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Merged
Bearbbcjtc merged 4 commits into from
Mar 21, 2026
Merged

Feat/202603 dataportal #19

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ddcd690
update portal image:1_1_11
Bearbbcjtc Mar 5, 2026
cc9e20a
Merge branch 'main' into feat/202603-dataportal
Bearbbcjtc Mar 7, 2026
70f65e4
update image 1_1_12
Bearbbcjtc Mar 7, 2026
24dd44b
add files data, modify followup link to demo via case
Bearbbcjtc Mar 21, 2026
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143 changes: 139 additions & 4 deletions ardac1prd/portal.ardac.org/values.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -111,12 +111,15 @@
type: molecular_test
- index: ardac_lab
type: lab
- index: file_collect_index
type: file
configIndex:
- ardac_case-array-config
- ardac_follow_up-array-config
- ardac_biospecimen-array-config
- ardac_lab_result-array-config
- ardac_lab-array-config
- file_collect_index-array-config

hatchery:
enabled: true
Expand Down Expand Up @@ -176,7 +179,7 @@

indexd:
enabled: true
defaultPrefix: "dg.XXXX/"

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182:41 [comments] too few spaces before comment: expected 2
externalSecrets:
dbcreds: "ardac1prd-default-indexd-creds"
createK8sServiceCredsSecret: true
Expand Down Expand Up @@ -207,7 +210,7 @@
enabled: true
image:
repository: bearbbhao/ardac-portal
tag: "1_1_11"
tag: "1_1_12"
gitops:
json: |
{
Expand Down Expand Up @@ -285,21 +288,21 @@
"name": "Studies"
},
{
"node": "case",

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"name": "Participants"
},
{
"node": "follow_up",
"name": "Follow_ups"
}
]

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},
"navigation": {
"title": "ARDaC: AlcHepNet Research Data Commons",
"items": [
{
"icon": "dictionary",
"link": "/DD",

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"color": "#421C52",
"name": "Dictionary",
"tooltip": ""
Expand All @@ -313,7 +316,7 @@
{
"icon": "files",
"link": "/files",
"name": "Files",

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"tooltip": ""
},
{
Expand Down Expand Up @@ -393,7 +396,7 @@
"study_id": {
"chartType": "count",
"title": "Studys"
},

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"gender": {
"chartType": "fullPie",
"title": "Sex"
Expand Down Expand Up @@ -1199,6 +1202,124 @@
],
"accessibleValidationField": "project_id"
}
},
{
"tabTitle": "Data Files",
"charts": {
"experimental_strategy": {
"chartType": "bar",
"title": "Experimental Strategy"
},
"data_category": {
"chartType": "pie",
"title": "Data Category"
},
"data_type": {
"chartType": "bar",
"title": "Data Type"
},
"data_format": {
"chartType": "pie",
"title": "Data Format"
}
},
"filters": {
"tabs": [
{
"title": "Data File",
"fields": [
"experimental_strategy",
"data_category",
"data_type",
"data_format"
]
}
]
},
"table": {
"enabled": true,
"fields": [
"submitter_id",
"file_name",
"experimental_strategy",
"data_category",
"data_type",
"data_format"
]
},
"dropdowns": {
"download": {
"title": "Download"
}
},
"buttons": [
{
"enabled": true,
"type": "manifest",
"title": "Download Manifest",
"leftIcon": "datafile",
"rightIcon": "download",
"fileName": "manifest.json",
"dropdownId": "download"
},
{
"enabled": true,
"type": "data-json",
"title": "Download Metadata (JSON)",
"leftIcon": "datafile",
"rightIcon": "download",
"fileName": "data_files.json",
"dropdownId": "download"
}
],
"guppyConfig": {
"dataType": "file",
"nodeCountTitle": "File_collections",
"fieldMapping": [
{
"field": "pat_id",
"name": "Patient Id"
},
{
"field": "visit_day",
"name": "Assessment Date"
},
{
"field": "study_site",
"name": "Clinical site"
},
{
"field": "case_arm",
"name": "Treatment Arm"
},
{
"field": "project_id",
"name": "Project"
},
{
"field": "observational",
"name": "Observational"
},
{
"field": "clinical_trial",
"name": "Clinical Trial"
},
{
"field": "gender",
"name": "sex"
}
],
"manifestMapping": {
"resourceIndexType": "file",
"resourceIdField": "object_id",
"referenceIdFieldInResourceIndex": "_case_id",
"referenceIdFieldInDataIndex": "_case_id"
},
"accessibleFieldCheckList": [
"project_id"
],
"accessibleValidationField": "project_id"
}
}
],
"featureFlags": {
Expand Down Expand Up @@ -1249,7 +1370,7 @@
--g3-default-btn__bg-color: var(--g3-color__white);
--g3-default-btn__border-color: var(--g3-color__gray);
--g3-default-btn__border-color--hover: var(--g3-color__black);

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--g3-disabled-btn__color: var(--g3-color__lightgray);
--g3-disabled-btn__bg-color: var(--g3-color__white);
--g3-disabled-btn__border-color: var(--g3-color__silver);
Expand Down Expand Up @@ -1508,8 +1629,8 @@
requests:
cpu: "500m"
memory: "2Gi"
limits:

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cpu: "1000m"

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memory: "4Gi"
spark:
requests:
Expand Down Expand Up @@ -1647,7 +1768,7 @@
- Heavy Drinker with Alcoholic Hepatits: AH cases
- Heavy Drinker without Alcoholic Hepatits: Heavy Drinking Controls
- Healthy Donor: Healthy Controls
- path: demographics[gender,race,ethnicity,year_of_birth,age_at_index]
- path: cases.demographics[gender,race,ethnicity,year_of_birth,age_at_index]
value_mappings:
- female: Female
- male: Male
Expand Down Expand Up @@ -1687,7 +1808,7 @@
- name: varices_diagnosis_date
- name: weight
aggregated_props:
- name: laboratory_test

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path: molecular_tests
src: laboratory_test
fn: set
Expand All @@ -1709,7 +1830,7 @@
- path: follow_ups[follow_up_id:submitter_id, visit_day].cases[pat_id:submitter_id, case_arm:actarm].studies[study_name, study_id:submitter_id]
- path: follow_ups.cases[pat_id:submitter_id, case_arm:actarm, case_group:cohort, study_site, aki_status, days_180_aki, days_180_survival, days_90_aki, days_90_survival, days_to_aki]
- path: labs[lab_id:submitter_id, lab_name:name_of_institute, PI_name]
- path: follow_ups.demographics[gender, race, ethnicity, year_of_birth, age_at_index]
- path: follow_ups.cases.demographics[gender, race, ethnicity, year_of_birth, age_at_index]

- name: ardac_lab_result
doc_type: molecular_test
Expand All @@ -1718,7 +1839,7 @@
parent_props:
- path: follow_ups[follow_up_id:submitter_id, visit_day].cases[pat_id:submitter_id, case_arm:actarm].studies[study_name, study_id:submitter_id]
- path: follow_ups.cases[pat_id:submitter_id, case_arm:actarm, case_group:cohort, study_site, aki_status, days_180_aki, days_180_survival, days_90_aki, days_90_survival, days_to_aki]
- path: follow_ups.demographics[gender, race, ethnicity, year_of_birth, age_at_index]
- path: follow_ups.cases.demographics[gender, race, ethnicity, year_of_birth, age_at_index]
- path: aliquots.labs[lab_id:submitter_id, lab_name:name_of_institute, PI_name]
props:
- name: project_id
Expand Down Expand Up @@ -1748,3 +1869,17 @@
path: aliquots.molecular_tests
src: laboratory_test
fn: set

- name: file_collect_index
doc_type: file
type: collector
category: data_file
root: None
props:
- name: submitter_id
- name: file_name
- name: experimental_strategy
- name: data_category
- name: data_type
- name: data_format
- name: source_node
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