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Commit 53d25e72 authored by Olivier Langella's avatar Olivier Langella
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Ods2Csv bug found by T. Balliau is fixed

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with 235 additions and 158 deletions
.gitignore
+ 1
− 1
View file @ 53d25e72
......@@ -4,4 +4,4 @@
/build
/build_ubuntu.xml
/build.xml
mascotdatfile_log4j.log
mascotdatfile_log4j.log*
lib/libodsstream.jar
+ 0
− 0
View file @ 53d25e72
No preview for this file type
lib/ods2csv.jar
+ 0
− 0
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No preview for this file type
src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_peptide_list.java
+ 1
− 0
View file @ 53d25e72
......@@ -120,6 +120,7 @@ public class print_ods_peptide_list extends printOdsBase {
}
odsTable.writeLine();
// out.write("\n");
logger.debug("printing group " + group.getNumber()+" end");
}
}
src/fr/inra/pappso/xtandempipeline/output/CsvRedundantPeptideOutput.java
+ 3
− 3
View file @ 53d25e72
......@@ -39,10 +39,10 @@ public class CsvRedundantPeptideOutput extends OdsRedundantPeptideOutput {
public CsvRedundantPeptideOutput(OutputStream outputStream)
throws MSMSException {
ods2csv = new Ods2Csv();
ods2csv.setSinkOutputStream(outputStream);
ods2csv.setNumericFormat(NumericFormat.en);
ods2csv.setSeparator('\t');
try {
ods2csv.setSinkOutputStream(outputStream);
ods2csv.setNumericFormat(NumericFormat.en);
ods2csv.setSeparator('\t');
odsTable = ods2csv.getOdsDocPipedOutput();
} catch (Exception e) {
String message = "error getting OdsDocPipedOutput "
......
src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java
+ 17
− 0
View file @ 53d25e72
......@@ -72,6 +72,10 @@ public class OdsRedundantPeptideOutput {
String message = "DatatypeConfigurationException " + e.getMessage();
logger.error(message);
throw new MSMSException(message);
} catch (Exception e) {
String message = "Exception " + e.getMessage();
logger.error(message);
throw new MSMSException(message);
}
}
......@@ -84,6 +88,10 @@ public class OdsRedundantPeptideOutput {
String message = "XMLStreamException " + e.getMessage();
logger.error(message);
throw new MSMSException(message);
} catch (Exception e) {
String message = "Exception " + e.getMessage();
logger.error(message);
throw new MSMSException(message);
}
}
......@@ -202,6 +210,11 @@ public class OdsRedundantPeptideOutput {
+ e.getMessage();
logger.error(message);
throw new MSMSException(message);
} catch (Exception e) {
String message = "Exception in write(Identification ident) "
+ e.getMessage();
logger.error(message);
throw new MSMSException(message);
}
}
......@@ -237,6 +250,10 @@ public class OdsRedundantPeptideOutput {
+ e.getMessage();
logger.error(message);
throw new MSMSException(message);
} catch (Exception e) {
String message = "Exception in writeHeaders() " + e.getMessage();
logger.error(message);
throw new MSMSException(message);
}
}
......
src/fr/inra/pappso/xtandempipeline/thread/printing_base.java
+ 25
− 2
View file @ 53d25e72
......@@ -8,6 +8,7 @@ import java.util.HashSet;
import fr.inra.pappso.csv2ods.Ods2Csv;
import fr.inra.pappso.libodsstream.OdsDocWriter;
import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.Protein;
import fr.inra.pappso.xtandempipeline.class_msms.config;
......@@ -228,6 +229,8 @@ public class printing_base extends process {
}
protected void printPeptideList(OdsDocWriter odsDoc) throws Exception {
logger.debug("printPeptideList begin");
// Verification pas arrete
if (this.isStop())
throw new StopException("");
......@@ -248,10 +251,18 @@ public class printing_base extends process {
for (Identification ident : this.identifications) {
writer.write(ident);
}
logger.debug("printPeptideList end");
if (this.isCsv) {
odsDoc.close();
logger.debug("csv file closed "
+ this.getfileout().getAbsolutePath() + "_peptide_list.txt");
}
}
protected void printOldPeptideList(OdsDocWriter odsDoc) throws Exception {
// Verification pas arrete
logger.debug("printOldPeptideList begin");
if (this.isStop())
throw new StopException("");
this.add_current_progress();
......@@ -270,8 +281,20 @@ public class printing_base extends process {
// output.open(this.getfileout().getAbsolutePath() + "_peptide.txt");
// peptide list
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_peptide_list(odsDoc));
try {
ident.print_result(new print_ods_peptide_list(odsDoc));
} catch (Exception e) {
String message = "error in ident.print_result :\n"
+ e.getMessage();
logger.error(message);
throw new MSMSException(message);
}
}
logger.debug("printOldPeptideList end");
if (this.isCsv) {
odsDoc.close();
logger.debug("csv file closed "
+ this.getfileout().getAbsolutePath() + "_peptide.txt");
}
}
}
src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java
+ 65
− 52
View file @ 53d25e72
......@@ -19,60 +19,73 @@ public class printing_combine extends printing_base {
this.set_view("Printing protein file results");
OdsDocWriter odsDoc;
if (this.isCsv) {
Ods2Csv ods2csv = new Ods2Csv();
ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ "_protein.txt");
odsDoc = ods2csv.getOdsDocPipedOutput();
} else {
odsDoc = new OdsDocWriter(this.getfileout().getAbsolutePath()
+ ".ods");
odsDoc.writeSheet("proteins");
}
// msms_output output = new msms_output();
// output.open(this.getfileout().getAbsolutePath() + "_protein.txt");
// protein view
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_protein_to_combined(odsDoc));
}
if (this.isCsv) {
odsDoc.close();
}
this.printOldPeptideList(odsDoc);
if (this.isCsv) {
odsDoc.close();
}
// Verification pas arrete
if (this.isStop())
throw new StopException("");
this.add_current_progress();
this.set_view("Printing compar file results");
if (this.isCsv) {
Ods2Csv ods2csv = new Ods2Csv();
ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ "_compar.txt");
odsDoc = ods2csv.getOdsDocPipedOutput();
} else {
odsDoc.writeSheet("compar");
}
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_compar(odsDoc, ident.getMsRunSet()));
}
if (this.isCsv) {
OdsDocWriter odsDoc = null;
try {
logger.debug("Print combine results proteins");
if (this.isCsv) {
Ods2Csv ods2csv = new Ods2Csv();
ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ "_protein.txt");
odsDoc = ods2csv.getOdsDocPipedOutput();
} else {
odsDoc = new OdsDocWriter(this.getfileout().getAbsolutePath()
+ ".ods");
odsDoc.writeSheet("proteins");
}
// msms_output output = new msms_output();
// output.open(this.getfileout().getAbsolutePath() +
// "_protein.txt");
// protein view
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_protein_to_combined(odsDoc));
}
if (this.isCsv) {
odsDoc.close();
}
logger.debug("Print combine results old peptides");
this.printOldPeptideList(odsDoc);
if (this.isCsv) {
odsDoc.close();
}
// Verification pas arrete
if (this.isStop())
throw new StopException("");
this.add_current_progress();
this.set_view("Printing compar file results");
logger.debug("Print combine results compar");
if (this.isCsv) {
Ods2Csv ods2csv = new Ods2Csv();
ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ "_compar.txt");
odsDoc = ods2csv.getOdsDocPipedOutput();
} else {
odsDoc.writeSheet("compar");
}
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_compar(odsDoc, ident
.getMsRunSet()));
}
if (this.isCsv) {
odsDoc.close();
}
logger.debug("Print combine new peptide");
this.printPeptideList(odsDoc);
odsDoc.close();
} catch (Exception e) {
throw e;
} finally {
if (odsDoc != null) {
odsDoc.close();
}
}
this.printPeptideList(odsDoc);
odsDoc.close();
this.add_current_progress();
}
......
src/fr/inra/pappso/xtandempipeline/thread/printing_indiv.java
+ 46
− 33
View file @ 53d25e72
......@@ -5,7 +5,6 @@ import fr.inra.pappso.libodsstream.OdsDocWriter;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.config;
import fr.inra.pappso.xtandempipeline.class_msms.Identification;
import fr.inra.pappso.xtandempipeline.filter_print.print_ods_peptide_list;
import fr.inra.pappso.xtandempipeline.filter_print.print_ods_protein_to_indiv;
public class printing_indiv extends printing_base {
......@@ -19,40 +18,55 @@ public class printing_indiv extends printing_base {
this.set_view("Printing protein file results");
OdsDocWriter odsDoc;
if (this.isCsv) {
Ods2Csv ods2csv = new Ods2Csv();
ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ "_protein.txt");
odsDoc = ods2csv.getOdsDocPipedOutput();
} else {
odsDoc = new OdsDocWriter(this.getfileout().getAbsolutePath()
+ ".ods");
odsDoc.writeSheet("proteins");
}
// msms_output output = new msms_output();
// output.open(this.getfileout().getAbsolutePath() + "_protein.txt");
// protein view
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_protein_to_indiv(odsDoc, ident
.getMsRunSet()));
}
if (this.isCsv) {
OdsDocWriter odsDoc = null;
try {
logger.debug("Print indiv results proteins");
if (this.isCsv) {
Ods2Csv ods2csv = new Ods2Csv();
ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ "_protein.txt");
odsDoc = ods2csv.getOdsDocPipedOutput();
} else {
odsDoc = new OdsDocWriter(this.getfileout().getAbsolutePath()
+ ".ods");
odsDoc.writeSheet("proteins");
}
// msms_output output = new msms_output();
// output.open(this.getfileout().getAbsolutePath() +
// "_protein.txt");
// protein view
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_protein_to_indiv(odsDoc, ident
.getMsRunSet()));
}
if (this.isCsv) {
odsDoc.close();
}
logger.debug("Print indiv results old peptides");
this.printOldPeptideList(odsDoc);
logger.debug("after printOldPeptideList(odsDoc)");
if (this.isCsv) {
logger.debug("try to close");
odsDoc.close();
}
logger.debug("Print indiv results new peptides");
this.printPeptideList(odsDoc);
odsDoc.close();
} catch (Exception e) {
throw e;
} finally {
if (odsDoc != null) {
odsDoc.close();
}
}
this.printOldPeptideList(odsDoc);
if (this.isCsv) {
odsDoc.close();
}
this.printPeptideList(odsDoc);
odsDoc.close();
// Verification pas arrete
if (this.isStop())
throw new StopException("");
......@@ -60,5 +74,4 @@ public class printing_indiv extends printing_base {
}
}
src/fr/inra/pappso/xtandempipeline/thread/printing_phosphopeptide.java
+ 77
− 67
View file @ 53d25e72
......@@ -20,76 +20,86 @@ public class printing_phosphopeptide extends printing_base {
this.set_view("Printing protein file results");
OdsDocWriter odsDoc;
if (this.isCsv) {
Ods2Csv ods2csv = new Ods2Csv();
ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ "_protein.txt");
odsDoc = ods2csv.getOdsDocPipedOutput();
} else {
odsDoc = new OdsDocWriter(this.getfileout().getAbsolutePath()
+ ".ods");
odsDoc.writeSheet("proteins");
}
// protein view
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_protein_to_phosphopeptide(odsDoc));
}
if (this.isCsv) {
odsDoc.close();
}
// Verification pas arrete
if (this.isStop())
throw new StopException("");
this.add_current_progress();
this.set_view("Printing peptide file results");
if (this.isCsv) {
Ods2Csv ods2csv = new Ods2Csv();
ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ "_peptide.txt");
odsDoc = ods2csv.getOdsDocPipedOutput();
} else {
odsDoc.writeSheet("peptides");
}
// output.open(this.getfileout().getAbsolutePath() + "_peptide.txt");
// peptide list
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_peptide_list_to_phosphopeptide(
odsDoc));
}
if (this.isCsv) {
OdsDocWriter odsDoc = null;
try {
if (this.isCsv) {
Ods2Csv ods2csv = new Ods2Csv();
ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ "_protein.txt");
odsDoc = ods2csv.getOdsDocPipedOutput();
} else {
odsDoc = new OdsDocWriter(this.getfileout().getAbsolutePath()
+ ".ods");
odsDoc.writeSheet("proteins");
}
// protein view
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_protein_to_phosphopeptide(
odsDoc));
}
if (this.isCsv) {
odsDoc.close();
}
// Verification pas arrete
if (this.isStop())
throw new StopException("");
this.add_current_progress();
this.set_view("Printing peptide file results");
if (this.isCsv) {
Ods2Csv ods2csv = new Ods2Csv();
ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ "_peptide.txt");
odsDoc = ods2csv.getOdsDocPipedOutput();
} else {
odsDoc.writeSheet("peptides");
}
// output.open(this.getfileout().getAbsolutePath() +
// "_peptide.txt");
// peptide list
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_peptide_list_to_phosphopeptide(
odsDoc));
}
if (this.isCsv) {
odsDoc.close();
}
// Verification pas arrete
if (this.isStop())
throw new StopException("");
this.add_current_progress();
this.set_view("Printing compar file results");
if (this.isCsv) {
Ods2Csv ods2csv = new Ods2Csv();
ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ "_compar.txt");
odsDoc = ods2csv.getOdsDocPipedOutput();
} else {
odsDoc.writeSheet("compar");
}
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_compar_phospho(odsDoc, ident
.getMsRunSet()));
}
odsDoc.close();
} catch (Exception e) {
throw e;
} finally {
if (odsDoc != null) {
odsDoc.close();
}
}
// Verification pas arrete
if (this.isStop())
throw new StopException("");
this.add_current_progress();
this.set_view("Printing compar file results");
if (this.isCsv) {
Ods2Csv ods2csv = new Ods2Csv();
ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ "_compar.txt");
odsDoc = ods2csv.getOdsDocPipedOutput();
} else {
odsDoc.writeSheet("compar");
}
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_compar_phospho(odsDoc, ident
.getMsRunSet()));
}
odsDoc.close();
this.add_current_progress();
}
......
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