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add localdatabasepath to MetFragRest parameter parsing, closes #128
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@sneumann
sneumann committed Sep 4, 2023
1 parent 8e6b1fb commit 85cd7c5
Showing 1 changed file with 40 additions and 28 deletions.
68 changes: 40 additions & 28 deletions MetFragRest/src/main/java/de/ipbhalle/model/ProcessArguments.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,16 +21,17 @@ public class ProcessArguments {
private String precursoriontype;
private String peakliststring;
private String metfragdatabasetype;
private String localdatabasepath;
private String maximumtreedepth;
private String samplename;
// local database
private String localmetchemdatabase;
private String localmetchemdatabaseportnumber;
private String localmetchemdatabase;
private String localmetchemdatabaseportnumber;
private String localmetchemdatabaseserverip;
private String localmetchemdatabaseuser;
private String localmetchemdatabaseuser;
private String localmetchemdatabasepassword;
private String localmetchemdatabaselibrary;

public String toString() {
StringBuilder builder = new StringBuilder();
if(fragmentpeakmatchabsolutemassdeviation != null) builder.append("fragmentpeakmatchabsolutemassdeviation=" + fragmentpeakmatchabsolutemassdeviation + "\n");
Expand All @@ -41,33 +42,34 @@ public String toString() {
if(neutralprecursormass != null) builder.append("neutralprecursormass=" + neutralprecursormass + "\n");
if(neutralprecursormolecularformula != null) builder.append("neutralprecursormolecularformula=" + neutralprecursormolecularformula + "\n");
if(precursorionmode != null) builder.append("precursorionmode=" + precursorionmode + "\n");
if(precursoriontype != null) builder.append("precursoriontype=" + precursoriontype + "\n");
if(peakliststring != null) builder.append("peakliststring=" + peakliststring + "\n");
if(precursoriontype != null) builder.append("precursoriontype=" + precursoriontype + "\n");
if(peakliststring != null) builder.append("peakliststring=" + peakliststring + "\n");
if(metfragdatabasetype != null) builder.append("metfragdatabasetype=" + metfragdatabasetype + "\n");
if(localdatabasepath != null) builder.append("localdatabasepath=" + localdatabasepath + "\n");
if(maximumtreedepth != null) builder.append("maximumtreedepth=" + maximumtreedepth + "\n");
if(samplename != null) builder.append("samplename=" + samplename + "\n");
// local database
if(localmetchemdatabase != null) builder.append("localmetchemdatabase=" + localmetchemdatabase + "\n");
if(localmetchemdatabaseportnumber != null) builder.append("localmetchemdatabaseportnumber=" + localmetchemdatabaseportnumber + "\n");
if(localmetchemdatabaseserverip != null) builder.append("localmetchemdatabaseserverip=" + localmetchemdatabaseserverip + "\n");
if(localmetchemdatabaseuser != null) builder.append("localmetchemdatabaseuser=" + localmetchemdatabaseuser + "\n");
if(localmetchemdatabasepassword != null) builder.append("localmetchemdatabasepassword=" + localmetchemdatabasepassword + "\n");
if(localmetchemdatabaselibrary != null) builder.append("localmetchemdatabaselibrary=" + localmetchemdatabaselibrary + "\n");
if(localmetchemdatabase != null) builder.append("localmetchemdatabase=" + localmetchemdatabase + "\n");
if(localmetchemdatabaseportnumber != null) builder.append("localmetchemdatabaseportnumber=" + localmetchemdatabaseportnumber + "\n");
if(localmetchemdatabaseserverip != null) builder.append("localmetchemdatabaseserverip=" + localmetchemdatabaseserverip + "\n");
if(localmetchemdatabaseuser != null) builder.append("localmetchemdatabaseuser=" + localmetchemdatabaseuser + "\n");
if(localmetchemdatabasepassword != null) builder.append("localmetchemdatabasepassword=" + localmetchemdatabasepassword + "\n");
if(localmetchemdatabaselibrary != null) builder.append("localmetchemdatabaselibrary=" + localmetchemdatabaselibrary + "\n");

return builder.toString();
}

public MetFragGlobalSettings getSettingsObject(File resFolder) throws ParameterNotKnownException {
MetFragGlobalSettings settings = new MetFragGlobalSettings();
if(fragmentpeakmatchabsolutemassdeviation != null)
if(fragmentpeakmatchabsolutemassdeviation != null)
settings.set(VariableNames.ABSOLUTE_MASS_DEVIATION_NAME, ParameterDataTypes.getParameter(fragmentpeakmatchabsolutemassdeviation, VariableNames.ABSOLUTE_MASS_DEVIATION_NAME));
if(fragmentpeakmatchrelativemassdeviation != null)
if(fragmentpeakmatchrelativemassdeviation != null)
settings.set(VariableNames.RELATIVE_MASS_DEVIATION_NAME, ParameterDataTypes.getParameter(fragmentpeakmatchabsolutemassdeviation, VariableNames.RELATIVE_MASS_DEVIATION_NAME));
if(databasesearchrelativemassdeviation != null)
if(databasesearchrelativemassdeviation != null)
settings.set(VariableNames.DATABASE_RELATIVE_MASS_DEVIATION_NAME, ParameterDataTypes.getParameter(databasesearchrelativemassdeviation, VariableNames.DATABASE_RELATIVE_MASS_DEVIATION_NAME));
if(precursorcompoundids != null)
if(precursorcompoundids != null)
settings.set(VariableNames.PRECURSOR_DATABASE_IDS_NAME, ParameterDataTypes.getParameter(precursorcompoundids, VariableNames.PRECURSOR_DATABASE_IDS_NAME));
if(ionizedprecursormass != null)
if(ionizedprecursormass != null)
settings.set(VariableNames.PRECURSOR_ION_MASS_NAME, ParameterDataTypes.getParameter(ionizedprecursormass, VariableNames.PRECURSOR_ION_MASS_NAME));
if(neutralprecursormass != null)
settings.set(VariableNames.PRECURSOR_NEUTRAL_MASS_NAME, ParameterDataTypes.getParameter(neutralprecursormass, VariableNames.PRECURSOR_NEUTRAL_MASS_NAME));
Expand All @@ -81,11 +83,13 @@ public MetFragGlobalSettings getSettingsObject(File resFolder) throws ParameterN
settings.set(VariableNames.PEAK_LIST_STRING_NAME, ParameterDataTypes.getParameter(peakliststring, VariableNames.PEAK_LIST_STRING_NAME));
if(metfragdatabasetype != null)
settings.set(VariableNames.METFRAG_DATABASE_TYPE_NAME, ParameterDataTypes.getParameter(metfragdatabasetype, VariableNames.METFRAG_DATABASE_TYPE_NAME));
if(localdatabasepath != null)
settings.set(VariableNames.LOCAL_DATABASE_PATH_NAME, ParameterDataTypes.getParameter(localdatabasepath, VariableNames.LOCAL_DATABASE_PATH_NAME));
if(maximumtreedepth != null)
settings.set(VariableNames.MAXIMUM_TREE_DEPTH_NAME, ParameterDataTypes.getParameter(maximumtreedepth, VariableNames.MAXIMUM_TREE_DEPTH_NAME));
if(samplename != null)
settings.set(VariableNames.SAMPLE_NAME, ParameterDataTypes.getParameter(samplename, VariableNames.SAMPLE_NAME));
// local database
// local database
if(localmetchemdatabase != null)
settings.set(VariableNames.LOCAL_METCHEM_DATABASE_NAME, ParameterDataTypes.getParameter(localmetchemdatabase, VariableNames.LOCAL_METCHEM_DATABASE_NAME));
if(localmetchemdatabaseportnumber != null)
Expand All @@ -98,31 +102,31 @@ public MetFragGlobalSettings getSettingsObject(File resFolder) throws ParameterN
settings.set(VariableNames.LOCAL_METCHEM_DATABASE_PASSWORD_NAME, ParameterDataTypes.getParameter(localmetchemdatabasepassword, VariableNames.LOCAL_METCHEM_DATABASE_PASSWORD_NAME));
if(localmetchemdatabaselibrary != null)
settings.set(VariableNames.LOCAL_METCHEM_DATABASE_LIBRARY_NAME, ParameterDataTypes.getParameter(localmetchemdatabaselibrary, VariableNames.LOCAL_METCHEM_DATABASE_LIBRARY_NAME));


this.addAdditionalParameters(settings, resFolder);
return settings;
}

private void addAdditionalParameters(MetFragGlobalSettings settings, File resFolder) {
settings.set(VariableNames.METFRAG_PEAK_LIST_READER_NAME, FilteredStringTandemMassPeakListReader.class.getName());
settings.set(VariableNames.STORE_RESULTS_PATH_NAME, resFolder.getAbsolutePath());
if(!settings.containsKey(VariableNames.SAMPLE_NAME)) settings.set(VariableNames.SAMPLE_NAME, resFolder.getName());
settings.set(VariableNames.METFRAG_CANDIDATE_WRITER_NAME, new String[] {"CSV"});
}

public String getFragmentpeakmatchabsolutemassdeviation() {
return fragmentpeakmatchabsolutemassdeviation;
}

public void setFragmentpeakmatchabsolutemassdeviation(String fragmentPeakMatchAbsoluteMassDeviation) {
fragmentpeakmatchabsolutemassdeviation = fragmentPeakMatchAbsoluteMassDeviation;
}

public String getFragmentpeakmatchrelativemassdeviation() {
return fragmentpeakmatchrelativemassdeviation;
}

public void setFragmentpeakmatchrelativemassdeviation(String fragmentPeakMatchRelativeMassDeviation) {
fragmentpeakmatchrelativemassdeviation = fragmentPeakMatchRelativeMassDeviation;
}
Expand Down Expand Up @@ -199,6 +203,14 @@ public void setMetfragdatabasetype(String metfragdatabasetype) {
this.metfragdatabasetype = metfragdatabasetype;
}

public String getLocaldatabasepath() {
return localdatabasepath;
}

public void setLocaldatabasepath(String localdatabasepath) {
this.localdatabasepath = localdatabasepath;
}

public String getLocalmetchemdatabase() {
return localmetchemdatabase;
}
Expand Down Expand Up @@ -262,5 +274,5 @@ public String getSamplename() {
public void setSamplename(String samplename) {
this.samplename = samplename;
}

}

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