Merge branch 'master' of git.wur.nl:unlock/fairds

# Conflicts:
#	src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUNSET.java

src/main/java/nl/fairbydesign/backend/data/objects/DiskUsage.java

@@ -3,7 +3,8 @@ package nl.fairbydesign.backend.data.objects;
 public class DiskUsage {
     private String project;
     private String investigation;
-    private long size;
+    private long tapeSize;
+    private long diskSize;
 
     public void setProject(String project) {
         this.project = project;
@@ -13,13 +14,6 @@ public class DiskUsage {
         return project;
     }
 
-    public void setSize(long size) {
-        this.size = size;
-    }
-
-    public long getSize() {
-        return size;
-    }
 
     public String getInvestigation() {
         return investigation;
@@ -28,4 +22,20 @@ public class DiskUsage {
     public void setInvestigation(String investigation) {
         this.investigation = investigation;
     }
+
+    public void setTapeSize(long tapeSize) {
+        this.tapeSize = tapeSize;
+    }
+
+    public long getTapeSize() {
+        return tapeSize;
+    }
+
+    public void setDiskSize(long diskSize) {
+        this.diskSize = diskSize;
+    }
+
+    public long getDiskSize() {
+        return diskSize;
+    }
 }

src/main/java/nl/fairbydesign/backend/irods/Data.java

@@ -195,9 +195,10 @@ public class Data {
         // Obtain all disk usage for each project
         IRODSGenQueryBuilder queryBuilder = new IRODSGenQueryBuilder(true, null);
 
-        queryBuilder.addConditionAsGenQueryField(COL_COLL_NAME, QueryConditionOperators.LIKE, "/" + irodsAccount.getZone() + "/projects/" + process.getProjectIdentifier() + "/" + process.getInvestigationIdentifier() + "%");
+        queryBuilder.addConditionAsGenQueryField(COL_COLL_NAME, QueryConditionOperators.LIKE, "/" + irodsAccount.getZone() + "%" + process.getProjectIdentifier() + "/" + process.getInvestigationIdentifier() + "%");
 
         // Column name as default does a distinct?
+        queryBuilder.addSelectAsGenQueryValue(COL_R_RESC_NAME);
         queryBuilder.addSelectAsAgregateGenQueryValue(RodsGenQueryEnum.COL_DATA_SIZE, GenQueryField.SelectFieldTypes.SUM);
 
         // Set limit?
@@ -212,13 +213,15 @@ public class Data {
         DiskUsage diskUsage = new DiskUsage();
         diskUsage.setProject(process.getProjectIdentifier());
         diskUsage.setInvestigation(process.getInvestigationIdentifier());
+        diskUsage.setTapeSize(0);
+        diskUsage.setDiskSize(0);
         for (IRODSQueryResultRow irodsQueryResultRow : irodsQueryResultSetResults) {
-            String size = irodsQueryResultRow.getColumn(0).trim().strip();
-            if (StringUtils.isNumeric(size) && size.length() > 0) {
-                diskUsage.setSize(Long.parseLong(size) / (1024 * 1024 * 1024));
-            } else {
-                diskUsage.setSize(-1);
-            }
+            String resource = irodsQueryResultRow.getColumn(0);
+            String size = irodsQueryResultRow.getColumn(1).trim().strip();
+            if (resource.contains("archiveResc") && StringUtils.isNumeric(size) && size.length() > 0)
+                    diskUsage.setTapeSize(Long.parseLong(size) / (1024 * 1024 * 1024));
+            if (resource.contains("dataResc") && StringUtils.isNumeric(size) && size.length() > 0)
+                diskUsage.setDiskSize(Long.parseLong(size) / (1024 * 1024 * 1024));
         }
         return diskUsage;
     }

src/main/java/nl/fairbydesign/backend/ncbi/NCBI.java

@@ -6,8 +6,6 @@ import com.fasterxml.jackson.databind.MapperFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import nl.fairbydesign.backend.ncbi.objects.esearch.Root;
 import nl.fairbydesign.backend.parsers.ExcelGenerator;
-import org.apache.jena.sparql.function.library.print;
-import org.apache.poi.ddf.EscherTertiaryOptRecord;
 import org.jboss.logging.Logger;
 import org.json.JSONObject;
 import org.json.XML;
@@ -26,7 +24,6 @@ import java.util.HashSet;
 import java.util.Scanner;
 
 import static nl.fairbydesign.backend.ncbi.XLSX.setup;
-import static nl.fairbydesign.backend.ncbi.XLSX.studies;
 
 public class NCBI {
     public static final Logger logger = Logger.getLogger(ExcelGenerator.class);

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/BASECALL.java

-package nl.fairbydesign.backend.ncbi.objects.esample;
-
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-public class BASECALL {
-    @JsonProperty("match_edge")
-    public String getMatch_edge() {
-        return this.match_edge; }
-    public void setMatch_edge(String match_edge) {
-        this.match_edge = match_edge; }
-    String match_edge;
-    @JsonProperty("content")
-    public String getContent() {
-        return this.content; }
-    public void setContent(String content) {
-        this.content = content; }
-    String content;
-}

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPECTEDBASECALLTABLE.java

-package nl.fairbydesign.backend.ncbi.objects.esample;
-
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-public class EXPECTEDBASECALLTABLE {
-    @JsonProperty("BASECALL")
-    public BASECALL getBASECALL() {
-        return this.bASECALL; }
-    public void setBASECALL(BASECALL bASECALL) {
-        this.bASECALL = bASECALL; }
-    BASECALL bASECALL;
-}

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPERIMENT.java

@@ -21,15 +21,12 @@ public class EXPERIMENT{
     public void setCenter_name(String center_name) { 
 		 this.center_name = center_name; } 
     String center_name;
-
-    //String or Object needed
-    @JsonProperty("PROCESSING")
-    public Object getPROCESSING() {
-        return this.pROCESSING; }
-    public void setPROCESSING(Object pROCESSING) {
-        this.pROCESSING = pROCESSING; }
-    Object pROCESSING;
-
+    @JsonProperty("PROCESSING") 
+    public String getPROCESSING() { 
+		 return this.pROCESSING; } 
+    public void setPROCESSING(String pROCESSING) { 
+		 this.pROCESSING = pROCESSING; } 
+    String pROCESSING;
     @JsonProperty("alias") 
     public String getAlias() { 
 		 return this.alias; } 
@@ -60,10 +57,4 @@ public class EXPERIMENT{
     public void setSTUDY_REF(STUDYREF sTUDY_REF) { 
 		 this.sTUDY_REF = sTUDY_REF; } 
     STUDYREF sTUDY_REF;
-    @JsonProperty("EXPERIMENT_LINKS")
-    public EXPERIMENTLINKS getEXPERIMENT_LINKS() {
-        return this.eXPERIMENT_LINKS; }
-    public void setEXPERIMENT_LINKS(EXPERIMENTLINKS eXPERIMENT_LINKS) {
-        this.eXPERIMENT_LINKS = eXPERIMENT_LINKS; }
-    EXPERIMENTLINKS eXPERIMENT_LINKS;
 }

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPERIMENTLINK.java

-package nl.fairbydesign.backend.ncbi.objects.esample;
-
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-public class EXPERIMENTLINK {
-    @JsonProperty("URL_LINK")
-    public URLLINK getURL_LINK() {
-        return this.uRL_LINK; }
-    public void setURL_LINK(URLLINK uRL_LINK) {
-        this.uRL_LINK = uRL_LINK; }
-    URLLINK uRL_LINK;
-}

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/EXPERIMENTLINKS.java

-package nl.fairbydesign.backend.ncbi.objects.esample;
-
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-public class EXPERIMENTLINKS {
-    @JsonProperty("EXPERIMENT_LINK")
-    public EXPERIMENTLINK getEXPERIMENT_LINK() {
-        return this.eXPERIMENT_LINK; }
-    public void setEXPERIMENT_LINK(EXPERIMENTLINK eXPERIMENT_LINK) {
-        this.eXPERIMENT_LINK = eXPERIMENT_LINK; }
-    EXPERIMENTLINK eXPERIMENT_LINK;
-}

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/PIPELINE.java

-package nl.fairbydesign.backend.ncbi.objects.esample;
-
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-public class PIPELINE {
-    @JsonProperty("PIPE_SECTION")
-    public PIPESECTION getPIPE_SECTION() {
-        return this.pIPE_SECTION; }
-    public void setPIPE_SECTION(PIPESECTION pIPE_SECTION) {
-        this.pIPE_SECTION = pIPE_SECTION; }
-    PIPESECTION pIPE_SECTION;
-}

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/PIPESECTION.java

-package nl.fairbydesign.backend.ncbi.objects.esample;
-
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-public class PIPESECTION {
-    @JsonProperty("STEP_INDEX")
-    public int getSTEP_INDEX() {
-        return this.sTEP_INDEX; }
-    public void setSTEP_INDEX(int sTEP_INDEX) {
-        this.sTEP_INDEX = sTEP_INDEX; }
-    int sTEP_INDEX;
-    @JsonProperty("VERSION")
-    public String getVERSION() {
-        return this.vERSION; }
-    public void setVERSION(String vERSION) {
-        this.vERSION = vERSION; }
-    String vERSION;
-    @JsonProperty("PREV_STEP_INDEX")
-    public String getPREV_STEP_INDEX() {
-        return this.pREV_STEP_INDEX; }
-    public void setPREV_STEP_INDEX(String pREV_STEP_INDEX) {
-        this.pREV_STEP_INDEX = pREV_STEP_INDEX; }
-    String pREV_STEP_INDEX;
-    @JsonProperty("PROGRAM")
-    public String getPROGRAM() {
-        return this.pROGRAM; }
-    public void setPROGRAM(String pROGRAM) {
-        this.pROGRAM = pROGRAM; }
-    String pROGRAM;
-}

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/PROCESSING.java

-package nl.fairbydesign.backend.ncbi.objects.esample;
-
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-public class PROCESSING {
-    @JsonProperty("PIPELINE")
-    public PIPELINE getPIPELINE() {
-        return this.pIPELINE; }
-    public void setPIPELINE(PIPELINE pIPELINE) {
-        this.pIPELINE = pIPELINE; }
-    PIPELINE pIPELINE;
-}

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/READSPEC.java

@@ -27,16 +27,4 @@ public class READSPEC{
     public void setREAD_TYPE(String rEAD_TYPE) { 
 		 this.rEAD_TYPE = rEAD_TYPE; } 
     String rEAD_TYPE;
-    @JsonProperty("EXPECTED_BASECALL_TABLE")
-    public EXPECTEDBASECALLTABLE getEXPECTED_BASECALL_TABLE() {
-        return this.eXPECTED_BASECALL_TABLE; }
-    public void setEXPECTED_BASECALL_TABLE(EXPECTEDBASECALLTABLE eXPECTED_BASECALL_TABLE) {
-        this.eXPECTED_BASECALL_TABLE = eXPECTED_BASECALL_TABLE; }
-    EXPECTEDBASECALLTABLE eXPECTED_BASECALL_TABLE;
-    @JsonProperty("RELATIVE_ORDER")
-    public RELATIVEORDER getRELATIVE_ORDER() {
-        return this.rELATIVE_ORDER; }
-    public void setRELATIVE_ORDER(RELATIVEORDER rELATIVE_ORDER) {
-        this.rELATIVE_ORDER = rELATIVE_ORDER; }
-    RELATIVEORDER rELATIVE_ORDER;
 }

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RELATIVEORDER.java

-package nl.fairbydesign.backend.ncbi.objects.esample;
-
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-public class RELATIVEORDER {
-    @JsonProperty("follows_read_index")
-    public int getFollows_read_index() {
-        return this.follows_read_index; }
-    public void setFollows_read_index(int follows_read_index) {
-        this.follows_read_index = follows_read_index; }
-    int follows_read_index;
-}

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUN.java

@@ -137,13 +137,6 @@ public class RUN {
 
     Bases bases;
 
-    @JsonProperty("xmlns")
-    public String getXmlns() {
-        return this.xmlns; }
-    public void setXmlns(String xmlns) {
-        this.xmlns = xmlns; }
-    String xmlns;
-
     @JsonProperty("center_name")
     public String getCenter_name() {
         return this.center_name;

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUNATTRIBUTE.java

@@ -15,10 +15,4 @@ public class RUNATTRIBUTE{
     public void setVALUE(String vALUE) { 
 		 this.vALUE = vALUE; } 
     String vALUE;
-    @JsonProperty("UNITS")
-    public String getUNITS() {
-        return this.uNITS; }
-    public void setUNITS(String uNITS) {
-        this.uNITS = uNITS; }
-    String uNITS;
 }

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUNSET.java

@@ -12,4 +12,14 @@ public class RUNSET{
     public void setRUN(ArrayList<RUN> rUN) {
 		 this.rUN = rUN; }
     ArrayList<RUN> rUN = new ArrayList<>();
-    }
\ No newline at end of file
+    }
+=======
+public class RUNSET{
+    @JsonProperty("RUN")
+    public RUN getRUN() {
+		 return this.rUN; } 
+    public void setRUN(RUN rUN) { 
+		 this.rUN = rUN; } 
+    RUN rUN;
+}
+>>>>>>> 3d2e7bc368880c32d40198f9fb320f8e742a6eea

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SAMPLE.java

@@ -3,66 +3,91 @@ package nl.fairbydesign.backend.ncbi.objects.esample;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 public class SAMPLE {
-    @JsonProperty("center_name")
-    public String getCenter_name() {
-        return this.center_name; }
-    public void setCenter_name(String center_name) {
-        this.center_name = center_name; }
-    String center_name;
-
     @JsonProperty("SAMPLE_NAME")
     public SAMPLENAME getSAMPLE_NAME() {
-        return this.sAMPLE_NAME; }
+        return this.sAMPLE_NAME;
+    }
+
     public void setSAMPLE_NAME(SAMPLENAME sAMPLE_NAME) {
-        this.sAMPLE_NAME = sAMPLE_NAME; }
+        this.sAMPLE_NAME = sAMPLE_NAME;
+    }
+
     SAMPLENAME sAMPLE_NAME;
 
     @JsonProperty("alias")
     public String getAlias() {
-        return this.alias; }
+        return this.alias;
+    }
+
     public void setAlias(String alias) {
-        this.alias = alias; }
+        this.alias = alias;
+    }
+
     String alias;
 
     @JsonProperty("IDENTIFIERS")
     public IDENTIFIERS getIDENTIFIERS() {
-        return this.iDENTIFIERS; }
+        return this.iDENTIFIERS;
+    }
+
     public void setIDENTIFIERS(IDENTIFIERS iDENTIFIERS) {
-        this.iDENTIFIERS = iDENTIFIERS; }
+        this.iDENTIFIERS = iDENTIFIERS;
+    }
+
     IDENTIFIERS iDENTIFIERS;
 
     @JsonProperty("accession")
     public String getAccession() {
-        return this.accession; }
+        return this.accession;
+    }
+
     public void setAccession(String accession) {
-        this.accession = accession; }
+        this.accession = accession;
+    }
+
     String accession;
 
     @JsonProperty("SAMPLE_ATTRIBUTES")
     public SAMPLEATTRIBUTES getSAMPLE_ATTRIBUTES() {
-        return this.sAMPLE_ATTRIBUTES; }
+        return this.sAMPLE_ATTRIBUTES;
+    }
+
     public void setSAMPLE_ATTRIBUTES(SAMPLEATTRIBUTES sAMPLE_ATTRIBUTES) {
-        this.sAMPLE_ATTRIBUTES = sAMPLE_ATTRIBUTES; }
+        this.sAMPLE_ATTRIBUTES = sAMPLE_ATTRIBUTES;
+    }
+
     SAMPLEATTRIBUTES sAMPLE_ATTRIBUTES;
 
     @JsonProperty("SAMPLE_LINKS")
     public SAMPLELINKS getSAMPLE_LINKS() {
-        return this.sAMPLE_LINKS; }
+        return this.sAMPLE_LINKS;
+    }
+
     public void setSAMPLE_LINKS(SAMPLELINKS sAMPLE_LINKS) {
-        this.sAMPLE_LINKS = sAMPLE_LINKS; }
+        this.sAMPLE_LINKS = sAMPLE_LINKS;
+    }
+
     SAMPLELINKS sAMPLE_LINKS;
 
     @JsonProperty("TITLE")
     public String getTITLE() {
-        return this.tITLE; }
+        return this.tITLE;
+    }
+
     public void setTITLE(String tITLE) {
-        this.tITLE = tITLE; }
+        this.tITLE = tITLE;
+    }
+
     String tITLE;
 
     @JsonProperty("DESCRIPTION")
     public String getDESCRIPTION() {
-        return this.dESCRIPTION; }
+        return this.dESCRIPTION;
+    }
+
     public void setDESCRIPTION(String dESCRIPTION) {
-        this.dESCRIPTION = dESCRIPTION; }
+        this.dESCRIPTION = dESCRIPTION;
+    }
+
     String dESCRIPTION;
 }

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SAMPLELINK.java

@@ -9,10 +9,4 @@ public class SAMPLELINK{
     public void setXREF_LINK(XREFLINK xREF_LINK) { 
 		 this.xREF_LINK = xREF_LINK; } 
     XREFLINK xREF_LINK;
-    @JsonProperty("URL_LINK")
-    public URLLINK getURL_LINK() {
-        return this.uRL_LINK; }
-    public void setURL_LINK(URLLINK uRL_LINK) {
-        this.uRL_LINK = uRL_LINK; }
-    URLLINK uRL_LINK;
 }

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/SUBMISSION.java

@@ -2,27 +2,13 @@ package nl.fairbydesign.backend.ncbi.objects.esample;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
 
-import java.util.Date;
-
 public class SUBMISSION{
-    @JsonProperty("submission_date")
-    public Date getSubmission_date() {
-        return this.submission_date; }
-    public void setSubmission_date(Date submission_date) {
-        this.submission_date = submission_date; }
-    Date submission_date;
     @JsonProperty("center_name")
     public String getCenter_name() { 
 		 return this.center_name; } 
     public void setCenter_name(String center_name) { 
 		 this.center_name = center_name; } 
     String center_name;
-    @JsonProperty("broker_name")
-    public String getBroker_name() {
-        return this.broker_name; }
-    public void setBroker_name(String broker_name) {
-        this.broker_name = broker_name; }
-    String broker_name;
     @JsonProperty("alias") 
     public String getAlias() { 
 		 return this.alias; } 

src/main/java/nl/fairbydesign/backend/parsers/ExcelValidator.java

@@ -60,7 +60,7 @@ public class ExcelValidator {
     public static final String FORWARD_FILENAME = "Forward filename";
     public static final String OBSERVATION_UNIT_IDENTIFIER = "Observation unit identifier";
     public static final String SAMPLE_IDENTIFIER = "Sample identifier";
-    public static final String FILE_NAME = "FileName";
+    public static final String FILE_NAME = "Filename";
     public static final String ASSAY_IDENTIFIER = "Assay identifier";
     public static final String SAME_AS = "Same as";
     public static final String LIBRARY_NAME = "Library name";
@@ -756,17 +756,17 @@ public class ExcelValidator {
         AssayType assayType;
         if (sheet.getSheetName().endsWith("AmpliconAssay")) {
             assayType = AssayType.Amplicon;
-        } else if (sheet.getSheetName().endsWith("AmpliconLibraryAssay")) {
+        } else if (sheet.getSheetName().endsWith("AmpliconLibrary")) {
             assayType = AssayType.AmpliconLibrary;
-        } else if (sheet.getSheetName().endsWith("RNAseqAssay")) {
+        } else if (sheet.getSheetName().endsWith("RNA")) {
             assayType = AssayType.Transcriptomics;
         } else if (sheet.getSheetName().toLowerCase().endsWith("illumina")) {
             assayType = AssayType.Genomics;
         } else if (sheet.getSheetName().toLowerCase().endsWith("nanopore")) {
             assayType = AssayType.Genomics;
-        } else if (sheet.getSheetName().endsWith("ProteomicsAssay")) {
+        } else if (sheet.getSheetName().endsWith("Proteomics")) {
             assayType = AssayType.Proteomics;
-        } else if (sheet.getSheetName().endsWith("MetabolomicsAssay")) {
+        } else if (sheet.getSheetName().endsWith("Metabolomics")) {
             assayType = AssayType.Metabolomics;
         } else {
             throw new Exception("The sheet " + sheet.getSheetName() + " is of an unsupported assay type");
@@ -923,7 +923,7 @@ public class ExcelValidator {
                     // parsedHeaders.addAll(Arrays.asList(ASSAY_DESCRIPTION, ASSAY_TITLE, ASSAY_IDENTIFIER, PLATFORM));
 
                     if (fileCell.getCellType().equals(CellType.BLANK)) {
-                        logging("No file found for " + assay.getIdentifier());
+//                            logging("No file found for " + assay.getResource().getURI());
                     } else {
                         String fileName = getStringValueCell(fileCell);
                         // Check the FileNameForwardPath and FileNameReversePath first