Data Commons" - }, - { - "src": "/src/img/createdby.png", - "href": "https://ctds.uchicago.edu/", - "alt": "Center for Translational Data Science at the University of Chicago" - } ] },