Merge pull request #11 from qbicsoftware/feature/sample-and-dataset-t…

…ransfer add sample and dataset transfer/update (most cases), fix some issues
qbicsoftware · Oct 15, 2024 · e00052d · e00052d
2 parents 052edf7 + dd3000a
commit e00052d
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Showing 18 changed files with 696 additions and 177 deletions.
diff --git a/src/main/java/life/qbic/io/PetabParser.java b/src/main/java/life/qbic/io/PetabParser.java
@@ -13,6 +13,7 @@
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
+import java.util.Set;
 import life.qbic.model.petab.PetabMetadata;
 
 public class PetabParser {
@@ -94,4 +95,7 @@ private File findYaml(File directory) {
     return null;
   }
 
-}
+  public void addPatientIDs(String outputPath, Set<String> patientIDs) {
+    System.err.println("found patient ids: "+patientIDs);
+  }
+}
diff --git a/src/main/java/life/qbic/io/commandline/DownloadPetabCommand.java b/src/main/java/life/qbic/io/commandline/DownloadPetabCommand.java
@@ -28,14 +28,15 @@ public class DownloadPetabCommand implements Runnable {
 
     @Override
     public void run() {
+      App.readConfig();
       OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(),
           auth.getOpenbisAS(), auth.getOpenbisDSS());
       OpenbisConnector openbis = new OpenbisConnector(authentication);
 
       List<DataSet> datasets = openbis.findDataSets(Collections.singletonList(datasetCode));
 
       if(datasets.isEmpty()) {
-        System.out.println(datasetCode+" not found");
+        System.out.println("Dataset "+datasetCode+" not found");
         return;
       }
       DatasetWithProperties result = new DatasetWithProperties(datasets.get(0));
@@ -54,6 +55,7 @@ public void run() {
       try {
         System.out.println("Adding dataset identifier to metaInformation.yaml.");
         parser.addDatasetId(outputPath, datasetCode);
+        parser.addPatientIDs(outputPath, patientIDs);
       } catch (IOException e) {
         System.out.println("Could not add dataset identifier.");
         throw new RuntimeException(e);

diff --git a/src/main/java/life/qbic/io/commandline/FindDatasetsCommand.java b/src/main/java/life/qbic/io/commandline/FindDatasetsCommand.java
@@ -9,7 +9,6 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
 import life.qbic.App;
@@ -24,29 +23,56 @@
     description = "lists datasets and their details for a given experiment code")
 public class FindDatasetsCommand implements Runnable {
 
-  @Parameters(arity = "1", paramLabel = "experiment", description = "The code of the experiment data is attached to")
-  private String experimentCode;
-  @Option(arity = "1", paramLabel = "<space>", description = "Optional openBIS spaces to filter samples", names = {"-s", "--space"})
+  @Parameters(arity = "1", paramLabel = "openBIS obejct", description =
+      "The code of the experiment "
+          + "or sample data is attached to.")
+  private String objectCode;
+  @Option(arity = "1", paramLabel = "<space>", description = "Optional openBIS spaces to filter "
+      + "found datasets by", names = {"-s", "--space"})
   private String space;
   @Mixin
   OpenbisAuthenticationOptions auth = new OpenbisAuthenticationOptions();
 
-    @Override
+  @Override
     public void run() {
+      App.readConfig();
       List<String> spaces = new ArrayList<>();
       if (space != null) {
         System.out.println("Querying experiment in space: " + space + "...");
         spaces.add(space);
       } else {
         System.out.println("Querying experiment in all available spaces...");
       }
+      if(objectCode.contains("/")) {
+        String[] splt = objectCode.split("/");
+        objectCode = splt[splt.length-1];
+        System.out.println("Query is not an object code, querying for: " + objectCode+" instead.");
+      }
       OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(),
           auth.getOpenbisAS());
       OpenbisConnector openbis = new OpenbisConnector(authentication);
-      List<DataSet> datasets = openbis.listDatasetsOfExperiment(spaces, experimentCode).stream()
-          .sorted(Comparator.comparing(
-              (DataSet d) -> d.getExperiment().getProject().getSpace().getCode())).collect(
-              Collectors.toList());
+
+      List<DataSet> datasetsOfExp = openbis.listDatasetsOfExperiment(spaces, objectCode).stream()
+            .sorted(Comparator.comparing(
+                (DataSet d) -> d.getExperiment().getProject().getSpace().getCode()))
+            .collect(Collectors.toList());
+
+      List<DataSet> datasets = new ArrayList<>();
+
+      if(!datasetsOfExp.isEmpty()) {
+        System.err.println("Found "+datasetsOfExp.size()+" datasets for experiment "+objectCode);
+        datasets.addAll(datasetsOfExp);
+      }
+      List<DataSet> datasetsOfSample = openbis.listDatasetsOfSample(spaces, objectCode).stream()
+            .sorted(Comparator.comparing(
+                (DataSet d) -> d.getExperiment().getProject().getSpace().getCode()))
+            .collect(Collectors.toList());
+
+      if(!datasetsOfSample.isEmpty()) {
+        System.err.println("Found "+datasetsOfSample.size()+" datasets for sample "+objectCode);
+        datasets.addAll(datasetsOfSample);
+      }
+
       Map<String, String> properties = new HashMap<>();
       if (!datasets.isEmpty()) {
         Set<String> patientIDs = openbis.findPropertiesInSampleHierarchy("PATIENT_DKFZ_ID",
@@ -64,7 +90,7 @@ public void run() {
       }).collect(Collectors.toList());
       int datasetIndex = 0;
       System.out.println();
-      System.out.printf("Found %s datasets for experiment %s:%n", datasets.size(), experimentCode);
+      System.out.printf("Found %s datasets for %s:%n", datasets.size(), objectCode);
       for (DatasetWithProperties dataSet : datasetWithProperties) {
         datasetIndex++;
         System.out.println("["+datasetIndex+"]");

diff --git a/src/main/java/life/qbic/io/commandline/OpenbisAuthenticationOptions.java b/src/main/java/life/qbic/io/commandline/OpenbisAuthenticationOptions.java
@@ -7,7 +7,6 @@
 import java.net.URL;
 import java.util.StringJoiner;
 import life.qbic.App;
-import life.qbic.io.PropertyReader;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import picocli.CommandLine;
@@ -38,7 +37,8 @@ public class OpenbisAuthenticationOptions {
   public String getOpenbisUser() {
     if(openbisUser == null && App.configProperties.containsKey("user")) {
       openbisUser = App.configProperties.get("user");
-    } else {
+    }
+    if(openbisUser == null) {
       log.error("No openBIS user provided.");
       System.exit(2);
     }
@@ -49,13 +49,21 @@ public String getOpenbisDSS() {
     if(dss_url == null && App.configProperties.containsKey("dss")) {
       dss_url = App.configProperties.get("dss");
     }
+    if(dss_url == null) {
+      log.error("No openBIS datastore server URL provided.");
+      System.exit(2);
+    }
     return dss_url;
   }
 
   public String getOpenbisAS() {
     if(as_url == null && App.configProperties.containsKey("as")) {
       as_url = App.configProperties.get("as");
     }
+    if(as_url == null) {
+      log.error("No openBIS application server URL provided.");
+      System.exit(2);
+    }
     return as_url;
   }
 

diff --git a/src/main/java/life/qbic/io/commandline/SampleHierarchyCommand.java b/src/main/java/life/qbic/io/commandline/SampleHierarchyCommand.java
@@ -35,6 +35,7 @@ public class SampleHierarchyCommand implements Runnable {
 
     @Override
     public void run() {
+      App.readConfig();
       List<String> summary = new ArrayList<>();
       List<String> spaces = new ArrayList<>();
         if(space!=null) {

diff --git a/src/main/java/life/qbic/io/commandline/SeekAuthenticationOptions.java b/src/main/java/life/qbic/io/commandline/SeekAuthenticationOptions.java
@@ -5,7 +5,6 @@
 
 import java.util.StringJoiner;
 import life.qbic.App;
-import life.qbic.io.PropertyReader;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import picocli.CommandLine;
@@ -31,17 +30,19 @@ public class SeekAuthenticationOptions {
   public String getSeekUser() {
     if(seekUser == null && App.configProperties.containsKey("seek_user")) {
       seekUser = App.configProperties.get("seek_user");
-    } else {
+    }
+    if (seekUser == null) {
       log.error("No SEEK user/email provided.");
       System.exit(2);
     }
     return seekUser;
   }
 
   public String getSeekURL() {
-    if(seek_url == null && App.configProperties.containsKey("seek_url")) {
+    if(seek_url != null || App.configProperties.containsKey("seek_url")) {
       seek_url = App.configProperties.get("seek_url");
-    } else {
+    }
+    if(seek_url == null) {
       log.error("No URL to the SEEK address provided.");
       System.exit(2);
     }

diff --git a/src/main/java/life/qbic/io/commandline/SpaceStatisticsCommand.java b/src/main/java/life/qbic/io/commandline/SpaceStatisticsCommand.java
@@ -41,6 +41,7 @@ public class SpaceStatisticsCommand implements Runnable {
 
     @Override
     public void run() {
+      App.readConfig();
       List<String> summary = new ArrayList<>();
       List<String> blackList = new ArrayList<>(Arrays.asList("ELN_SETTINGS", "MATERIAL.GLOBAL"));
       List<String> spaces = new ArrayList<>();