List of usage examples for org.apache.commons.collections15 OrderedMap get
V get(Object key);
From source file:org.isatools.isacreator.gui.DataEntryForm.java
/** * Adds the fields describing a section to a Container (e.g. JPanel, Box, etc.) * * @param containerToAddTo @see JPanel, @see Box, @see Container * @param sectionToAddTo - @see InvestigationFileSection as a reference for where the fields are being added * @param fieldValues - Map of field name to values. * @param referenceObject - A @see DataEntryReferenceObject which gives information about *///from w ww .j a v a 2s. c o m public void addFieldsToPanel(Container containerToAddTo, InvestigationFileSection sectionToAddTo, OrderedMap<String, String> fieldValues, DataEntryReferenceObject referenceObject) { if (fieldDefinitions == null) { fieldDefinitions = new ListOrderedMap<String, JComponent>(); } Set<String> ontologyFields = referenceObject.getOntologyTerms(sectionToAddTo); Set<String> fieldsToIgnore = referenceObject.getFieldsToIgnore(); for (String fieldName : fieldValues.keySet()) { if (!fieldsToIgnore.contains(fieldName)) { FieldObject fieldDescriptor = referenceObject.getFieldDefinition(fieldName); if (!fieldDescriptor.isHidden()) { String tmpFieldName = fieldName; if (realNamesToAliases.containsKey(fieldName)) { tmpFieldName = realNamesToAliases.get(fieldName); } JPanel fieldPanel = createFieldPanel(1, 2); JLabel fieldLabel = createLabel(tmpFieldName); JComponent textComponent; if (fieldDescriptor.getDatatype() == DataTypes.STRING || fieldDescriptor.getDatatype() == DataTypes.ONTOLOGY_TERM || fieldDescriptor.getDatatype() == DataTypes.DATE) { textComponent = new RoundedJTextField(10); } else if (fieldDescriptor.getDatatype() == DataTypes.LONG_STRING) { textComponent = new JTextArea(); ((JTextArea) textComponent).setSelectionColor(UIHelper.LIGHT_GREEN_COLOR); ((JTextArea) textComponent).setSelectedTextColor(UIHelper.BG_COLOR); ((JTextArea) textComponent).setWrapStyleWord(true); ((JTextArea) textComponent).setLineWrap(true); textComponent.setBackground(UIHelper.BG_COLOR); textComponent.setBorder(UIHelper.GREEN_ROUNDED_BORDER); } else if (fieldDescriptor.getDatatype() == DataTypes.LIST) { textComponent = new JComboBox(fieldDescriptor.getFieldList()); } else { textComponent = new RoundedJTextField(10); } if (textComponent instanceof JTextArea || textComponent instanceof JTextComponent) { ((JTextComponent) textComponent) .setText(fieldValues.get(fieldName).equals("") ? fieldDescriptor.getDefaultVal() : fieldValues.get(fieldName)); } textComponent.setToolTipText(fieldDescriptor.getDescription()); UIHelper.renderComponent(textComponent, UIHelper.VER_11_PLAIN, UIHelper.DARK_GREEN_COLOR, false); fieldPanel.add(fieldLabel); if (textComponent instanceof JTextArea) { JScrollPane invDescScroll = new JScrollPane(textComponent, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); invDescScroll.setPreferredSize(new Dimension(200, 75)); invDescScroll.getViewport().setBackground(UIHelper.BG_COLOR); ((JTextArea) textComponent).getDocument().addDocumentListener(new DocumentChangeListener()); IAppWidgetFactory.makeIAppScrollPane(invDescScroll); fieldPanel.add( UIHelper.createTextEditEnableJTextArea(invDescScroll, (JTextArea) textComponent)); } else if (textComponent instanceof JTextComponent) { if (fieldDescriptor.getDatatype() == DataTypes.ONTOLOGY_TERM || ontologyFields.contains(fieldName)) { fieldPanel.add(createOntologyDropDown(fieldName, (JTextComponent) textComponent, true, false, fieldDescriptor.getRecommmendedOntologySource())); } else if (fieldDescriptor.getDatatype() == DataTypes.DATE) { fieldPanel.add(createDateDropDown((JTextComponent) textComponent)); } else if (fieldDescriptor.isAcceptsFileLocations()) { fieldPanel.add(createFileField((JTextComponent) textComponent)); } else { fieldPanel.add(textComponent); } ((JTextComponent) textComponent).getDocument() .addDocumentListener(new DocumentChangeListener()); } else { fieldPanel.add(textComponent); } fieldDefinitions.put(tmpFieldName, textComponent); containerToAddTo.add(fieldPanel); containerToAddTo.add(Box.createVerticalStrut(5)); } } } }
From source file:org.isatools.isacreator.io.importisa.InvestigationImport.java
/** * imports the Investigation file into a Map data structure. * * @param investigationFile- File object representing Investigation file to be loaded. * @return Map is formatted like so:/*ww w. java 2s . c o m*/ * (Main section name) e.g. Investigation-1 * -> Section name e.g. InvestigationFileSection e.g. InvestigationFileSection.ONTOLOGY_SECTION * -> Label for the ontology section e.g. Term Source Name * -> Values for the given section/label e.g. OBI * EFO * etc */ public Pair<Boolean, OrderedMap<String, OrderedMap<InvestigationFileSection, OrderedMap<String, List<String>>>>> importInvestigationFile( File investigationFile) throws IOException { OrderedMap<String, OrderedMap<InvestigationFileSection, OrderedMap<String, List<String>>>> importedInvestigationFile = new ListOrderedMap<String, OrderedMap<InvestigationFileSection, OrderedMap<String, List<String>>>>(); List<String[]> investigationFileContents = loadFile(investigationFile); String currentMajorSection = "Investigation-1"; int studyCount = 1; importedInvestigationFile.put(currentMajorSection, new ListOrderedMap<InvestigationFileSection, OrderedMap<String, List<String>>>()); InvestigationFileSection currentMinorSection = null; for (String[] line : investigationFileContents) { InvestigationFileSection tmpSection; if ((tmpSection = InvestigationFileSection.convertToInstance(line[0])) != null) { currentMinorSection = tmpSection; if (currentMinorSection == InvestigationFileSection.STUDY_SECTION) { currentMajorSection = "Study-" + studyCount; studyCount++; importedInvestigationFile.put(currentMajorSection, new ListOrderedMap<InvestigationFileSection, OrderedMap<String, List<String>>>()); } importedInvestigationFile.get(currentMajorSection).put(currentMinorSection, new ListOrderedMap<String, List<String>>()); } else { String lineLabel = line[0].trim(); if (!StringUtils.isEmpty(lineLabel)) { String valueToTitleCase = lineLabel; if (lineLabel.contains("Comment")) valueToTitleCase = StringProcessing.removeSpaceFromQualifiedField( StringProcessing.convertStringToTitleCase(lineLabel)); //System.out.println(valueToTitleCase); if (!importedInvestigationFile.get(currentMajorSection).get(currentMinorSection) .containsKey(valueToTitleCase)) { importedInvestigationFile.get(currentMajorSection).get(currentMinorSection) .put(valueToTitleCase, new ArrayList<String>()); } if (line.length > 1) { for (int index = 1; index < line.length; index++) { importedInvestigationFile.get(currentMajorSection).get(currentMinorSection) .get(valueToTitleCase).add(line[index]); } } } } } return new Pair<Boolean, OrderedMap<String, OrderedMap<InvestigationFileSection, OrderedMap<String, List<String>>>>>( isValidInvestigationSections(importedInvestigationFile), importedInvestigationFile); }
From source file:org.isatools.isacreator.io.importisa.InvestigationImport.java
/** * Checks to make sure all required Investigation file sections have been entered * * @param investigationFile - Map containing investigation file structure * @return - true if valid, false otherwise. *///from w ww . ja v a2s. co m private boolean isValidInvestigationSections( OrderedMap<String, OrderedMap<InvestigationFileSection, OrderedMap<String, List<String>>>> investigationFile) { InvestigationStructureLoader loader = new InvestigationStructureLoader(); Map<InvestigationFileSection, InvestigationSection> sections = loader.loadInvestigationStructure(); MessageFormat fmt = new MessageFormat( "The field {0} is missing from the {1} section of the investigation file"); for (String mainSection : investigationFile.keySet()) { // checking major section, e.g. study or investigation Set<InvestigationFileSection> majorSectionParts = new HashSet<InvestigationFileSection>(); for (InvestigationFileSection section : investigationFile.get(mainSection).keySet()) { majorSectionParts.add(section); Set<String> minorSectionParts = new HashSet<String>(); // we also want to check if the salient information for each minor section is in place. for (String sectionLabelsAndValues : investigationFile.get(mainSection).get(section).keySet()) { minorSectionParts.add(sectionLabelsAndValues.toLowerCase()); } SetUtils<String> setUtils = new SetUtils<String>(); Set<String> requiredValuesAsLowercase = setUtils .getLowerCaseSetContents(sections.get(section).getRequiredValues()); Pair<Boolean, Set<String>> equalityResult = setUtils.compareSets(minorSectionParts, requiredValuesAsLowercase, false); if (!equalityResult.fst) { for (String sectionValue : equalityResult.snd) { messages.add(new ErrorMessage(ErrorLevel.ERROR, fmt.format(new Object[] { sectionValue, section }))); } } // check minor section for salient information } // check major section for salient information // the mainsection string is investigation-1 or study-2 - here we strip away from - onwards. Set<InvestigationFileSection> requiredSections = loader .getRequiredSections(mainSection.substring(0, mainSection.lastIndexOf("-"))); SetUtils<InvestigationFileSection> setUtils = new SetUtils<InvestigationFileSection>(); Pair<Boolean, Set<InvestigationFileSection>> equalityResult = setUtils.compareSets(majorSectionParts, requiredSections, true); // if false, if (!equalityResult.fst) { if (equalityResult.snd != null) { for (InvestigationFileSection section : equalityResult.snd) { messages.add(new ErrorMessage(ErrorLevel.ERROR, fmt.format( new Object[] { section, mainSection.substring(0, mainSection.lastIndexOf("-")) }))); } } else { messages.add(new ErrorMessage(ErrorLevel.ERROR, "Incorrect number of sections defined for " + mainSection.substring(0, mainSection.lastIndexOf("-")))); } } } // if the message size is 0, there are no errors... return messages.size() == 0; }
From source file:org.isatools.isacreator.io.importisa.StructureToInvestigationMapper.java
public Pair<Boolean, Investigation> createInvestigationFromDataStructure( OrderedMap<String, OrderedMap<InvestigationFileSection, OrderedMap<String, List<String>>>> investigationStructure) { Investigation investigation = null;//from www . j a v a 2 s . c om List<Study> studies = new ArrayList<Study>(); for (String majorSection : investigationStructure.keySet()) { if (majorSection.contains("Investigation")) { investigation = processInvestigation(investigationStructure.get(majorSection)); System.out.println(investigation.getInvestigationTitle()); } if (majorSection.contains("Study")) { Study newStudy = processStudy(investigationStructure.get(majorSection)); studies.add(newStudy); } } if (investigation != null) { for (Study study : studies) { investigation.addStudy(study); } } return new Pair<Boolean, Investigation>(validateInvestigationFile(investigation), investigation); }
From source file:org.isatools.isacreator.io.importisa.StructureToInvestigationMapper.java
private Investigation processInvestigation( OrderedMap<InvestigationFileSection, OrderedMap<String, List<String>>> investigationSections) { Set<OntologySourceRefObject> ontologySources = new HashSet<OntologySourceRefObject>(); List<Contact> contacts = new ArrayList<Contact>(); List<Publication> publications = new ArrayList<Publication>(); Investigation tmpInvestigation = null; OrderedMap<InvestigationFileSection, Set<String>> sectionFields = new ListOrderedMap<InvestigationFileSection, Set<String>>(); for (InvestigationFileSection investigationSection : investigationSections.keySet()) { if (investigationSection == InvestigationFileSection.INVESTIGATION_SECTION) { Pair<Set<String>, Investigation> processedInvestigationSection = processInvestigationSection( investigationSections.get(investigationSection)); sectionFields.put(investigationSection, processedInvestigationSection.fst); tmpInvestigation = processedInvestigationSection.snd; } else if (investigationSection == InvestigationFileSection.ONTOLOGY_SECTION) { Pair<Set<String>, List<OntologySourceRefObject>> processedOntologySection = processOntologySourceReferences( investigationSections.get(investigationSection)); sectionFields.put(investigationSection, processedOntologySection.fst); ontologySources = new HashSet<OntologySourceRefObject>(processedOntologySection.snd); } else if (investigationSection == InvestigationFileSection.INVESTIGATION_PUBLICATIONS_SECTION) { Pair<Set<String>, List<Publication>> processedPublicationSection = processPublication( investigationSection, investigationSections.get(investigationSection)); sectionFields.put(investigationSection, processedPublicationSection.fst); publications = processedPublicationSection.snd; } else if (investigationSection == InvestigationFileSection.INVESTIGATION_CONTACTS_SECTION) { Pair<Set<String>, List<Contact>> processedContactSection = processContacts(investigationSection, investigationSections.get(investigationSection)); sectionFields.put(investigationSection, processedContactSection.fst); contacts = processedContactSection.snd; }//from w w w.j a v a 2 s . c o m } if (tmpInvestigation != null) { OntologyManager.setOntologySources(ontologySources); tmpInvestigation.addToPublications(publications); tmpInvestigation.addToContacts(contacts); tmpInvestigation.addToReferenceObject(sectionFields); } return tmpInvestigation; }
From source file:org.isatools.isacreator.io.importisa.StructureToInvestigationMapper.java
private Study processStudy( OrderedMap<InvestigationFileSection, OrderedMap<String, List<String>>> studySections) { Study study = null;/* w w w .j a v a 2 s .co m*/ List<Protocol> protocols = new ArrayList<Protocol>(); List<Factor> factors = new ArrayList<Factor>(); List<Contact> contacts = new ArrayList<Contact>(); List<Publication> publications = new ArrayList<Publication>(); List<Assay> assays = new ArrayList<Assay>(); List<StudyDesign> studyDesigns = new ArrayList<StudyDesign>(); OrderedMap<InvestigationFileSection, Set<String>> sectionFields = new ListOrderedMap<InvestigationFileSection, Set<String>>(); for (InvestigationFileSection studySection : studySections.keySet()) { if (studySection == InvestigationFileSection.STUDY_SECTION) { Pair<Set<String>, Study> processedStudySection = processStudySection( studySections.get(studySection)); study = processedStudySection.snd; sectionFields.put(studySection, processedStudySection.fst); } else if (studySection == InvestigationFileSection.STUDY_FACTORS) { Pair<Set<String>, List<Factor>> processedFactorsSection = processFactors( studySections.get(studySection)); sectionFields.put(studySection, processedFactorsSection.fst); factors = processedFactorsSection.snd; } else if (studySection == InvestigationFileSection.STUDY_DESIGN_SECTION) { Pair<Set<String>, List<StudyDesign>> processedStudyDesignSection = processStudyDesigns( studySections.get(studySection)); sectionFields.put(studySection, processedStudyDesignSection.fst); studyDesigns = processedStudyDesignSection.snd; } else if (studySection == InvestigationFileSection.STUDY_ASSAYS) { Pair<Set<String>, List<Assay>> processedAssaySection = processAssay( studySections.get(studySection)); sectionFields.put(studySection, processedAssaySection.fst); assays = processedAssaySection.snd; } else if (studySection == InvestigationFileSection.STUDY_PUBLICATIONS) { Pair<Set<String>, List<Publication>> processedPublicationSection = processPublication(studySection, studySections.get(studySection)); sectionFields.put(studySection, processedPublicationSection.fst); publications = processedPublicationSection.snd; } else if (studySection == InvestigationFileSection.STUDY_PROTOCOLS) { Pair<Set<String>, List<Protocol>> processedProtocolSection = processProtocol( studySections.get(studySection)); sectionFields.put(studySection, processedProtocolSection.fst); protocols = processedProtocolSection.snd; } else if (studySection == InvestigationFileSection.STUDY_CONTACTS) { Pair<Set<String>, List<Contact>> processedContactSection = processContacts(studySection, studySections.get(studySection)); sectionFields.put(studySection, processedContactSection.fst); contacts = processedContactSection.snd; } } if (study != null) { study.addToAssays(assays); study.setProtocols(protocols); study.setContacts(contacts); study.setStudyDesigns(studyDesigns); study.setFactors(factors); study.setPublications(publications); // we want to add new fields, but want to keep the general working of the configuration. So we do just that. // new fields (unknown) will be treated as Strings, other known values will acquire the properties // specified of them in the configuration XML. study.addToReferenceObject(sectionFields); } return study; }
From source file:org.isatools.isacreator.io.importisa.StructureToInvestigationMapper.java
private int getLoopCount(OrderedMap<String, List<String>> assayStructure) { return assayStructure.get(assayStructure.firstKey()).size(); }
From source file:org.isatools.isacreator.model.ISASection.java
public void addToReferenceObject(OrderedMap<InvestigationFileSection, Set<String>> sectionFields) { for (InvestigationFileSection section : sectionFields.keySet()) { if (!referenceObject.getSectionDefinition().containsKey(section)) { referenceObject.getSectionDefinition().put(section, new ListOrderedSet<String>()); }//w ww .j av a 2 s.c o m referenceObject.getSectionDefinition().get(section).addAll(sectionFields.get(section)); } }