small fixes and features

src/main/java/life/qbic/io/commandline/AuthenticationOptions.java

@@ -8,6 +8,8 @@
 import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.StringJoiner;
 import java.util.TreeMap;
 import org.apache.logging.log4j.LogManager;
@@ -29,13 +31,13 @@ public class AuthenticationOptions {
 
   @Option(
       names = {"-as", "-as_url"},
-      description = "ApplicationServer URL",
+      description = "OpenBIS ApplicationServer URL",
       scope = CommandLine.ScopeType.INHERIT)
   private String as_url;
 
   @Option(
       names = {"-dss", "--dss_url"},
-      description = "DatastoreServer URL",
+      description = "OpenBIS DatastoreServer URL",
       scope = CommandLine.ScopeType.INHERIT)
   private String dss_url;
 
@@ -85,14 +87,14 @@ public String getSeekURL() {
     return seek_url;
   }
 
-  public String getDSS() {
+  public String getOpenbisDSS() {
     if(dss_url == null & configPath!=null && !configPath.isBlank()) {
       dss_url = ReadProperties.getProperties(configPath).get("dss");
     }
     return dss_url;
   }
 
-  public String getAS() {
+  public String getOpenbisAS() {
     if(as_url == null & configPath!=null && !configPath.isBlank()) {
       as_url = ReadProperties.getProperties(configPath).get("as");
     }
@@ -107,6 +109,16 @@ public char[] getOpenbisPassword() {
     return openbisPasswordOptions.getPassword();
   }
 
+  public String getOpenbisBaseURL() throws MalformedURLException {
+    URL asURL = new URL(as_url);
+    String res = asURL.getProtocol()+ "://" +asURL.getHost();
+    if(asURL.getPort()!=-1) {
+      res+=":"+asURL.getPort();
+    }
+    System.err.println(res);
+    return res;
+  }
+
   /**
    * <a href="https://picocli.info/#_optionally_interactive">official picocli documentation example</a>
    */

src/main/java/life/qbic/io/commandline/DownloadPetabCommand.java

@@ -27,7 +27,7 @@ public class DownloadPetabCommand implements Runnable {
 
     @Override
     public void run() {
-      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS(), auth.getDSS());
+      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));

src/main/java/life/qbic/io/commandline/FindDatasetsCommand.java

@@ -39,7 +39,7 @@ public void run() {
       } else {
         System.out.println("Querying experiment in all available spaces...");
       }
-      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS());
+      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(

src/main/java/life/qbic/io/commandline/SampleHierarchyCommand.java

@@ -43,7 +43,7 @@ public void run() {
         } else {
           summary.add("Querying samples in all available spaces...");
         }
-        OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS());
+        OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getOpenbisAS());
         OpenbisConnector openbis = new OpenbisConnector(authentication);
         Map<SampleTypeConnection, Integer> hierarchy = openbis.queryFullSampleHierarchy(spaces);
 

src/main/java/life/qbic/io/commandline/SpaceStatisticsCommand.java

@@ -50,7 +50,7 @@ public void run() {
       } else {
         summary.add("Querying samples in all available spaces...");
       }
-      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS());
+      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getOpenbisAS());
       OpenbisConnector openbis = new OpenbisConnector(authentication);
 
       if (spaces.isEmpty()) {

src/main/java/life/qbic/io/commandline/TransferDataToSeekCommand.java

@@ -76,7 +76,7 @@ public void run() {
     System.out.println("Connecting to openBIS...");
 
     OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(),
-        auth.getAS(), auth.getDSS());
+        auth.getOpenbisAS(), auth.getOpenbisDSS());
 
     openbis = new OpenbisConnector(authentication);
 
@@ -106,8 +106,8 @@ public void run() {
     byte[] httpCredentials = Base64.encodeBase64(
         (auth.getSeekUser() + ":" + new String(auth.getSeekPassword())).getBytes());
     try {
-      seek = new SEEKConnector(auth.getSeekURL(), httpCredentials, "seek_test",
-          "lisym default study");
+      seek = new SEEKConnector(auth.getSeekURL(), httpCredentials, auth.getOpenbisBaseURL(),
+          "seek_test", "lisym default study");
       translator = seek.getTranslator();
     } catch (URISyntaxException | IOException | InterruptedException e) {
       throw new RuntimeException(e);

src/main/java/life/qbic/io/commandline/TransferSampleTypesToSeekCommand.java

@@ -28,16 +28,16 @@ public void run() {
     System.out.println("auth...");
 
     OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(),
-        auth.getAS(), auth.getDSS());
+        auth.getOpenbisAS(), auth.getOpenbisDSS());
     System.out.println("openbis...");
 
     openbis = new OpenbisConnector(authentication);
 
     byte[] httpCredentials = Base64.encodeBase64(
         (auth.getSeekUser() + ":" + new String(auth.getSeekPassword())).getBytes());
     try {
-      seek = new SEEKConnector(auth.getSeekURL(), httpCredentials, "seek_test",
-          "lisym default study");
+      seek = new SEEKConnector(auth.getSeekURL(), httpCredentials, auth.getOpenbisBaseURL(),
+          "seek_test", "lisym default study");
       translator = seek.getTranslator();
     } catch (URISyntaxException | IOException | InterruptedException e) {
       throw new RuntimeException(e);

src/main/java/life/qbic/io/commandline/UploadDatasetCommand.java

@@ -32,7 +32,7 @@ public class UploadDatasetCommand implements Runnable {
 
     @Override
     public void run() {
-      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS(), auth.getDSS());
+      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getOpenbisAS(), auth.getOpenbisDSS());
       openbis = new OpenbisConnector(authentication);
 
       if(!pathValid(dataPath)) {

src/main/java/life/qbic/io/commandline/UploadPetabResultCommand.java

@@ -33,7 +33,7 @@ public class UploadPetabResultCommand implements Runnable {
 
     @Override
     public void run() {
-      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS(), auth.getDSS());
+      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getOpenbisAS(), auth.getOpenbisDSS());
       openbis = new OpenbisConnector(authentication);
 
       if(!pathValid(dataPath)) {

src/main/java/life/qbic/model/OpenbisSeekTranslator.java

@@ -2,7 +2,6 @@
 
 import static java.util.Map.entry;
 
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.DataType;
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
@@ -16,13 +15,13 @@
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
 import java.util.Set;
 import life.qbic.model.isa.GenericSeekAsset;
 import life.qbic.model.isa.ISAAssay;
-import life.qbic.model.isa.ISADataFile;
 import life.qbic.model.isa.ISASample;
 import life.qbic.model.isa.ISASampleType;
 import life.qbic.model.isa.ISASampleType.SampleAttribute;
@@ -34,12 +33,24 @@ public class OpenbisSeekTranslator {
   private final String DEFAULT_PROJECT_ID;
   private final String DEFAULT_STUDY_ID;
   private final String DEFAULT_TRANSFERRED_SAMPLE_TITLE = "openBIS Name";
+  private final String openBISBaseURL;
 
-  public OpenbisSeekTranslator(String defaultProjectID, String defaultStudyID) {
+  public OpenbisSeekTranslator(String openBISBaseURL, String defaultProjectID, String defaultStudyID) {
+    this.openBISBaseURL = openBISBaseURL;
     this.DEFAULT_PROJECT_ID = defaultProjectID;
     this.DEFAULT_STUDY_ID = defaultStudyID;
   }
 
+  private String generateOpenBISLinkFromPermID(String entityType, String permID) {
+    StringBuilder builder = new StringBuilder();
+    builder.append(openBISBaseURL);
+    builder.append("#entity=");
+    builder.append(entityType);
+    builder.append("&permId=");
+    builder.append(permID);
+    return builder.toString();
+  }
+
   Map<String, String> experimentTypeToAssayClass = Map.ofEntries(
       entry("00_MOUSE_DATABASE", "EXP"),
       entry("00_PATIENT_DATABASE", "EXP"),
@@ -63,8 +74,8 @@ public OpenbisSeekTranslator(String defaultProjectID, String defaultStudyID) {
           new SampleAttributeType("8", "String", "String")),
       entry(DataType.HYPERLINK, new SampleAttributeType("8", "String", "String")),
       entry(DataType.XML, new SampleAttributeType("7", "Text", "Text")),
-      entry(DataType.SAMPLE, //should be handled before mapping types
-          new SampleAttributeType("8", "String", "String")),
+      entry(DataType.SAMPLE, //we link the sample as URL to openBIS for now
+          new SampleAttributeType("5", "Web link", "String")),
       entry(DataType.DATE, new SampleAttributeType("2", "Date time", "Date"))
   );
 
@@ -150,12 +161,23 @@ public SeekStructure translate(OpenbisExperimentWithDescendants experiment,
 
       //try to put all attributes into sample properties, as they should be a 1:1 mapping
       Map<String, String> typeCodesToNames = new HashMap<>();
+      Set<String> propertiesLinkingSamples = new HashSet<>();
       for (PropertyAssignment a : sampleType.getPropertyAssignments()) {
-        typeCodesToNames.put(a.getPropertyType().getCode(), a.getPropertyType().getLabel());
+        String code = a.getPropertyType().getCode();
+        String label = a.getPropertyType().getLabel();
+        DataType type = a.getPropertyType().getDataType();
+        typeCodesToNames.put(code, label);
+        if(type.equals(DataType.SAMPLE)) {
+          propertiesLinkingSamples.add(code);
+        }
       }
       Map<String, Object> attributes = new HashMap<>();
       for(String code : sample.getProperties().keySet()) {
-        attributes.put(typeCodesToNames.get(code), sample.getProperties().get(code));
+        String value = sample.getProperty(code);
+        if(propertiesLinkingSamples.contains(code)) {
+          value = generateOpenBISLinkFromPermID("SAMPLE", value);
+        }
+        attributes.put(typeCodesToNames.get(code), value);
       }
 
       attributes.put(DEFAULT_TRANSFERRED_SAMPLE_TITLE, sample.getIdentifier().getIdentifier());

src/main/java/life/qbic/model/download/SEEKConnector.java

@@ -30,7 +30,6 @@
 import life.qbic.model.isa.ISASample;
 import life.qbic.model.isa.ISASampleType;
 import life.qbic.model.isa.ISAStudy;
-import org.apache.commons.codec.binary.Base64;
 import org.apache.http.client.utils.URIBuilder;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -41,13 +40,56 @@ public class SEEKConnector {
   private String apiURL;
   private byte[] credentials;
   private OpenbisSeekTranslator translator;
+  private final String DEFAULT_PROJECT_ID;
 
-  public SEEKConnector(String apiURL, byte[] httpCredentials, String defaultProjectTitle,
-      String defaultStudyTitle) throws URISyntaxException, IOException, InterruptedException {
+  public SEEKConnector(String apiURL, byte[] httpCredentials, String openBISBaseURL,
+      String defaultProjectTitle, String defaultStudyTitle) throws URISyntaxException, IOException,
+      InterruptedException {
     this.apiURL = apiURL;
     this.credentials = httpCredentials;
-    translator = new OpenbisSeekTranslator("1", //searchNodeWithTitle("projects", defaultProjectTitle),
-        "1");//searchNodeWithTitle("studies", defaultStudyTitle));
+    Optional<String> projectID = getProjectWithTitle(defaultProjectTitle);
+    if(projectID.isEmpty()) {
+      throw new RuntimeException("Failed to find project with title: " + defaultProjectTitle+". "
+          + "Please provide an existing default project.");
+    }
+    DEFAULT_PROJECT_ID = projectID.get();
+
+    translator = new OpenbisSeekTranslator(openBISBaseURL, DEFAULT_PROJECT_ID,
+        searchNodeWithTitle("studies", defaultStudyTitle));
+  }
+
+  /**
+   * Lists projects and returns the optional identifier of the one matching the provided ID.
+   * Necessary because project search does not seem to work.
+   * @param projectTitle the title to search for
+   * @return
+   */
+  private Optional<String> getProjectWithTitle(String projectTitle)
+      throws IOException, InterruptedException, URISyntaxException {
+    String endpoint = apiURL+"/projects/";
+    HttpRequest request = HttpRequest.newBuilder()
+        .uri(new URI(endpoint))
+        .headers("Content-Type", "application/json")
+        .headers("Accept", "application/json")
+        .headers("Authorization", "Basic " + new String(credentials))
+        .GET().build();
+    HttpResponse<String> response = HttpClient.newBuilder().build()
+        .send(request, BodyHandlers.ofString());
+    if(response.statusCode() == 200) {
+      JsonNode rootNode = new ObjectMapper().readTree(response.body());
+      JsonNode hits = rootNode.path("data");
+      for (Iterator<JsonNode> it = hits.elements(); it.hasNext(); ) {
+        JsonNode hit = it.next();
+        String id = hit.get("id").asText();
+        String title = hit.get("attributes").get("title").asText();
+        if(title.equals(projectTitle)) {
+          return Optional.of(id);
+        }
+      }
+    } else {
+      throw new RuntimeException("Failed : HTTP error code : " + response.statusCode());
+    }
+    return Optional.empty();
   }
 
   public String addAssay(ISAAssay assay)
@@ -231,13 +273,16 @@ public String uploadStreamContent(String blobEndpoint,
     HttpRequest request = HttpRequest.newBuilder()
         .uri(new URI(blobEndpoint))
         .headers("Content-Type", "application/octet-stream")
-        .headers("Accept", "application/octet-stream")
+        .headers("Accept", "*/*")
         .headers("Authorization", "Basic " + new String(credentials))
         .PUT(BodyPublishers.ofInputStream(streamSupplier)).build();
 
     HttpResponse<String> response = HttpClient.newBuilder().build()
         .send(request, BodyHandlers.ofString());
 
+    System.err.println("response was: "+response);
+    System.err.println("response body: "+response.body());
+
     if(response.statusCode()!=200) {
       System.err.println(response.body());
       throw new RuntimeException("Failed : HTTP error code : " + response.statusCode());
@@ -276,9 +321,9 @@ public Optional<AssetToUpload> createAssetForFile(DataSetFile file, String asset
       if(!file.getPath().isBlank() && !file.isDirectory()) {
         File f = new File(file.getPath());
         String datasetCode = file.getDataSetPermId().toString();
-        String assetName = datasetCode+": "+f.getName();
-        GenericSeekAsset isaFile = new GenericSeekAsset("data_files", assetName, file.getPath(),
-            Arrays.asList("1"));//TODO
+        String assetName = datasetCode+": "+f.getName();//TODO what do we want to call the asset?
+        GenericSeekAsset isaFile = new GenericSeekAsset(assetType, assetName, file.getPath(),
+            Arrays.asList(DEFAULT_PROJECT_ID));
         isaFile.withAssays(assays);
         String fileExtension = f.getName().substring(f.getName().lastIndexOf(".")+1);
         String annotation = translator.dataFormatAnnotationForExtension(fileExtension);
@@ -298,9 +343,9 @@ public List<AssetToUpload> createAssets(List<DataSetFile> filesInDataset,
       if(!file.getPath().isBlank() && !file.isDirectory()) {
         File f = new File(file.getPath());
         String datasetCode = file.getDataSetPermId().toString();
-        String assetName = datasetCode+": "+f.getName();//TODO?
+        String assetName = datasetCode+": "+f.getName();//TODO what do we want to call the asset?
         GenericSeekAsset isaFile = new GenericSeekAsset("data_files", assetName, file.getPath(),
-            Arrays.asList("1"));
+            Arrays.asList(DEFAULT_PROJECT_ID));
         isaFile.withAssays(assays);
         String fileExtension = f.getName().substring(f.getName().lastIndexOf(".")+1);
         String annotation = translator.dataFormatAnnotationForExtension(fileExtension);
@@ -384,7 +429,7 @@ private Map<String, String> parseSampleTypesJSON(String json) throws JsonProcess
 
   private String searchNodeWithTitle(String nodeType, String title)
       throws URISyntaxException, IOException, InterruptedException {
-    String endpoint = apiURL+"/search/";
+    String endpoint = apiURL+"/search";
     URIBuilder builder = new URIBuilder(endpoint);
     builder.setParameter("q", title).setParameter("search_type", nodeType);
 
@@ -402,8 +447,7 @@ private String searchNodeWithTitle(String nodeType, String title)
       JsonNode hits = rootNode.path("data");
       for (Iterator<JsonNode> it = hits.elements(); it.hasNext(); ) {
         JsonNode hit = it.next();
-        System.err.println(hit.asText());
-        if(hit.get("title").asText().equals(title)) {
+        if(hit.get("attributes").get("title").asText().equals(title)) {
           return hit.get("id").asText();
         }
       }
@@ -458,6 +502,7 @@ public AssayWithQueuedAssets createNode(SeekStructure nodeWithChildren, boolean
       throws URISyntaxException, IOException, InterruptedException {
     String assayID = addAssay(nodeWithChildren.getAssay());
     for(ISASample sample : nodeWithChildren.getSamples()) {
+      sample.setAssayIDs(Arrays.asList(assayID));
       createSample(sample);
     }