Sync fork 8

.github/workflows/ghcr-actions.yml

@@ -18,7 +18,7 @@ jobs:
       packages: write
     steps:
       - name: Delete 'PR' containers older than one month
-        uses: snok/container-retention-policy@v3.0.0
+        uses: snok/container-retention-policy@v3.0.1
         with:
           account: ${{ github.repository_owner }}
           image-names: sensitive-data-archive

charts/sda-svc/templates/api-deploy.yaml

@@ -100,6 +100,7 @@ spec:
         - name: inbox
           mountPath: "/inbox"
     {{- end }}
+      enableServiceLinks: false
       volumes:
     {{- if not .Values.global.vaultSecrets }}
         - name: config

charts/sda-svc/templates/auth-deploy.yaml

@@ -99,6 +99,7 @@ spec:
         - name: c4gh
           mountPath: {{ template "c4ghPath" . }}
       {{- end }}
+      enableServiceLinks: false
       volumes:
       {{- if not .Values.global.vaultSecrets }}
         {{- if and (.Values.global.auth.resignJwt) (not .Values.global.vaultSecrets) }}

charts/sda-svc/templates/doa-deploy.yaml

@@ -281,6 +281,7 @@ spec:
         - name: archive
           mountPath: {{ .Values.global.archive.volumePath | quote }}
       {{- end }}
+      enableServiceLinks: false
       volumes:
         - name: tmp
           emptyDir: {}

charts/sda-svc/templates/download-deploy.yaml

@@ -100,6 +100,7 @@ spec:
         - name: archive
           mountPath: {{ .Values.global.archive.volumePath | quote }}
       {{- end }}
+      enableServiceLinks: false
       volumes:
       {{- if and (not .Values.global.pkiService) .Values.global.tls.enabled }}
         - name: tls

charts/sda-svc/templates/finalize-deploy.yaml

@@ -92,6 +92,7 @@ spec:
         - name: backup
           mountPath: {{ .Values.global.backupArchive.volumePath | quote }}
     {{- end }}
+      enableServiceLinks: false
       volumes:
       {{- if not .Values.global.vaultSecrets }}
         - name: config

charts/sda-svc/templates/ingest-deploy.yaml

@@ -95,6 +95,7 @@ spec:
         - name: inbox
           mountPath: {{ .Values.global.inbox.path | quote }}
       {{- end }}
+      enableServiceLinks: false
       volumes:
     {{- if not .Values.global.vaultSecrets }}
         - name: config

charts/sda-svc/templates/intercept-deploy.yaml

@@ -70,6 +70,7 @@ spec:
         - name: tls
           mountPath: {{ template "tlsPath" . }}
       {{- end }}
+      enableServiceLinks: false
       volumes:
         - name: config
           projected:

charts/sda-svc/templates/mapper-deploy.yaml

@@ -71,6 +71,7 @@ spec:
         - name: inbox
           mountPath: {{ .Values.global.inbox.path | quote }}
       {{- end }}
+      enableServiceLinks: false
       volumes:
       {{- if not .Values.global.vaultSecrets }}
         - name: config

charts/sda-svc/templates/re-encrypt-deploy.yaml

@@ -73,6 +73,7 @@ spec:
         - name: tls
           mountPath: {{ template "tlsPath" . }}
         {{- end }}
+      enableServiceLinks: false
       volumes:
       {{- if not .Values.global.vaultSecrets }}
         - name: config

charts/sda-svc/templates/release-test-deploy.yml

@@ -89,6 +89,7 @@ spec:
       command: [ "/bin/bash" ]
       args:
         - "/release-test-app/release-test.sh"
+  enableServiceLinks: false
   volumes:
     {{- if and (not .Values.global.pkiService) .Values.global.tls.enabled }}
       - name: certs

charts/sda-svc/templates/s3-inbox-deploy.yaml

@@ -115,6 +115,7 @@ spec:
           mountPath: {{ include "jwtPath" . }}
         {{- end }}
       {{- end }}
+      enableServiceLinks: false
       volumes:
       {{- if and (not .Values.global.pkiService) .Values.global.tls.enabled }}
         - name: tls

charts/sda-svc/templates/sftp-inbox-deploy.yaml

@@ -164,6 +164,7 @@ spec:
           mountPath: "/etc/ssl/certs/java"
         - name: tmp
           mountPath: /tmp/
+      enableServiceLinks: false
       volumes:
         - name: tmp
           emptyDir: {}

charts/sda-svc/templates/sync-deploy.yaml

@@ -92,6 +92,7 @@ spec:
           - name: tls
             mountPath: {{ template "tlsPath" . }}
   {{- end }}
+      enableServiceLinks: false
       volumes:
       {{- if and (not .Values.global.pkiService) .Values.global.tls.enabled }}
         - name: tls

charts/sda-svc/templates/syncapi-deploy.yaml

@@ -92,6 +92,7 @@ spec:
         - name: tls
           mountPath: {{ template "tlsPath" . }}
       {{- end }}
+      enableServiceLinks: false
       volumes:
       {{- if not .Values.global.vaultSecrets }}
         - name: config

charts/sda-svc/templates/verify-deploy.yaml

@@ -74,6 +74,7 @@ spec:
         - name: archive
           mountPath: {{ .Values.global.archive.volumePath | quote }}
         {{- end }}
+      enableServiceLinks: false
       volumes:
       {{- if and (not .Values.global.pkiService) .Values.global.tls.enabled }}
         - name: tls

sda-doa/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>3.5.5</version>
+        <version>3.5.6</version>
         <relativePath/>
     </parent>
     <groupId>no.uio.ifi</groupId>
@@ -21,7 +21,7 @@
         <dependency>
             <groupId>com.google.code.gson</groupId>
             <artifactId>gson</artifactId>
-            <version>2.13.1</version>
+            <version>2.13.2</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
@@ -84,7 +84,7 @@
         <dependency>
             <groupId>io.minio</groupId>
             <artifactId>minio</artifactId>
-            <version>8.5.17</version>
+            <version>8.6.0</version>
         </dependency>
         <dependency>
             <groupId>net.logstash.logback</groupId>
@@ -110,7 +110,7 @@
         <dependency>
             <groupId>no.elixir</groupId>
             <artifactId>crypt4gh</artifactId>
-            <version>3.0.33</version>
+            <version>3.0.34</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.slf4j</groupId>
@@ -121,7 +121,7 @@
         <dependency>
             <groupId>no.elixir</groupId>
             <artifactId>clearinghouse</artifactId>
-            <version>3.0.8</version>
+            <version>3.0.10</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.slf4j</groupId>
@@ -134,6 +134,11 @@
             <artifactId>snakeyaml</artifactId>
             <version>2.5</version>
         </dependency>
+        <dependency>
+            <groupId>com.squareup.okhttp3</groupId>
+            <artifactId>okhttp-jvm</artifactId>
+            <version>5.1.0</version>
+        </dependency>
     </dependencies>
 
     <build>

sda-download/api/api.md

@@ -59,25 +59,19 @@ For example, given a dataset name `https://doi.org/abc/123`, one can do `GET /me
 [
     {
         "fileId": "urn:file:1",
-        "datasetId": "dataset_1",
         "displayFileName": "file_1.txt.c4gh",
-        "fileName": "hash",
-        "fileSize": 60,
+        "filePath": "directory/file_1.txt.c4gh",
         "decryptedFileSize": 32,
         "decryptedFileChecksum": "hash",
         "decryptedFileChecksumType": "SHA256",
-        "fileStatus": "READY"
     },
     {
         "fileId": "urn:file:2",
-        "datasetId": "dataset_1",
         "displayFileName": "file_2.txt.c4gh",
-        "fileName": "hash",
-        "fileSize": 60,
+        "filePath": "directory/file_2.txt.c4gh",       
         "decryptedFileSize": 32,
         "decryptedFileChecksum": "hash",
         "decryptedFileChecksumType": "SHA256",
-        "fileStatus": "READY"
     },
 ]
 ```

sda-download/api/s3/s3.go

@@ -72,7 +72,7 @@
 		return
 	}
 	c.XML(http.StatusAccepted, LocationConstraint{
 		XMLns:    "http://s3.amazonaws.com/doc/2006-03-01/",
 		Location: "us-west-2",
 	})
 }
@@ -185,13 +185,13 @@
 	})
 }
 
-func getFileInfo(c *gin.Context) (fileInfo *database.FileInfo, err error) {
+func getFileStableID(c *gin.Context) (fileStableID string, err error) {
 	// Get file info for the given file path (or abort)
 	filename := c.Param("filename")
 	if !strings.HasSuffix(c.Param("filename"), ".c4gh") {
 		filename = c.Param("filename") + ".c4gh"
 	}
-	fileInfo, err = database.GetDatasetFileInfo(c.Param("dataset"), filename)
+	fileStableID, err = database.GetDatasetFileStableID(c.Param("dataset"), filename)
 	if err != nil {
 		if err.Error() == "sql: no rows in result set" {
 			c.AbortWithStatus(http.StatusNotFound)
@@ -202,7 +202,7 @@
 		return
 	}
 
-	return fileInfo, nil
+	return fileStableID, nil
 }
 
 // GetObject respondes to an S3 GetObject request. This request returns S3
@@ -213,7 +213,7 @@
 func GetObject(c *gin.Context) {
 	log.Debugf("S3 GetObject request, context: %v", c.Params)
 
-	fileInfo, err := getFileInfo(c)
+	fileStableID, err := getFileStableID(c)
 	if err != nil {
 		return
 	}
@@ -222,7 +222,7 @@
 	c.Set("S3", true)
 
 	// set the fileID so that download knows what file to download
-	c.Params = append(c.Params, gin.Param{Key: "fileid", Value: fileInfo.FileID})
+	c.Params = append(c.Params, gin.Param{Key: "fileid", Value: fileStableID})
 
 	// Download the file
 	sda.Download(c)
@@ -236,7 +236,7 @@
 func GetEcnryptedObject(c *gin.Context) {
 	log.Debugf("S3 GetEncryptedObject request, context: %v", c.Params)
 
-	fileInfo, err := getFileInfo(c)
+	fileStableID, err := getFileStableID(c)
 	if err != nil {
 		return
 	}
@@ -245,7 +245,7 @@
 	c.Set("S3", true)
 
 	// set the fileID so that download knows what file to download
-	c.Params = append(c.Params, gin.Param{Key: "fileid", Value: fileInfo.FileID})
+	c.Params = append(c.Params, gin.Param{Key: "fileid", Value: fileStableID})
 
 	// set the encrypted parameter so that download gets the encrypted file instead
 	c.Params = append(c.Params, gin.Param{Key: "type", Value: "encrypted"})