Merge pull request #2408 from opencb/TASK-5618

TASK-5618 - Port Patch 1.10.2 -> 2.0.0

opencga-app/app/analysis/resources/README

@@ -1,55 +1,6 @@
 README
 
-
-In this folder, users should store external files to be used by some OpenCGA analysis.
-
-1) roleInCancer.txt[.gz]
-
-This file is used by interpretation clinical analysis, e.g., Tiering and TEAM analysis.
-
-It stores those genes which contain mutations that have been casually implicated in cancer. This information can be downloaded
-from the Cancer Gene Census (CGC) at https://cancer.sanger.ac.uk/census
-
-The file consists of two tab-separated columns: the first one contains the gene name, and the second, the role in cancer, i.e.: oncogne,
-TSG, fusion. In addition, lines starting with # are considered comments and will be ignored.
-
-Sample of a roleInCancer file:
-
-#Gene name	Role in Cancer
-A1CF	oncogene
-ABI1	TSG, fusion
-ABL1	oncogene, fusion
-ABL2	oncogene, fusion
-ACKR3	oncogene, fusion
-ACSL3	fusion
-...
-...
-
-
-2) actionableVariants_xxx.txt[.gz] where xxx = assembly, e.g.: grch37
-
-This file is used by interpretation clinical analysis, e.g., TEAM analysis.
-
-It stores variants that were identified as clinically actionable variants. The file consists of the following twelve tab-separated columns:
-  - Chromosome
-  - Start
-  - Stop
-  - Reference allele
-  - Alternate allele
-  - dbSNP ID
-  - ClinVar Variant ID
-  - HGVS
-  - Phenotype list
-  - Clinical significance
-  - Review status
-  - Submitter categories
-
-In addition, lines starting with # are considered comments and will be ignored.
-
-Sample fo an actionableVariants file:
-
-#Chromosome	Start	Stop	ReferenceAllele	AlternateAllele	dbSNP ID    ClinVar Variant ID  hgvs	PhenotypeList   ClinicalSignificance	ReviewStatus	SubmitterCategories
-2	47702269	47702269	C	T   rs28929483  1753    NM_000251.2(MSH2):c.1865C>T (p.Pro622Leu)   Hereditary cancer-predisposing syndrome;Hereditary nonpolyposis colon cancer;Lynch syndrome;Lynch syndrome I    Pathogenic			reviewed by expert panel	3
-2	47657020	47657020	C	T   rs63751108  1755    NM_000251.2(MSH2):c.1216C>T (p.Arg406Ter)   Carcinoma of colon;Hereditary cancer-predisposing syndrome;Hereditary nonpolyposis colon cancer;Lynch syndrome;Lynch syndrome I;not provided    Pathogenic		reviewed by expert panel	3
-...
-...
+This directory is designated for OpenCGA analyses to download the necessary external data.
+For instance, during the first Exomiser analysis, the files '2109_hg38.zip' and '2109_phenotype.zip' will be downloaded
+from the OpenCGA analysis URL and stored in the 'exomiser' folder within this directory. Subsequent Exomiser analyses will
+then access this folder to read these files.

opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile

@@ -25,11 +25,11 @@ RUN apt-get update -y && DEBIAN_FRONTEND="noninteractive" TZ="Europe/London" apt
 WORKDIR /opt/opencga/signature.tools.lib
 
 RUN git fetch origin --tags && \
-    git checkout tags/v2.4.2 && \
+    git checkout tags/v2.4.4 && \
     sed -i '/Mmusculus/d' DESCRIPTION && \
     sed -i '/Cfamiliaris/d' DESCRIPTION && \
     sed -i '/1000genomes/d' DESCRIPTION && \
-    R -e 'options(timeout = 300);devtools::install(repos="https://www.stats.bris.ac.uk/R/")' && \
+    R -e 'options(timeout = 3600);devtools::install(repos="https://www.stats.bris.ac.uk/R/")' && \
     ## Clean up
     rm -rf /var/lib/apt/lists/* /tmp/* /opt/opencga/signature.tools.lib/.git && \
     strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5

opencga-app/app/misc/scripts/hadoop-ssh.sh

@@ -1,45 +1,45 @@
 #!/usr/bin/env sh
 
 
-if [ -z ${HADOOP_SSH_USER} ] ; then
+if [ -z "${HADOOP_SSH_USER}" ] ; then
   echo "Undefined HADOOP_SSH_USER" 1>&2
   exit 1
 fi
 
-if [ -z ${HADOOP_SSH_HOST} ] ; then
+if [ -z "${HADOOP_SSH_HOST}" ] ; then
   echo "Undefined HADOOP_SSH_HOST" 1>&2
   exit 1
 fi
 
 SSHPASS_CMD=
-if [ -z ${SSHPASS} ] ; then
+if [ -z "${SSHPASS}" ] ; then
   # If empty, assume ssh-key exists in the system
   SSHPASS_CMD=""
 else
   # If non zero, use sshpass command
-  SSHPASS_CMD="sshpass -e"
+  SSHPASS_CMD="sshpass -e "
 fi
 
 SSH_OPTS="-o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -o ServerAliveInterval=60"
-if [ ! -z ${HADOOP_SSH_KEY} ] && [ -f ${HADOOP_SSH_KEY} ] ; then
+if [ -n "${HADOOP_SSH_KEY}" ] && [ -f "${HADOOP_SSH_KEY}" ] ; then
   SSH_OPTS="${SSH_OPTS} -i ${HADOOP_SSH_KEY}"
 fi
 
 echo "Connect to Hadoop edge node ${HADOOP_SSH_USER}@${HADOOP_SSH_HOST}" 1>&2
 
-echo "${SSHPASS_CMD} ssh ${SSH_OPTS} ${HADOOP_SSH_USER}@${HADOOP_SSH_HOST}" 1>&2
+echo "${SSHPASS_CMD}ssh ${SSH_OPTS} ${HADOOP_SSH_USER}@${HADOOP_SSH_HOST}" 1>&2
 
 # Escape args with single quotes
 CMD=
-for arg in $@ ; do
+for arg in "$@" ; do
     # Escape single quote, if any :
 #    arg=`echo $arg | sed "s/'/'\"'\"'/g"`   # aaa'aaa --> 'aaa'"'"'aaa'
-    arg=`echo $arg | sed "s/'/'\\\\\\''/g"` # aaa'aaa --> 'aaa'\''aaa'
+    arg=$(echo "$arg" | sed "s/'/'\\\\\\''/g") # aaa'aaa --> 'aaa'\''aaa'
     CMD="${CMD}'${arg}' "
 done
 echo ${CMD}
 
-${SSHPASS_CMD} ssh ${SSH_OPTS} ${HADOOP_SSH_USER}@${HADOOP_SSH_HOST} /bin/bash << EOF
+${SSHPASS_CMD} ssh ${SSH_OPTS} "${HADOOP_SSH_USER}@${HADOOP_SSH_HOST}" /bin/bash << EOF
 
 export HADOOP_CLASSPATH=${HADOOP_CLASSPATH}
 export HADOOP_USER_CLASSPATH_FIRST=${HADOOP_USER_CLASSPATH_FIRST}

opencga-app/src/main/java/org/opencb/opencga/app/cli/CommandExecutor.java

@@ -17,16 +17,25 @@
 package org.opencb.opencga.app.cli;
 
 import com.beust.jcommander.JCommander;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Level;
 import org.apache.logging.log4j.core.config.Configurator;
+import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.utils.FileUtils;
 import org.opencb.commons.utils.PrintUtils;
+import org.opencb.opencga.app.cli.main.utils.CommandLineUtils;
 import org.opencb.opencga.app.cli.session.SessionManager;
 import org.opencb.opencga.client.config.ClientConfiguration;
 import org.opencb.opencga.client.exceptions.ClientException;
+import org.opencb.opencga.client.rest.OpenCGAClient;
 import org.opencb.opencga.core.config.Configuration;
 import org.opencb.opencga.core.config.storage.StorageConfiguration;
+import org.opencb.opencga.core.response.RestResponse;
+import org.opencb.opencga.server.generator.models.RestCategory;
+import org.opencb.opencga.server.generator.models.RestEndpoint;
+import org.opencb.opencga.server.generator.models.RestParameter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -36,6 +45,7 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.List;
 
 /**
  * Created by imedina on 19/04/16.
@@ -281,6 +291,95 @@ public CommandExecutor setSessionManager(SessionManager sessionManager) {
         return this;
     }
 
+
+    public String getObjectAsJSON(String objectCategory, String objectPath, OpenCGAClient openCGAClient) throws Exception {
+        StringBuilder jsonInString = new StringBuilder("\n");
+        try {
+            ObjectMap queryParams = new ObjectMap();
+            queryParams.putIfNotEmpty("category", objectCategory);
+            RestResponse<List> response = openCGAClient.getMetaClient().api(queryParams);
+            ObjectMapper jsonObjectMapper = new ObjectMapper();
+            for (List list : response.getResponses().get(0).getResults()) {
+                List<RestCategory> categories = jsonObjectMapper.convertValue(list, new TypeReference<List<RestCategory>>() {});
+                for (RestCategory category : categories) {
+                    for (RestEndpoint endpoint : category.getEndpoints()) {
+                        if (objectPath.equals(endpoint.getPath())) {
+                            boolean enc = false;
+                            for (RestParameter parameter : endpoint.getParameters()) {
+                                //jsonInString += parameter.getName()+":"+parameter.getAllowedValues()+"\n";
+                                if (parameter.getData() != null) {
+                                    enc = true;
+                                    jsonInString.append(printBody(parameter.getData(), ""));
+                                }
+                            }
+                            if (!enc) {
+                                jsonInString.append("No model available");
+                            }
+                            //
+                        }
+                    }
+                }
+            }
+        } catch (Exception e) {
+            jsonInString = new StringBuilder("Data model not found.");
+            CommandLineUtils.error(e);
+        }
+        return jsonInString.toString();
+    }
+
+    private String printBody(List<RestParameter> data, String tabs) {
+        String res = "";
+        res += "{\n";
+        String tab = "    " + tabs;
+        for (RestParameter parameter : data) {
+            if (parameter.getData() == null) {
+                res += printParameter(parameter, tab);
+            } else {
+                res += tab + "\"" +parameter.getName() + "\"" + ": [" + printBody(parameter.getData(), tab) + "],\n";
+            }
+        }
+        res += tabs + "}";
+        return res;
+
+    }
+
+    private String printParameter(RestParameter parameter, String tab) {
+
+        return tab + "\"" + parameter.getName() + "\"" + ":" + printParameterValue(parameter) + ",\n";
+    }
+
+    private String printParameterValue(RestParameter parameter) {
+
+        if(!StringUtils.isEmpty(parameter.getAllowedValues())){
+            return parameter.getAllowedValues().replace(" ", "|");
+        }
+        switch (parameter.getType()) {
+            case "Boolean":
+            case "java.lang.Boolean":
+                return "false";
+            case "Long":
+            case "Float":
+            case "Double":
+            case "Integer":
+            case "int":
+            case "double":
+            case "float":
+            case "long":
+                return "0";
+            case "List":
+                return "[\"\"]";
+            case "Date":
+                return "\"dd/mm/yyyy\"";
+            case "Map":
+                return "{\"key\": \"value\"}";
+            case "String":
+                return "\"\"";
+            default:
+                return "\"-\"";
+        }
+    }
+
+
     public Logger getLogger() {
         return logger;
     }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2024-03-04 OpenCB
+* Copyright 2015-2024-03-06 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
@@ -60,7 +60,7 @@ public abstract class OpenCgaCompleter implements Completer {
             .map(Candidate::new)
             .collect(toList());
 
-    private List<Candidate> clinicalList = asList( "acl-update","annotation-sets-load","clinical-configuration-update","create","distinct","interpretation-distinct","interpretation-search","interpretation-info","interpreter-cancer-tiering-run","interpreter-exomiser-run","interpreter-team-run","interpreter-tiering-run","interpreter-zetta-run","load","rga-aggregation-stats","rga-gene-query","rga-gene-summary","rga-index-run","rga-individual-query","rga-individual-summary","rga-variant-query","rga-variant-summary","search","variant-query","acl","delete","update","annotation-sets-annotations-update","info","interpretation-create","interpretation-clear","interpretation-delete","interpretation-revert","interpretation-update")
+    private List<Candidate> clinicalList = asList( "acl-update","annotation-sets-load","clinical-configuration-update","create","distinct","interpretation-distinct","interpretation-search","interpretation-info","interpreter-cancer-tiering-run","interpreter-exomiser-run","interpreter-team-run","interpreter-tiering-run","interpreter-zetta-run","load","rga-aggregation-stats","rga-gene-query","rga-gene-summary","rga-index-run","rga-individual-query","rga-individual-summary","rga-variant-query","rga-variant-summary","search","variant-query","acl","delete","update","annotation-sets-annotations-update","info","interpretation-create","interpretation-clear","interpretation-delete","interpretation-revert","interpretation-update","report-update")
             .stream()
             .map(Candidate::new)
             .collect(toList());

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2024-03-04 OpenCB
+* Copyright 2015-2024-03-06 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
@@ -161,6 +161,7 @@ public OpencgaCliOptionsParser() {
         analysisClinicalSubCommands.addCommand("interpretation-delete", analysisClinicalCommandOptions.deleteInterpretationCommandOptions);
         analysisClinicalSubCommands.addCommand("interpretation-revert", analysisClinicalCommandOptions.revertInterpretationCommandOptions);
         analysisClinicalSubCommands.addCommand("interpretation-update", analysisClinicalCommandOptions.updateInterpretationCommandOptions);
+        analysisClinicalSubCommands.addCommand("report-update", analysisClinicalCommandOptions.updateReportCommandOptions);
 
         jobsCommandOptions = new JobsCommandOptions(commonCommandOptions, jCommander);
         jCommander.addCommand("jobs", jobsCommandOptions);

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java

@@ -202,6 +202,9 @@ public void execute() throws Exception {
             case "interpretation-update":
                 queryResponse = updateInterpretation();
                 break;
+            case "report-update":
+                queryResponse = updateReport();
+                break;
             default:
                 logger.error("Subcommand not valid");
                 break;
@@ -1485,4 +1488,48 @@ private RestResponse<Interpretation> updateInterpretation() throws Exception {
         }
         return openCGAClient.getClinicalAnalysisClient().updateInterpretation(commandOptions.clinicalAnalysis, commandOptions.interpretation, interpretationUpdateParams, queryParams);
     }
+
+    private RestResponse<ClinicalReport> updateReport() throws Exception {
+        logger.debug("Executing updateReport in Analysis - Clinical command line");
+
+        AnalysisClinicalCommandOptions.UpdateReportCommandOptions commandOptions = analysisClinicalCommandOptions.updateReportCommandOptions;
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotEmpty("include", commandOptions.include);
+        queryParams.putIfNotEmpty("exclude", commandOptions.exclude);
+        queryParams.putIfNotEmpty("study", commandOptions.study);
+        queryParams.putIfNotNull("supportingEvidencesAction", commandOptions.supportingEvidencesAction);
+        queryParams.putIfNotNull("includeResult", commandOptions.includeResult);
+        if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
+            queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
+        }
+
+
+        ClinicalReport clinicalReport = null;
+        if (commandOptions.jsonDataModel) {
+            RestResponse<ClinicalReport> res = new RestResponse<>();
+            res.setType(QueryType.VOID);
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalysis}/report/update"));
+            return res;
+        } else if (commandOptions.jsonFile != null) {
+            clinicalReport = JacksonUtils.getDefaultObjectMapper()
+                    .readValue(new java.io.File(commandOptions.jsonFile), ClinicalReport.class);
+        } else {
+            ObjectMap beanParams = new ObjectMap();
+            putNestedIfNotEmpty(beanParams, "title",commandOptions.title, true);
+            putNestedIfNotEmpty(beanParams, "overview",commandOptions.overview, true);
+            putNestedIfNotEmpty(beanParams, "discussion.author",commandOptions.discussionAuthor, true);
+            putNestedIfNotEmpty(beanParams, "discussion.date",commandOptions.discussionDate, true);
+            putNestedIfNotEmpty(beanParams, "discussion.text",commandOptions.discussionText, true);
+            putNestedIfNotEmpty(beanParams, "logo",commandOptions.logo, true);
+            putNestedIfNotEmpty(beanParams, "signedBy",commandOptions.signedBy, true);
+            putNestedIfNotEmpty(beanParams, "signature",commandOptions.signature, true);
+            putNestedIfNotEmpty(beanParams, "date",commandOptions.date, true);
+
+            clinicalReport = JacksonUtils.getDefaultObjectMapper().copy()
+                    .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
+                    .readValue(beanParams.toJson(), ClinicalReport.class);
+        }
+        return openCGAClient.getClinicalAnalysisClient().updateReport(commandOptions.clinicalAnalysis, clinicalReport, queryParams);
+    }
 }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java

@@ -106,7 +106,11 @@ private RestResponse<String> model() throws Exception {
         logger.debug("Executing model in Meta command line");
 
         MetaCommandOptions.ModelCommandOptions commandOptions = metaCommandOptions.modelCommandOptions;
-        return openCGAClient.getMetaClient().model();
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotEmpty("model", commandOptions.model);
+
+        return openCGAClient.getMetaClient().model(queryParams);
     }
 
     private RestResponse<String> ping() throws Exception {