upload added

.gitlab-ci.yml

@@ -14,8 +14,9 @@ test_build_dev:
   stage: test_build
   script:
     - ./build.sh
-    - FILENAME=./iRODSKubernetes.jar
-    - /upload.sh $FILENAME
+    - curl --insecure --user $USERNAME:$PASSWORD -T ./iRODSKubernetes.jar sftp://download.systemsbiology.nl/unlock/
+    # - FILENAME=./iRODSKubernetes.jar
+    # - /upload.sh $FILENAME
   only:
     - dev
 
@@ -24,7 +25,8 @@ test_build_master:
   stage: test_build
   script:
     - ./build.sh
-    - FILENAME=./iRODSKubernetes.jar
-    - /upload.sh $FILENAME
+    - curl --insecure --user $USERNAME:$PASSWORD -T ./iRODSKubernetes.jar sftp://download.systemsbiology.nl/unlock/
+    # - FILENAME=./iRODSKubernetes.jar
+    # - /upload.sh $FILENAME
   only:
     - master

src/main/java/nl/munlock/objects/WorkflowHDT.java

+package nl.munlock.objects;
+
+import nl.munlock.Generic;
+import nl.munlock.yaml.MetaGenomics;
+import nl.munlock.yaml.Yaml;
+import org.apache.log4j.Logger;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+
+public class WorkflowMetagenomics extends Workflow {
+    private static final Logger log = Generic.getLogger(WorkflowMetagenomics.class, Yaml.debug);
+
+    public String destination;
+    public HashMap<String, String> irods = new HashMap<>();
+    public ArrayList<FileClass> forward_reads = new ArrayList<>();
+    public ArrayList<FileClass> reverse_reads = new ArrayList<>();
+    public ArrayList<FileClass> pacbio_reads = new ArrayList<>();
+    public String kraken_database; //  = new ArrayList<>();
+    public boolean isolate;
+    public boolean metagenomics;
+    public Map<String, String> clazz;
+
+    public void addIRODS(String irodsPath) {
+        irods.put(irods.size() + "_irods", irodsPath);
+    }
+
+    public void setDestination(String destination) {
+        this.destination = destination;
+    }
+
+    public String getDestination() {
+        return destination;
+    }
+
+    public ArrayList<FileClass> getForward_reads() {
+        return forward_reads;
+    }
+
+    public void addForward_reads(String forward_reads) throws Exception {
+        addIRODS(forward_reads);
+        FileClass fileClass = new FileClass();
+        fileClass.setClazz("File");
+        fileClass.setLocation(forward_reads);
+        this.forward_reads.add(fileClass);
+    }
+
+
+    public boolean isIsolate() {
+        return isolate;
+    }
+
+    public void setIsolate(boolean isolate) {
+        this.isolate = isolate;
+    }
+
+    public ArrayList<FileClass> getReverse_reads() {
+        return reverse_reads;
+    }
+
+    public void addReverse_reads(String reverse_reads) throws Exception {
+        addIRODS(reverse_reads);
+        FileClass fileClass = new FileClass();
+        fileClass.setClazz("File");
+        fileClass.setLocation(reverse_reads);
+        this.reverse_reads.add(fileClass);
+    }
+
+    public ArrayList<FileClass> getPacbio() {
+        return pacbio_reads;
+    }
+
+    public void addPacbio(String pacbio) throws Exception {
+        addIRODS(pacbio);
+        FileClass fileClass = new FileClass();
+        fileClass.setClazz("File");
+        fileClass.setLocation(pacbio);
+        this.pacbio_reads.add(fileClass);
+    }
+
+    public boolean isMetagenomics() {
+        return metagenomics;
+    }
+
+    public void setMetagenomics(boolean metagenomics) {
+        this.metagenomics = metagenomics;
+    }
+
+    public String getKraken_database() {
+        return kraken_database;
+    }
+
+    public void setKraken_database(String kraken_database) throws Exception {
+        this.kraken_database = kraken_database;
+//        FileClass fileClass = new FileClass();
+//        fileClass.setClazz("Directory");
+//        fileClass.setLocation(kraken_database);
+//        this.kraken_database.add(fileClass);
+    }
+}

src/main/java/nl/munlock/options/workflow/CommandOptionsHDT.java

+package nl.munlock.options.workflow;
+
+import com.beust.jcommander.JCommander;
+import com.beust.jcommander.Parameter;
+import com.beust.jcommander.ParameterException;
+
+import java.lang.reflect.Field;
+
+public class CommandOptionsNGTAX extends CommandOptionsYAML {
+
+    @Parameter(names = {"-length"}, description = "Read length used in NGTAX (default maximum length)")
+    public int read_len = 0;
+
+    @Parameter(names = {"-minimumThreshold"}, description = "Minimum threshold detectable, expressed in percentage")
+    public double minimumThreshold = 0.1;
+
+    @Parameter(names = {"-referenceDB"}, description = "Reference database to disable provide empty string -referenceDB ''")
+    public String reference_db = "/unlock/references/databases/Silva/SILVA_132_SSURef_tax_silva.fasta.gz";
+
+
+    public CommandOptionsNGTAX(String args[]) {
+        try {
+            JCommander jc = new JCommander(this);
+            jc.parse(args);
+
+            // if any of the nl.wur.ssb.options is null...
+            boolean failed = false;
+            for (Field f : getClass().getDeclaredFields())
+                if (f.get(this) == null) {
+                    System.err.println(f + " system variable not found, see help for more information");
+                    failed = true;
+                }
+
+            if (this.help || failed) {
+                throw new ParameterException("something failed");
+            }
+        } catch (ParameterException | IllegalAccessException pe) {
+            int exitCode = 64;
+            if (this.help) {
+                exitCode = 0;
+            }
+            System.out.println(pe.getMessage());
+            new JCommander(this).usage();
+            System.out.println("  * required parameter");
+            System.exit(exitCode);
+        }
+    }
+}

src/main/java/nl/munlock/yaml/HDT.java

+package nl.munlock.yaml;public class HDT {
+}