core: add minimumRequirements to Workflow, #TASK-6445

opencga-analysis/src/main/java/org/opencb/opencga/analysis/binary/BinaryExecutor.java

@@ -5,7 +5,7 @@
 import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.utils.DockerUtils;
 import org.opencb.opencga.analysis.tools.OpenCgaToolScopeStudy;
-import org.opencb.opencga.analysis.utils.InputFileUtils;
+import org.opencb.opencga.catalog.utils.InputFileUtils;
 import org.opencb.opencga.core.common.TimeUtils;
 import org.opencb.opencga.core.exceptions.ToolException;
 import org.opencb.opencga.core.models.common.Enums;

opencga-analysis/src/main/java/org/opencb/opencga/analysis/workflow/NextFlowExecutor.java

@@ -11,7 +11,7 @@
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.commons.utils.DockerUtils;
 import org.opencb.opencga.analysis.tools.OpenCgaToolScopeStudy;
-import org.opencb.opencga.analysis.utils.InputFileUtils;
+import org.opencb.opencga.catalog.utils.InputFileUtils;
 import org.opencb.opencga.catalog.db.api.WorkflowDBAdaptor;
 import org.opencb.opencga.core.common.JacksonUtils;
 import org.opencb.opencga.core.common.TimeUtils;

opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/JobManager.java

@@ -37,6 +37,7 @@
 import org.opencb.opencga.catalog.io.IOManagerFactory;
 import org.opencb.opencga.catalog.models.InternalGetDataResult;
 import org.opencb.opencga.catalog.utils.CatalogFqn;
+import org.opencb.opencga.catalog.utils.InputFileUtils;
 import org.opencb.opencga.catalog.utils.ParamUtils;
 import org.opencb.opencga.catalog.utils.UuidUtils;
 import org.opencb.opencga.core.api.FieldConstants;
@@ -379,7 +380,12 @@ private void autoCompleteNewJob(String organizationId, Study study, Job job, Jwt
             job.setInput(Collections.emptyList());
         } else {
             // We only check input files if the job does not depend on other job that might be creating the necessary file.
-            List<File> inputFiles = getJobInputFilesFromParams(study.getFqn(), job, tokenPayload.getToken());
+            List<File> inputFiles;
+            if (job.getTool().getId().equalsIgnoreCase("binary") || job.getTool().getId().equalsIgnoreCase("workflow")) {
+                inputFiles = getWorkflowJobInputFilesFromParams(study.getFqn(), job, tokenPayload.getToken());
+            } else {
+                inputFiles = getJobInputFilesFromParams(study.getFqn(), job, tokenPayload.getToken());
+            }
             job.setInput(inputFiles);
         }
 
@@ -433,7 +439,6 @@ public OpenCGAResult<Job> kill(String studyStr, String jobId, String token) thro
         }
     }
 
-
     public List<File> getJobInputFilesFromParams(String study, Job job, String token) throws CatalogException {
         // Look for input files
         String fileParamSuffix = "file";
@@ -457,10 +462,9 @@ public List<File> getJobInputFilesFromParams(String study, Job job, String token
                     // We look for files in the dynamic params
                     Map<String, Object> dynamicParams = (Map<String, Object>) entry.getValue();
                     for (Map.Entry<String, Object> subEntry : dynamicParams.entrySet()) {
-                        String subEntryKey = subEntry.getKey().toLowerCase();
-                        if (!subEntryKey.contains("profile") && subEntryKey.endsWith(fileParamSuffix)) {
+                        if (subEntry.getKey().toLowerCase().endsWith(fileParamSuffix)) {
                             // We assume that every variable ending in 'file' corresponds to input files that need to be accessible in
-                            // catalog (except words such as 'profile')
+                            // catalog
                             try {
                                 // Validate the user has access to the file
                                 File file = catalogManager.getFileManager().get(study, (String) subEntry.getValue(),
@@ -478,6 +482,46 @@ public List<File> getJobInputFilesFromParams(String study, Job job, String token
         return inputFiles;
     }
 
+    public List<File> getWorkflowJobInputFilesFromParams(String study, Job job, String token) throws CatalogException {
+        InputFileUtils inputFileUtils = new InputFileUtils(catalogManager);
+        // Look for input files
+        List<File> inputFiles = new ArrayList<>();
+        if (job.getParams() != null) {
+            for (Map.Entry<String, Object> entry : job.getParams().entrySet()) {
+                if (entry.getValue() instanceof String) {
+                    String fileStr = (String) entry.getValue();
+                    if (inputFileUtils.isValidOpenCGAFile(fileStr)) {
+                        try {
+                            File file = inputFileUtils.getOpenCGAFile(study, fileStr, token);
+                            inputFiles.add(file);
+                        } catch (CatalogException e) {
+                            throw new CatalogException("Cannot find file '" + entry.getValue() + "' from job param '" + entry.getKey()
+                                    + "'; (study = " + study + ") :" + e.getMessage(), e);
+                        }
+                    }
+                } else if (entry.getValue() instanceof Map) {
+                    // We look for files in the dynamic params
+                    Map<String, Object> dynamicParams = (Map<String, Object>) entry.getValue();
+                    for (Map.Entry<String, Object> subEntry : dynamicParams.entrySet()) {
+                        if (subEntry.getValue() instanceof String) {
+                            String fileStr = (String) subEntry.getValue();
+                            if (inputFileUtils.isValidOpenCGAFile(fileStr)) {
+                                try {
+                                    File file = inputFileUtils.getOpenCGAFile(study, fileStr, token);
+                                    inputFiles.add(file);
+                                } catch (CatalogException e) {
+                                    throw new CatalogException("Cannot find file '" + subEntry.getValue() + "' from variable '"
+                                            + entry.getKey() + "." + subEntry.getKey() + "'. ", e);
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
+        return inputFiles;
+    }
+
     public OpenCGAResult<Job> retry(String studyStr, JobRetryParams jobRetry, Enums.Priority priority, String jobId, String jobDescription,
                                     List<String> jobDependsOn, List<String> jobTags, String jobScheduledStartTime, String token)
             throws CatalogException {

opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/WorkflowManager.java

@@ -561,7 +561,6 @@ private WorkflowDBAdaptor.QueryParams getFieldFilter(List<String> idList) throws
 
     private void validateNewWorkflow(Workflow workflow, String userId) throws CatalogParameterException {
         ParamUtils.checkIdentifier(workflow.getId(), ID.key());
-        ParamUtils.checkObj(workflow.getType(), TYPE.key());
         if (workflow.getManager() == null) {
             workflow.setManager(new WorkflowSystem());
         }
@@ -571,6 +570,7 @@ private void validateNewWorkflow(Workflow workflow, String userId) throws Catalo
         if (StringUtils.isEmpty(workflow.getManager().getVersion())) {
             workflow.getManager().setVersion("24.04.4");
         }
+        workflow.setType(ParamUtils.defaultObject(workflow.getType(), Workflow.Type.OTHER));
         workflow.setTags(workflow.getTags() != null ? workflow.getTags() : Collections.emptyList());
         workflow.setScripts(workflow.getScripts() != null ? workflow.getScripts() : Collections.emptyList());
         boolean main = false;

opencga-analysis/src/main/java/org/opencb/opencga/analysis/utils/InputFileUtils.java → opencga-catalog/src/main/java/org/opencb/opencga/catalog/utils/InputFileUtils.java

@@ -1,4 +1,4 @@
-package org.opencb.opencga.analysis.utils;
+package org.opencb.opencga.catalog.utils;
 
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.CatalogManager;
@@ -16,8 +16,7 @@ public class InputFileUtils {
     private final CatalogManager catalogManager;
 
     private static final Pattern OPERATION_PATTERN = Pattern.compile("^(?i)(ocga://|opencga://|file://)(.+)$");
-
-    private final static Logger logger = LoggerFactory.getLogger(InputFileUtils.class);
+    private final Logger logger = LoggerFactory.getLogger(InputFileUtils.class);
 
     public InputFileUtils(CatalogManager catalogManager) {
         this.catalogManager = catalogManager;

opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java

@@ -317,8 +317,13 @@ public class FieldConstants {
     public static final String WORKFLOW_SCRIPTS_DESCRIPTION = "List of scripts used by the Workflow.";
     public static final String WORKFLOW_TAGS_DESCRIPTION = "List of tags.";
     public static final String WORKFLOW_VARIABLES_DESCRIPTION = "List of variables accepted by the Workflow.";
+    public static final String WORKFLOW_MINIMUM_REQUIREMENTS_DESCRIPTION = "Minimum requirements to execute the workflow.";
     public static final String WORKFLOW_INTERNAL_DESCRIPTION = "Workflow internal information.";
 
+    public static final String WORKFLOW_MIN_REQUIREMENTS_CPU_DESCRIPTION = "Minimum number of cpu cores required to execute the workflow.";
+    public static final String WORKFLOW_MIN_REQUIREMENTS_MEMORY_DESCRIPTION = "Minimum memory required to execute the workflow"
+            + " (expressed in GB).";
+
     public static final String WORKFLOW_SYSTEM_ID_DESCRIPTION = "Workflow system id. Valid values: NEXTFLOW.";
     public static final String WORKFLOW_SYSTEM_VERSION_DESCRIPTION = "Workflow system version to use.";
 

opencga-core/src/main/java/org/opencb/opencga/core/models/workflow/Workflow.java

@@ -51,6 +51,9 @@ public class Workflow extends PrivateStudyUid {
     @DataField(id = "variables", description = FieldConstants.WORKFLOW_VARIABLES_DESCRIPTION)
     private List<Variable> variables;
 
+    @DataField(id = "minimumRequirements", description = FieldConstants.WORKFLOW_MINIMUM_REQUIREMENTS_DESCRIPTION)
+    private WorkflowMinimumRequirements minimumRequirements;
+
     @DataField(id = "internal", description = FieldConstants.WORKFLOW_INTERNAL_DESCRIPTION)
     private WorkflowInternal internal;
 
@@ -66,7 +69,7 @@ public class Workflow extends PrivateStudyUid {
     public enum Type {
         CLINICAL_INTERPRETATION,
         SECONDARY_ANALYSIS,
-        RESEARCH,
+        RESEARCH_ANALYSIS,
         OTHER
     }
 
@@ -75,7 +78,8 @@ public Workflow() {
 
     public Workflow(String id, String name, String description, boolean draft, Type type, WorkflowSystem manager,
                     WorkflowRepository repository, List<WorkflowScript> scripts, List<String> tags, List<Variable> variables,
-                    WorkflowInternal internal, String creationDate, String modificationDate, Map<String, Object> attributes) {
+                    WorkflowMinimumRequirements minimumRequirements, WorkflowInternal internal, String creationDate,
+                    String modificationDate, Map<String, Object> attributes) {
         this.id = id;
         this.name = name;
         this.description = description;
@@ -86,6 +90,7 @@ public Workflow(String id, String name, String description, boolean draft, Type
         this.scripts = scripts;
         this.tags = tags;
         this.variables = variables;
+        this.minimumRequirements = minimumRequirements;
         this.internal = internal;
         this.creationDate = creationDate;
         this.modificationDate = modificationDate;
@@ -108,6 +113,7 @@ public String toString() {
         sb.append(", scripts=").append(scripts);
         sb.append(", tags=").append(tags);
         sb.append(", variables=").append(variables);
+        sb.append(", minimumRequirements=").append(minimumRequirements);
         sb.append(", internal=").append(internal);
         sb.append(", creationDate='").append(creationDate).append('\'');
         sb.append(", modificationDate='").append(modificationDate).append('\'');
@@ -240,6 +246,15 @@ public Workflow setVariables(List<Variable> variables) {
         return this;
     }
 
+    public WorkflowMinimumRequirements getMinimumRequirements() {
+        return minimumRequirements;
+    }
+
+    public Workflow setMinimumRequirements(WorkflowMinimumRequirements minimumRequirements) {
+        this.minimumRequirements = minimumRequirements;
+        return this;
+    }
+
     public WorkflowInternal getInternal() {
         return internal;
     }

opencga-core/src/main/java/org/opencb/opencga/core/models/workflow/WorkflowCreateParams.java

@@ -37,6 +37,9 @@ public class WorkflowCreateParams {
     @DataField(id = "variables", description = FieldConstants.WORKFLOW_VARIABLES_DESCRIPTION)
     private List<Variable> variables;
 
+    @DataField(id = "minimumRequirements", description = FieldConstants.WORKFLOW_MINIMUM_REQUIREMENTS_DESCRIPTION)
+    private WorkflowMinimumRequirements minimumRequirements;
+
     @DataField(id = "scripts", description = FieldConstants.WORKFLOW_SCRIPTS_DESCRIPTION)
     private List<WorkflowScript> scripts;
 
@@ -53,8 +56,9 @@ public WorkflowCreateParams() {
     }
 
     public WorkflowCreateParams(String id, String name, String description, WorkflowSystem manager, Workflow.Type type, List<String> tags,
-                                boolean draft, WorkflowRepository repository, List<Variable> variables, List<WorkflowScript> scripts,
-                                String creationDate, String modificationDate, Map<String, Object> attributes) {
+                                boolean draft, WorkflowRepository repository, List<Variable> variables,
+                                WorkflowMinimumRequirements minimumRequirements, List<WorkflowScript> scripts, String creationDate,
+                                String modificationDate, Map<String, Object> attributes) {
         this.id = id;
         this.name = name;
         this.description = description;
@@ -64,6 +68,7 @@ public WorkflowCreateParams(String id, String name, String description, Workflow
         this.draft = draft;
         this.repository = repository;
         this.variables = variables;
+        this.minimumRequirements = minimumRequirements;
         this.scripts = scripts;
         this.creationDate = creationDate;
         this.modificationDate = modificationDate;
@@ -82,6 +87,7 @@ public String toString() {
         sb.append(", draft=").append(draft);
         sb.append(", repository=").append(repository);
         sb.append(", variables=").append(variables);
+        sb.append(", minimumRequirements=").append(minimumRequirements);
         sb.append(", scripts=").append(scripts);
         sb.append(", creationDate='").append(creationDate).append('\'');
         sb.append(", modificationDate='").append(modificationDate).append('\'');
@@ -91,8 +97,8 @@ public String toString() {
     }
 
     public Workflow toWorkflow() {
-        return new Workflow(id, name, description, draft, type, manager, repository, scripts, tags, variables, new WorkflowInternal(),
-                creationDate, modificationDate, attributes);
+        return new Workflow(id, name, description, draft, type, manager, repository, scripts, tags, variables, minimumRequirements,
+                new WorkflowInternal(), creationDate, modificationDate, attributes);
     }
 
     public String getId() {
@@ -176,6 +182,15 @@ public WorkflowCreateParams setVariables(List<Variable> variables) {
         return this;
     }
 
+    public WorkflowMinimumRequirements getMinimumRequirements() {
+        return minimumRequirements;
+    }
+
+    public WorkflowCreateParams setMinimumRequirements(WorkflowMinimumRequirements minimumRequirements) {
+        this.minimumRequirements = minimumRequirements;
+        return this;
+    }
+
     public List<WorkflowScript> getScripts() {
         return scripts;
     }

opencga-core/src/main/java/org/opencb/opencga/core/models/workflow/WorkflowMinimumRequirements.java

@@ -0,0 +1,48 @@
+package org.opencb.opencga.core.models.workflow;
+
+import org.opencb.commons.annotations.DataField;
+import org.opencb.opencga.core.api.FieldConstants;
+
+public class WorkflowMinimumRequirements {
+
+    @DataField(id = "cpu", description = FieldConstants.WORKFLOW_MIN_REQUIREMENTS_CPU_DESCRIPTION)
+    private int cpu;
+
+    @DataField(id = "memory", description = FieldConstants.WORKFLOW_MIN_REQUIREMENTS_MEMORY_DESCRIPTION)
+    private int memory;
+
+    public WorkflowMinimumRequirements() {
+    }
+
+    public WorkflowMinimumRequirements(int cpu, int memory) {
+        this.cpu = cpu;
+        this.memory = memory;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("WorkflowMinimumRequirements{");
+        sb.append("cpu=").append(cpu);
+        sb.append(", memory=").append(memory);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public int getCpu() {
+        return cpu;
+    }
+
+    public WorkflowMinimumRequirements setCpu(int cpu) {
+        this.cpu = cpu;
+        return this;
+    }
+
+    public int getMemory() {
+        return memory;
+    }
+
+    public WorkflowMinimumRequirements setMemory(int memory) {
+        this.memory = memory;
+        return this;
+    }
+}

opencga-core/src/main/java/org/opencb/opencga/core/models/workflow/WorkflowUpdateParams.java

@@ -36,6 +36,9 @@ public class WorkflowUpdateParams {
     @DataField(id = "variables", description = FieldConstants.WORKFLOW_VARIABLES_DESCRIPTION)
     private List<Variable> variables;
 
+    @DataField(id = "minimumRequirements", description = FieldConstants.WORKFLOW_MINIMUM_REQUIREMENTS_DESCRIPTION)
+    private WorkflowMinimumRequirements minimumRequirements;
+
     @DataField(id = "creationDate", indexed = true, description = FieldConstants.GENERIC_CREATION_DATE_DESCRIPTION)
     private String creationDate;
 
@@ -50,7 +53,8 @@ public WorkflowUpdateParams() {
 
     public WorkflowUpdateParams(String name, String description, WorkflowSystem manager, Workflow.Type type, List<String> tags,
                                 boolean draft, WorkflowRepository repository, List<WorkflowScript> scripts, List<Variable> variables,
-                                String creationDate, String modificationDate, Map<String, Object> attributes) {
+                                WorkflowMinimumRequirements minimumRequirements, String creationDate, String modificationDate,
+                                Map<String, Object> attributes) {
         this.name = name;
         this.description = description;
         this.manager = manager;
@@ -60,6 +64,7 @@ public WorkflowUpdateParams(String name, String description, WorkflowSystem mana
         this.repository = repository;
         this.scripts = scripts;
         this.variables = variables;
+        this.minimumRequirements = minimumRequirements;
         this.creationDate = creationDate;
         this.modificationDate = modificationDate;
         this.attributes = attributes;
@@ -77,6 +82,7 @@ public String toString() {
         sb.append(", repository=").append(repository);
         sb.append(", scripts=").append(scripts);
         sb.append(", variables=").append(variables);
+        sb.append(", minimumRequirements=").append(minimumRequirements);
         sb.append(", creationDate='").append(creationDate).append('\'');
         sb.append(", modificationDate='").append(modificationDate).append('\'');
         sb.append(", attributes=").append(attributes);