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TASK-7645 - Integrated Clinical Preprocessing, Variant Assessment, and Reporting #128

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TASK-7645 - Integrated Clinical Preprocessing, Variant Assessment, and Reporting #128

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fab7c14
lib: support multiple values for same key, #TASK-7610
pfurio Nov 14, 2025
ad76281
Merge branch 'develop' into TASK-7610
pfurio Nov 28, 2025
27db4a8
Merge branch 'develop' into TASK-7610
j-coll Nov 28, 2025
c19e138
Merge branch 'TASK-7610' of github.com:opencb/java-common-libs into T…
pfurio Nov 28, 2025
cbb5f54
Merge branch 'develop' into TASK-7645
pfurio Dec 4, 2025
b22aa8d
Merge branch 'develop' into TASK-7610
pfurio Dec 4, 2025
1a0310d
Merge branch 'TASK-7610' into TASK-7645
pfurio Dec 4, 2025
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56 changes: 34 additions & 22 deletions commons-lib/src/main/java/org/opencb/commons/utils/DockerUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,13 +26,13 @@ public class DockerUtils {
* @param inputBindings Array of bind mounts for docker input volumes (source-target)
* @param outputBinding Bind mount for docker output volume (source-target)
* @param cmdParams Image command parameters
* @param dockerParams Docker parameters
* @param dockerParams Docker parameters (each key can have multiple values, e.g., for multiple --env settings)
* @return The command line
* @throws IOException IO exception
*/
public static String buildCommandLine(String image, List<AbstractMap.SimpleEntry<String, String>> inputBindings,
AbstractMap.SimpleEntry<String, String> outputBinding, String cmdParams,
Map<String, String> dockerParams) throws IOException {
Map<String, List<String>> dockerParams) throws IOException {
return buildCommandLine(image, inputBindings, Collections.singletonList(outputBinding), cmdParams, dockerParams);
}

Expand All @@ -43,13 +43,13 @@ public static String buildCommandLine(String image, List<AbstractMap.SimpleEntry
* @param inputBindings Array of bind mounts for docker input volumes (source-target)
* @param outputBindings Array of bind mount for docker output volume (source-target)
* @param cmdParams Image command parameters
* @param dockerParams Docker parameters
* @param dockerParams Docker parameters (each key can have multiple values, e.g., for multiple --env settings)
* @return The command line
* @throws IOException IO exception
*/
public static String buildCommandLine(String image, List<AbstractMap.SimpleEntry<String, String>> inputBindings,
List<AbstractMap.SimpleEntry<String, String>> outputBindings, String cmdParams,
Map<String, String> dockerParams) throws IOException {
Map<String, List<String>> dockerParams) throws IOException {
// Sanity check
if (outputBindings == null || outputBindings.isEmpty()) {
throw new IllegalArgumentException("Missing output binding(s)");
Expand All @@ -65,16 +65,28 @@ public static String buildCommandLine(String image, List<AbstractMap.SimpleEntry
setUser = false;
}
for (String key : dockerParams.keySet()) {
if (key.equals("user") && StringUtils.isEmpty(dockerParams.get("user"))) {
// User wants to disable user setting
continue;
}
if (!key.startsWith("-")) {
commandLine.append("--");
}
commandLine.append(key).append(" ");
if (StringUtils.isNotEmpty(dockerParams.get(key))) {
commandLine.append(dockerParams.get(key)).append(" ");
List<String> values = dockerParams.get(key);
if (values == null || values.isEmpty()) {
if (key.equals("user")) {
// User wants to disable user setting
continue;
}
// Parameter without value (flag)
if (!key.startsWith("-")) {
commandLine.append("--");
}
commandLine.append(key).append(" ");
} else {
// Parameter with value(s) - can have multiple values for same key
for (String value : values) {
if (!key.startsWith("-")) {
commandLine.append("--");
}
commandLine.append(key).append(" ");
if (StringUtils.isNotEmpty(value)) {
commandLine.append(value).append(" ");
}
}
}
}
}
Expand Down Expand Up @@ -198,7 +210,7 @@ public static boolean login(String registry, String username, String password) t
* @param inputBindings Array of bind mounts for docker input volumes (source-target)
* @param outputBinding Bind mount for docker output volume (source-target)
* @param cmdParams Image command parameters
* @param dockerParams Docker parameters
* @param dockerParams Docker parameters (each key can have multiple values, e.g., for multiple --env settings)
* @param registry Docker registry URL
* @param username Optional Docker registry username
* @param password Optional Docker registry password
Expand All @@ -207,7 +219,7 @@ public static boolean login(String registry, String username, String password) t
*/
public static String run(String image, List<AbstractMap.SimpleEntry<String, String>> inputBindings,
AbstractMap.SimpleEntry<String, String> outputBinding, String cmdParams,
Map<String, String> dockerParams, String registry, String username, String password) throws IOException {
Map<String, List<String>> dockerParams, String registry, String username, String password) throws IOException {
return run(image, inputBindings, outputBinding != null ? Collections.singletonList(outputBinding) : null,
cmdParams, dockerParams, registry, username, password);
}
Expand All @@ -219,13 +231,13 @@ public static String run(String image, List<AbstractMap.SimpleEntry<String, Stri
* @param inputBindings Array of bind mounts for docker input volumes (source-target)
* @param outputBinding Bind mount for docker output volume (source-target)
* @param cmdParams Image command parameters
* @param dockerParams Docker parameters
* @param dockerParams Docker parameters (each key can have multiple values, e.g., for multiple --env settings)
* @return The command line
* @throws IOException IO exception
*/
public static String run(String image, List<AbstractMap.SimpleEntry<String, String>> inputBindings,
AbstractMap.SimpleEntry<String, String> outputBinding, String cmdParams,
Map<String, String> dockerParams) throws IOException {
Map<String, List<String>> dockerParams) throws IOException {
return run(image, inputBindings, outputBinding != null ? Collections.singletonList(outputBinding) : null, cmdParams, dockerParams);
}

Expand All @@ -236,13 +248,13 @@ public static String run(String image, List<AbstractMap.SimpleEntry<String, Stri
* @param inputBindings Array of bind mounts for docker input volumes (source-target)
* @param outputBindings Array of bind mount for docker output volume (source-target)
* @param cmdParams Image command parameters
* @param dockerParams Docker parameters
* @param dockerParams Docker parameters (each key can have multiple values, e.g., for multiple --env settings)
* @return The command line
* @throws IOException IO exception
*/
public static String run(String image, List<AbstractMap.SimpleEntry<String, String>> inputBindings,
List<AbstractMap.SimpleEntry<String, String>> outputBindings, String cmdParams,
Map<String, String> dockerParams) throws IOException {
Map<String, List<String>> dockerParams) throws IOException {
return run(image, inputBindings, outputBindings, cmdParams, dockerParams, null, null, null);
}

Expand All @@ -253,7 +265,7 @@ public static String run(String image, List<AbstractMap.SimpleEntry<String, Stri
* @param inputBindings Array of bind mounts for docker input volumes (source-target)
* @param outputBindings Array of bind mount for docker output volume (source-target)
* @param cmdParams Image command parameters
* @param dockerParams Docker parameters
* @param dockerParams Docker parameters (each key can have multiple values, e.g., for multiple --env settings)
* @param registry Optional Docker registry URL (null if not using private registry)
* @param username Optional Docker registry username
* @param password Optional Docker registry password
Expand All @@ -262,7 +274,7 @@ public static String run(String image, List<AbstractMap.SimpleEntry<String, Stri
*/
public static String run(String image, List<AbstractMap.SimpleEntry<String, String>> inputBindings,
List<AbstractMap.SimpleEntry<String, String>> outputBindings, String cmdParams,
Map<String, String> dockerParams, String registry, String username, String password) throws IOException {
Map<String, List<String>> dockerParams, String registry, String username, String password) throws IOException {

checkDockerDaemonAlive();

Expand Down
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