OpenUpSA · Segundev · Sep 11, 2025 · Sep 12, 2025 · Sep 13, 2025 · Sep 25, 2025
diff --git a/api/rest.http b/api/rest.http
@@ -6,19 +6,19 @@
 @test_file_md5 = cc70b8e811b39c98a938edf87145e34d
 
 # Fixed IDs for Keycloak permissions
-@study_id = study1
-@analysis_id = analysis001
+@study_id = cholera-267
+@analysis_id = analysis003
 
 # Authentication config
-@username = admin
+@username = system.admin@agari.tech
 @password = pass123
 @realm = agari
 @client_id = dms
-@client_secret = dms-secret
+@client_secret = VDyLEjGR3xDQvoQlrHq5AB6OwbW0Refc
 
 ### 1. LOGIN to get access token
 # @name login
-POST http://keycloak.local/realms/{{realm}}/protocol/openid-connect/token
+POST https://keycloak-staging.openup.org.za/realms/{{realm}}/protocol/openid-connect/token
 Content-Type: application/x-www-form-urlencoded
 
 username={{username}}
@@ -31,7 +31,7 @@ username={{username}}
 @token = {{login.response.body.access_token}}
 
 ### 2. CREATE STUDY
-POST http://song.local/studies/{{study_id}}/
+POST https://song-staging.openup.org.za/studies/{{study_id}}/
 Authorization: Bearer {{token}}
 Content-Type: application/json
 
@@ -46,21 +46,39 @@ Content-Type: application/json
   }
 }
 
+
+### 2.b GET STUDIES
+
+GET https://song-ilifu.openup.org.za/studies/all
+
+
 ### 3a. SUBMIT ANALYSIS
 # @name submitAnalysis
-POST http://song.local/submit/{{study_id}}/
+POST https://song-staging.openup.org.za/submit/{{study_id}}/
 Authorization: Bearer {{token}}
 Content-Type: application/json
 
-< ./data/analysis_submission.json
+< ./metadata/sample/test_data.json
 
 ### 3b. GET ANALYSIS DETAILS
 # Extract analysis_id from step 4 response and get full analysis details
 @submitted_analysis_id = {{submitAnalysis.response.body.analysisId}}
 # @name getAnalysis
-GET http://song.local/studies/{{study_id}}/analysis/{{submitted_analysis_id}}
+GET https://song-staging.openup.org.za/studies/{{study_id}}/analysis/{{submitted_analysis_id}}
 Authorization: Bearer {{token}}
 
+
+### 3c. GET SCHEMAS REGISTRATION
+GET https://song-staging.openup.org.za/schemas/
+
+### 3d. POST SCHEMAS
+POST https://song-staging.openup.org.za/schemas
+Authorization: Bearer {{token}}
+Content-Type: application/json
+
+< ./metadata/sample/test-schema.json
+
+
 ### 4a. INITIALIZE SCORE UPLOAD
 # Extract object_id from step 5 response
 @object_id = {{getAnalysis.response.body.files[0].objectId}}

diff --git a/api/schemas.http b/api/schemas.http
@@ -0,0 +1,101 @@
+# @folio = http://localhost:8000
+@folio = https://folio-staging.openup.org.za
+# @folio = https://folio-ilifu.openup.org.za
+
+# @keycloak = http://keycloak.local
+@keycloak = https://keycloak-staging.openup.org.za
+# @keycloak = https://keycloak-ilifu.openup.org.za
+
+@realm = agari
+@client_id = dms
+@client_secret = VDyLEjGR3xDQvoQlrHq5AB6OwbW0Refc
+
+@username = system.admin@agari.tech
+
+@password = pass123
+
+
+### 1. LOGIN to get access token
+# @name login
+POST {{keycloak}}/realms/{{realm}}/protocol/openid-connect/token
+Content-Type: application/x-www-form-urlencoded
+
+username={{username}}
+&password={{password}}
+&grant_type=password
+&client_id={{client_id}}
+&client_secret={{client_secret}}
+
+###
+@token = {{login.response.body.access_token}}
+
+
+##########################
+### PATHOGENS
+##########################
+
+# @name list_pathogens
+GET {{folio}}/pathogens
+
+###
+
+@pathogen_id = 88938f26-94a6-4ea9-8d16-18eb21e9772d
+
+# @name get_pathogen
+GET {{folio}}/pathogens/{{pathogen_id}}
+
+###
+
+# @update_pathogen
+PUT {{folio}}/pathogens/{{pathogen_id}}
+Authorization: Bearer {{token}}
+Content-Type: application/json
+
+{
+    "schema_id": "8f3fc228-df4f-4994-a20f-38ebfa4d61f2"
+}
+
+
+##########################
+### SCHEMAS
+##########################
+
+# @name list_schemas
+GET {{folio}}/schemas
+Authorization: Bearer {{token}} 
+
+###
+
+# @name register_schema
+POST {{folio}}/schemas/
+Authorization: Bearer {{token}}
+Content-Type: multipart/form-data; boundary=----WebKitFormBoundary456
+
+------WebKitFormBoundary456
+Content-Disposition: form-data; name="metadata"
+
+{
+    "pathogen_id": "{{pathogen_id}}",
+    "name": "mpox_schema",
+    "description": "Schema for mpox pathogen"
+}
+
+------WebKitFormBoundary456
+Content-Disposition: form-data; name="file"; filename="cholera-v5.json"
+Content-Type: application/json
+
+< ./metadata/schemas/mpox/custom-mpox-v5.json
+
+------WebKitFormBoundary456--
+
+
+
+###
+
+@schema_id = 108f50fa-7082-4525-a721-7cdef52d78bf
+
+# @name get_schema
+GET {{folio}}/schemas/{{schema_id}}
+Authorization: Bearer {{token}} 
+
+###
diff --git a/data/analysis_submission.json b/data/analysis_submission.json
diff --git a/data/test_data.fasta b/data/test_data.fasta
diff --git a/helm/keycloak/values.yaml b/helm/keycloak/values.yaml
@@ -27,6 +27,10 @@ ingress:
       paths:
         - path: /
           pathType: Prefix
+          service:
+            name: keycloak
+            port:
+              number: 8080 # <— explicitly tell ingress to target 8080
   tls: []
 
 extraEnv:
@@ -38,6 +42,12 @@ extraEnv:
     value: "false"
   - name: JAVA_OPTS_APPEND
     value: "-Djava.awt.headless=true -Djboss.modules.system.pkgs=org.jboss.byteman -Djava.net.preferIPv4Stack=true -server -Xms512m -Xmx768m"
+  - name: KC_HOSTNAME
+    value: keycloak-ilifu.openup.org.za
+  - name: KC_PROXY
+    value: "edge"
+  - name: KC_CORS_ORIGINS
+    value: "*"
 
 probes:
   liveness:
@@ -46,7 +56,7 @@ probes:
     enabled: true
     tcpSocket:
       port: 8080
-    initialDelaySeconds: 120 
+    initialDelaySeconds: 120
     periodSeconds: 30
     timeoutSeconds: 15
     failureThreshold: 12
@@ -59,14 +69,13 @@ keycloak:
     database: keycloakDb
     username: admin
     password: keycloak-db-pass-123
-  
+
   # Admin user
   admin:
     username: admin
     password: admin123
-  
+
   # Keycloak settings
-  hostname: keycloak.local
   healthEnabled: true
   startupMode: start-dev
 

diff --git a/metadata/museAlternative/index.html b/metadata/museAlternative/index.html
@@ -0,0 +1,113 @@
+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>TSV to JSON Converter</title>
+    <style>
+        body {
+            font-family: Arial, sans-serif;
+            max-width: 800px;
+            margin: 20px auto;
+            padding: 20px;
+        }
+
+        .file-section {
+            margin: 20px 0;
+            padding: 15px;
+            border: 1px solid #ccc;
+            border-radius: 5px;
+        }
+
+        button {
+            background-color: #4CAF50;
+            color: white;
+            padding: 10px 20px;
+            border: none;
+            border-radius: 4px;
+            cursor: pointer;
+            font-size: 16px;
+        }
+
+        button:hover {
+            background-color: #45a049;
+        }
+
+        button:disabled {
+            background-color: #cccccc;
+            cursor: not-allowed;
+        }
+
+        pre {
+            background-color: #f4f4f4;
+            padding: 15px;
+            border-radius: 5px;
+            overflow-x: auto;
+        }
+
+        .input-group {
+            margin: 10px 0;
+        }
+
+        label {
+            display: block;
+            margin-bottom: 5px;
+            font-weight: bold;
+        }
+
+        input[type="text"] {
+            width: 100%;
+            padding: 8px;
+            border: 1px solid #ccc;
+            border-radius: 4px;
+            box-sizing: border-box;
+        }
+    </style>
+</head>
+
+<body>
+    <h1>TSV to JSON Converter with File Metadata</h1>
+
+    <div class="file-section">
+        <h2>1. Upload TSV Metadata File</h2>
+        <input type="file" id="tsvInput" accept=".tsv" />
+    </div>
+
+    <div class="file-section">
+        <h2>2. Upload Genome Files (FASTA, GenBank, etc.)</h2>
+        <input type="file" id="genomeFiles" multiple accept=".fasta,.fa,.gb,.genbank,.fastq" />
+        <p><small>You can select multiple files</small></p>
+    </div>
+
+    <div class="file-section">
+        <h2>3. Study Information</h2>
+        <div class="input-group">
+            <label for="studyId">Study ID:</label>
+            <input type="text" id="studyId" placeholder="e.g., STUDY001" />
+        </div>
+        <div class="input-group">
+            <label for="analysisName">Analysis Type Name:</label>
+            <input type="text" id="analysisName" placeholder="e.g., Genome Assembly" />
+        </div>
+        <div class="input-group">
+            <label for="analysisVersion">Analysis Version:</label>
+            <input type="text" id="analysisVersion" placeholder="e.g., 1.0" />
+        </div>
+    </div>
+
+    <button id="processBtn" disabled>Process Files</button>
+
+    <div class="file-section">
+        <h2>Output:</h2>
+        <pre id="output">Upload files and click "Process Files" to see the result...</pre>
+    </div>
+
+    <!-- Include crypto-js library for MD5 hashing -->
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/crypto-js/4.1.1/crypto-js.min.js"></script>
+
+    <!-- Link your JS file -->
+    <script src="tsvtojson.js"></script>
+</body>
+
+</html>