Update approach in build.gradle to SequenceAnalysis dependencies (#124)

Author: bbimber

covidseq/build.gradle

@@ -12,7 +12,6 @@ dependencies {
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "apiJarFile")
-    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "runtimeElements")
 
     BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "published", depExtension: "module")
     BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "published", depExtension: "module")

primeseq/build.gradle

@@ -10,7 +10,6 @@ dependencies {
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "apiJarFile")
-    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "runtimeElements")
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:cluster", depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:jbrowse", depProjectConfig: "apiJarFile")
 

primeseq/src/org/labkey/primeseq/PrimeseqController.java

@@ -46,7 +46,9 @@
 import org.labkey.api.security.RequiresSiteAdmin;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.security.permissions.UpdatePermission;
+import org.labkey.api.sequenceanalysis.pipeline.HasJobParams;
 import org.labkey.api.sequenceanalysis.pipeline.JobResourceSettings;
+import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
 import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.PageFlowUtil;
@@ -55,8 +57,6 @@
 import org.labkey.api.view.HtmlView;
 import org.labkey.api.writer.PrintWriters;
 import org.labkey.primeseq.pipeline.MhcCleanupPipelineJob;
-import org.labkey.sequenceanalysis.SequencePipelineServiceImpl;
-import org.labkey.sequenceanalysis.pipeline.SequenceJob;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
@@ -411,7 +411,7 @@ public ApiResponse execute(GetResourceSettingsForJobForm form, BindException err
             }
 
             List<JSONObject> resourceSettings = new ArrayList<>();
-            for (JobResourceSettings settings : SequencePipelineServiceImpl.get().getResourceSettings())
+            for (JobResourceSettings settings : SequencePipelineService.get().getResourceSettings())
             {
                 if (settings.isAvailable(getContainer()))
                 {
@@ -448,7 +448,7 @@ else if (!sf.lookupContainer().hasPermission(getUser(), ReadPermission.class))
                 try
                 {
                     PipelineJob job = PipelineJob.readFromFile(json);
-                    if (!(job instanceof SequenceJob sj))
+                    if (!(job instanceof HasJobParams sj))
                     {
                         errors.reject(ERROR_MSG, "Altering cluster params is only supported for sequence jobs");
                         return null;
@@ -539,7 +539,7 @@ else if (!sf.lookupContainer().hasPermission(getUser(), ReadPermission.class))
                 try
                 {
                     job = PipelineJob.readFromFile(jobJson);
-                    if (!(job instanceof SequenceJob sj))
+                    if (!(job instanceof HasJobParams sj))
                     {
                         errors.reject(ERROR_MSG, "Changing cluster parameters is only supported for Sequence jobs");
                         return null;

tcrdb/build.gradle

@@ -8,7 +8,6 @@ repositories {
 dependencies {
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:singlecell", depProjectConfig: "apiJarFile")
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "apiJarFile")
-   BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "runtimeElements")
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile")
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "assay"), depProjectConfig: "apiJarFile")