/*
* Copyright (C) 2013 SeqWare
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import joptsimple.OptionException;
import net.sourceforge.seqware.common.metadata.Metadata;
import net.sourceforge.seqware.common.model.LibrarySelection;
import net.sourceforge.seqware.common.model.LibrarySource;
import net.sourceforge.seqware.common.model.LibraryStrategy;
import net.sourceforge.seqware.common.model.Organism;
import net.sourceforge.seqware.common.model.Platform;
import net.sourceforge.seqware.common.model.StudyType;
import net.sourceforge.seqware.common.util.Log;
import net.sourceforge.seqware.common.util.runtools.ConsoleAdapter;
import org.apache.commons.lang3.StringUtils;
/**
*
* @author mtaschuk
*/
public abstract class BatchMetadataParser {
public enum Field {
study_type, platform_id, organism_id, study_name, experiment_name, sequencer_run_name, library_strategy_accession, library_source_accession, library_selection_accession, library_source_template_type, tissue_origin, tissue_type, library_type, library_size_code, targeted_resequencing, tissue_preparation, run_file_path, barcode, number_of_lanes, study_center_project, study_center_name
}
private static String[] librarySourceTemplateTypeList = new String[] { "CH", "EX", "MR", "SM", "TR", "TS", "WG", "WT", "Other" };
private static String[] targetedResequencingList = new String[] { "Agilent SureSelect 244k Array", "Agilent SureSelect All Exon G3362",
"Agilent SureSelect ICGC/Sanger Exon", "AmpliSeq Cancer Panel v1", "AmpliSeq Comprehensive Cancer Panel",
"Illumina TruSeq Exome", "Ion AmpliSeq Cancer Panel v1", "Nimblegen 2.1M Human Exome (21191)", "Nimblegen Human Exome v2.0",
"Nimblegen ICGC Beta", "Nimblegen OICR Test (13668)", "TruSeq Amplicon - Cancer Panel", "Other" };
private static String[] tissueOriginList = new String[] { "Br", "Cb", "Ep", "Ki", "Li", "Lu", "Lv", "Lx", "Ly", "Nk", "nn", "Oc", "Ov",
"Pa", "Pr", "Sg", "Sp", "St", "Ta", "Tr", "Wm", "Other" };
private static String[] tissuePreparationList = new String[] { "Blood", "FFPE", "Fresh Frozen", "Other" };
private static String[] tissueTypeList = new String[] { "C", "M", "n", "P", "R", "X", "Other" };
private static String[] libraryTypeList = new String[] { "SE", "PE", "MP", "Other" };
private String lstety = "";
private String tare = "";
private String tior = "";
private String tipr = "";
private String tity = "";
private String lity = "PE";
private Integer lSize = 0;
private Metadata metadata;
protected final Map<String, String> fields;
protected final Map<String, String> defaults;
protected boolean interactive;
/**
* Handles prompting for a choice out of a list of choices using integers.
*
* @param sampleName
* the sample name used for the prompting message
* @param title
* the name of the field that is being set
* @param choices
* the list of choices for the value of 'title'
* @param deflt
* the default choice to fall back on, which can be one of the list of 'choices'. This is the string value, not the integer.
* @return
*/
protected String choiceOf(String sampleName, String title, String[] choices, String deflt) {
String choice = null;
int choiceInt = 0;
Log.stdout("\nFor sample " + sampleName + ", choose one of the following for " + title + " or enter 0 to skip:");
for (int i = 1; i <= choices.length; i++) {
Log.stdout(i + " : " + choices[i - 1]);
if (choices[i - 1].equals(deflt)) {
choiceInt = i;
}
}
while (choice == null) {
choiceInt = promptPositiveInteger(title, choiceInt, null, 1, choices.length);
if (choiceInt == 0) { // no selection
break;
} else if (choiceInt == choices.length) {
choice = ConsoleAdapter.getInstance().promptString("Please specify", null);
} else if (choiceInt <= 0 || choiceInt > choices.length) {
} else {
choice = choices[choiceInt - 1];
}
}
return choice;
}
public BatchMetadataParser(Metadata metadata, Map<String, String> fields, boolean interactive) {
this.metadata = metadata;
this.fields = fields;
this.defaults = new HashMap<>(fields);
this.interactive = interactive;
}
protected Integer findOrganismId(String organism) {
Integer organismId = null;
for (Organism o : metadata.getOrganisms()) {
if (o.getName().equals(organism)) {
organismId = o.getOrganismId();
}
}
return organismId;
}
/**
* Generates a RunInfo object with the given parameters. All fields are optional.
*
* @param runName
* @param studyTitle
* @param experimentName
* @param filePath
* @param platformId
* @param studyType
* @param assayType
* @param workflowType
* @return
*/
protected RunInfo generateRunInfo(String runName, String runDescription, String studyTitle, String studyDescription,
String studyCenterName, String studyCenterProject, String experimentName, String experimentDescription, String filePath,
int platformId, int studyType, boolean isPairedEnd, String workflowType, String assayType) {
RunInfo runInfo = new RunInfo();
// Study
KeyVal[] list = getKeyVals(metadata.getStudyTypes());
runInfo.setStudyTitle(promptString("Study Title", studyTitle, Field.study_name));
runInfo.setStudyDescription(studyDescription);
if (studyDescription == null) {
runInfo.setStudyDescription(runInfo.getStudyTitle());
}
runInfo.setStudyCenterName(promptString("Study Center Name", studyCenterName, Field.study_center_name));
runInfo.setStudyCenterProject(promptString("Study Center Project", studyCenterProject, Field.study_center_project));
runInfo.setStudyType(promptAccession("Study Type Accession", studyType, list, Field.study_type));
// Sequencer run
list = getKeyVals(metadata.getPlatforms());
runInfo.setRunName(promptString("Sequencer Run Name", runName, Field.sequencer_run_name));
runInfo.setRunDescription(runDescription);
if (runDescription == null) {
runInfo.setRunDescription(runInfo.getRunName());
}
runInfo.setRunFilePath(promptString("Sequencer run directory", filePath, Field.run_file_path));
runInfo.setPlatformId(promptAccession("Platform accession", platformId, list, Field.platform_id));
runInfo.setPairedEnd(isPairedEnd);
runInfo.setRunSkip(false);
// experiment
runInfo.setExperimentName(promptString("Experiment Name", experimentName, Field.experiment_name));
runInfo.setExperimentDescription(experimentDescription);
if (experimentDescription == null) {
runInfo.setExperimentDescription(runInfo.getExperimentName());
}
if (workflowType != null) {
runInfo.setWorkflowType(workflowType);
}
if (assayType != null) {
runInfo.setAssayType(assayType);
}
return runInfo;
}
/**
* Generates lane info with the given parameters. Lane number needs to be given. Everything else can be null or less than 0.
*
* @param laneNumber
* @param studyTypeAccession
* @return
*/
protected LaneInfo generateLaneInfo(String laneNumber, int studyTypeAccession) {
LaneInfo laneInfo = new LaneInfo();
laneInfo.setLaneNumber(laneNumber);
laneInfo.setLaneName(laneInfo.getLaneNumber());
laneInfo.setLaneDescription(laneInfo.getLaneNumber());
laneInfo.setLaneSkip(Boolean.FALSE);
laneInfo.setLaneCycleDescriptor("");
if (studyTypeAccession > 0) {
laneInfo.setStudyTypeAcc(studyTypeAccession);
} else {
KeyVal[] list = getKeyVals(metadata.getStudyTypes());
laneInfo.setStudyTypeAcc(promptAccession("Study Type Accession", studyTypeAccession, list, Field.study_type));
}
// See https://jira.oicr.on.ca/browse/SEQWARE-1561. Uncomment when fixed.
KeyVal[] list = getKeyVals(metadata.getLibraryStrategies());
laneInfo.setLibraryStrategyAcc(promptAccession("Library Strategy Accession", 1, list, Field.library_strategy_accession));
list = getKeyVals(metadata.getLibrarySelections());
laneInfo.setLibrarySelectionAcc(promptAccession("Library Selection Accession", 1, list, Field.library_selection_accession));
list = getKeyVals(metadata.getLibrarySource());
laneInfo.setLibrarySourceAcc(promptAccession("Library Source Accession", 1, list, Field.library_source_accession));
return laneInfo;
}
private KeyVal[] getKeyVals(List list) {
if (list == null || list.size() <= 0) return null;
KeyVal[] libs = new KeyVal[list.size()];
int i = 0;
for (Object o : list) {
if (o instanceof LibraryStrategy) {
LibraryStrategy l = (LibraryStrategy) o;
libs[i++] = new KeyVal(l.getLibraryStrategyId(), l.getName(), l.getDescription());
} else if (o instanceof LibrarySelection) {
LibrarySelection l = (LibrarySelection) o;
libs[i++] = new KeyVal(l.getLibrarySelectionId(), l.getName(), l.getDescription());
} else if (o instanceof LibrarySource) {
LibrarySource l = (LibrarySource) o;
libs[i++] = new KeyVal(l.getLibrarySourceId(), l.getName(), l.getDescription());
} else if (o instanceof StudyType) {
StudyType l = (StudyType) o;
libs[i++] = new KeyVal(l.getStudyTypeId(), l.getName(), l.getDescription());
} else if (o instanceof Platform) {
Platform l = (Platform) o;
libs[i++] = new KeyVal(l.getPlatformId(), l.getName(), l.getDescription());
} else if (o instanceof Organism) {
Organism l = (Organism) o;
libs[i++] = new KeyVal(l.getOrganismId(), l.getName(), String.valueOf(l.getNcbiTaxId()));
} else {
Log.error("The type of list was not recognized. Contact your local SeqWare developer.");
}
}
return libs;
}
private class KeyVal {
protected String key;
protected String value;
protected int id;
public KeyVal(int id, String key, String value) {
this.key = key;
this.value = value;
}
@Override
public String toString() {
return key + "\t" + value;
}
}
/**
* Generates a sample info object given the fields, and prompts for null fields if the interactive flag is on. The individualNumber and
* projectCode are required. Everything else can be null or less than 0.
*
* @param prettyName
* @param projectCode
* @param individualNumber
* @param librarySourceTemplateType
* @param tissueOrigin
* @param tissueType
* @param libraryType
* @param librarySizeCode
* @param barcode
* @param organismId
* @param targetedResequencing
* @param tissuePreparation
* @param iusDescription
* @param iusName
* @return
* @throws Exception
*/
protected SampleInfo generateSampleInfo(String prettyName, String projectCode, String individualNumber,
String librarySourceTemplateType, String tissueOrigin, String tissueType, String libraryType, String librarySizeCode,
String barcode, int organismId, String targetedResequencing, String tissuePreparation, String sampleDescription,
String iusName, String iusDescription) throws Exception {
// Sample
if (individualNumber == null || individualNumber.isEmpty() || projectCode == null || projectCode.isEmpty()) {
throw new Exception("Every sample needs a project code and individual number: You gave me " + projectCode + " and "
+ individualNumber);
}
SampleInfo sa = new SampleInfo();
sa.setIndividualNumber(individualNumber);
sa.setProjectCode(projectCode);
if (libraryType == null || libraryType.isEmpty()) {
libraryType = promptString(prettyName, "Library Type", libraryTypeList, this.lity, Field.library_type);
this.lity = libraryType;
}
sa.setLibraryType(libraryType);
if (librarySourceTemplateType == null || librarySourceTemplateType.isEmpty()) {
librarySourceTemplateType = promptString(prettyName, "Library Source Template Type", librarySourceTemplateTypeList,
this.lstety, Field.library_source_template_type);
this.lstety = librarySourceTemplateType;
}
sa.setLibrarySourceTemplateType(librarySourceTemplateType);
if (targetedResequencing == null || targetedResequencing.isEmpty()) {
targetedResequencing = promptString(prettyName, "Targeted Resequencing Type", targetedResequencingList, this.tare,
Field.targeted_resequencing);
this.tare = targetedResequencing;
}
sa.setTargetedResequencing(targetedResequencing);
if (tissueOrigin == null || tissueOrigin.isEmpty()) {
tissueOrigin = promptString(prettyName, "Tissue Origin", tissueOriginList, this.tior, Field.tissue_origin);
if (tissueOrigin == null || tissueOrigin.trim().isEmpty()) {
tissueOrigin = "nn";
} else {
this.tior = tissueOrigin;
}
}
sa.setTissueOrigin(tissueOrigin);
if (tissuePreparation == null || tissuePreparation.isEmpty()) {
tissuePreparation = promptString(prettyName, "Tissue Preparation", tissuePreparationList, this.tipr, Field.tissue_preparation);
this.tipr = tissuePreparation;
}
sa.setTissuePreparation(tissuePreparation);
if (tissueType == null || tissueType.isEmpty()) {
tissueType = promptString(prettyName, "Tissue Type", tissueTypeList, this.tity, Field.tissue_type);
if (tissueType == null || tissueType.trim().isEmpty()) {
tissueType = "n";
} else {
this.tity = tissueType;
}
}
sa.setTissueType(tissueType);
if (librarySizeCode == null || librarySizeCode.isEmpty() || !StringUtils.isNumeric(librarySizeCode)) {
Integer libSize = promptInteger(
"Library Size Code - a number code indicating the size of the band cut from the gel in base pairs", this.lSize,
Field.library_size_code);
if (libSize <= 0) {
librarySizeCode = "nn";
} else {
this.lSize = libSize;
librarySizeCode = libSize.toString();
}
}
sa.setLibrarySizeCode(librarySizeCode);
StringBuilder name = new StringBuilder();
name.append(projectCode).append("_").append(individualNumber);
name.append("_").append(tissueOrigin).append("_").append(tissueType).append("_").append(libraryType).append("_");
name.append(librarySizeCode).append("_").append(librarySourceTemplateType);
sa.setName(name.toString());
if (sampleDescription == null) {
if (interactive) {
sampleDescription = promptString("Optional: Sample Description", name.toString(), null);
} else {
sampleDescription = name.toString();
}
}
sa.setSampleDescription(sampleDescription);
if (organismId <= 0) {
List<Organism> organisms = new ArrayList<>(metadata.getOrganisms());
for (int i = 0; i < organisms.size(); i++) {
Log.stdout((i + 1) + " : " + organisms.get(i).getName());
}
organismId = promptPositiveInteger("Organism id", 34, Field.organism_id, 1, organisms.size());
if (organismId > 0 && organismId <= organisms.size()) {
organismId = organisms.get(organismId - 1).getOrganismId();
}
}
sa.setOrganismId(organismId);
// IUS
if (barcode == null || barcode.isEmpty()) {
barcode = promptString("Barcode", "NoIndex", Field.barcode);
}
sa.setBarcode(barcode);
if (iusName == null) {
if (interactive) {
iusName = promptString("Optional: Barcode name", barcode, null);
} else {
iusName = barcode;
}
}
sa.setIusName(iusName);
if (iusDescription == null) {
if (interactive) {
iusDescription = promptString("Optional: Barcode description", barcode, null);
} else {
iusDescription = barcode;
}
}
sa.setIusDescription(iusDescription);
sa.setIusSkip(false);
return sa;
}
protected int promptInteger(String description, int deflt, Field fieldName) throws OptionException {
Log.debug("checking for field '" + description + "'");
String d = extractDefault(fieldName, String.valueOf(deflt));
if (StringUtils.isNumeric(d)) {
deflt = Integer.parseInt(d);
}
// not using interactive input
if (!interactive) {
return Integer.parseInt(returnDefault((deflt > 0), String.valueOf(deflt), description, fieldName));
} // interactively work with the user to determine the choice
else {
Integer i = ConsoleAdapter.getInstance().promptInteger(description, deflt);
if (fieldName != null) {
defaults.put(fieldName.toString(), i.toString());
}
return i;
}
}
protected int promptAccession(String description, int deflt, KeyVal[] values, Field fieldName) throws OptionException {
Log.debug("checking for accession '" + description + "'");
String d = extractDefault(fieldName, String.valueOf(deflt));
if (StringUtils.isNumeric(d)) {
deflt = Integer.parseInt(d);
}
// not using interactive input
if (!interactive) {
return Integer.parseInt(returnDefault((deflt > 0), String.valueOf(deflt), description, fieldName));
} // interactively work with the user to determine the choice
else {
for (int i = 1; i <= values.length; i++) {
Log.stdout(i + " : " + values[i - 1].toString());
}
Integer i = promptPositiveInteger(description, deflt, fieldName, 1, values.length);
if (fieldName != null) {
defaults.put(fieldName.toString(), i.toString());
}
return i;
}
}
protected String promptString(String description, String deflt, Field fieldName) throws OptionException {
Log.debug("checking for field '" + description + "'");
deflt = extractDefault(fieldName, deflt);
// not using interactive input
if (!interactive) {
return returnDefault((deflt != null && !deflt.trim().isEmpty()), deflt, description, fieldName);
} // interactively work with the user to determine the choice
else {
String s = ConsoleAdapter.getInstance().promptString(description, deflt);
if (fieldName != null) {
defaults.put(fieldName.toString(), s);
}
return s;
}
}
/**
* Determine a value for a field 'title' of sample 'sampleName'. This method has different functionality depending on whether the Field
* is set (can be null), or the 'interactive' option is on.
*
* @param sampleName
* the sample name used for prompting
* @param title
* the name of the field being set
* @param choices
* the list of choices (Strings) that the user can select from in interactive mode
* @param deflt
* the default string if everything else fails
* @param fieldName
* the Field that is used for command-line defaults.
* @return the choice for the field, or an OptionException if other methods fail. This method can return null.
*/
protected String promptString(String sampleName, String title, String[] choices, String deflt, Field fieldName) {
Log.debug("checking for field '" + sampleName + "'");
deflt = extractDefault(fieldName, deflt);
// not using interactive input
if (!interactive) {
return returnDefault(((deflt != null && !deflt.trim().isEmpty())), deflt, title, fieldName);
} else {
String s = choiceOf(sampleName, title, choices, deflt);
if (fieldName != null) {
defaults.put(fieldName.toString(), s);
}
return s;
}
}
private String extractDefault(Field fieldName, String deflt) {
// choose the default from a previous prompt first
// then the command line option if it exists
// otherwise fall back on the given default
if (fieldName != null) {
String d = defaults.get(fieldName.toString());
if (d != null && !d.trim().isEmpty()) {
deflt = d;
} else {
String field = fields.get(fieldName.toString());
if (field != null && !field.trim().isEmpty()) {
deflt = field;
}
}
}
return deflt;
}
private String returnDefault(boolean useDefault, String deflt, String title, Field fieldName) throws OptionException {
if (useDefault) {
return deflt;
} else {
Exception e = new Exception("A value must be provided for " + title + ", using --field "
+ (fieldName == null ? "No field known" : fieldName.toString()));
throw new OptionException(fields.keySet(), e) {
};
}
}
protected int promptPositiveInteger(String description, int deflt, Field fieldName, int lowNum, int highNum) {
int value = -1;
while ((value > highNum || value < lowNum) && value != 0) {
value = promptInteger(description, deflt, fieldName);
}
return value;
}
protected void printSampleInfo(SampleInfo info, Appendable writer) {
try {
info.print(writer, metadata);
} catch (IOException ex) {
Log.warn("IO error when printing SampleInfo information! This should not happen!", ex);
}
}
protected void printRunInfo(RunInfo info, Appendable writer) {
try {
info.print(writer, metadata);
} catch (IOException ex) {
Log.warn("IO error when printing RunInfo information! This should not happen!", ex);
}
}
protected void printLaneInfo(LaneInfo info, Appendable writer) {
try {
info.print(writer, metadata);
} catch (IOException ex) {
Log.warn("IO error when printing LaneInfo information! This should not happen!", ex);
}
}
}