Examples of au.csiro.ontology.input.RF2Input

au.csiro.ontology.input.RF2Input
An RF set of input files. @author Alejandro Metke

        // for this import entry
        Map<String, RelationshipRow> relationshipMap = new HashMap<String, RelationshipRow>();


        Map<String, RefsetRow> cdMap = new HashMap<String, RefsetRow>();


        RF2Input input = (RF2Input) entry.getInput();


        InputType inputType = input.getInputType();
        Set<String> conceptsFiles = input.getConceptsFiles();
        log.info("Read concepts info");
        for(String conceptsFile : conceptsFiles) {
            final String message = "Unable to load concepts file. " +
                    "Please check your input configuration file. " +
                    "(input type = "+inputType+", file="+conceptsFile+")";
            try {
                loadConceptRows(modMap, conceptMap, input.getInputStream(conceptsFile));
            } catch (NullPointerException e) {
                log.error(message, e);
                throw new ImportException(message, e);
            } catch (IOException e) {
                log.error(message, e);
                throw new ImportException(message, e);
            }
        }


        // Load relationships
        Set<String> relationshipsFiles = input.getStatedRelationshipsFiles();
        if(relationshipsFiles == null || relationshipsFiles.isEmpty()) {
            log.info("Read inferred relationships info");
            relationshipsFiles = input.getRelationshipsFiles();
        } else {
            log.info("Read stated relationships info");
        }


        if(relationshipsFiles == null || relationshipsFiles.isEmpty()) {
            throw new ImportException("No relationships files was specified.");
        }


        for(String relationshipsFile : relationshipsFiles) {
            final String message = "Unable to load relationships file. Please check your input configuration " +
                    "file. (input type = " + inputType+", file=" + relationshipsFile+")";
            try {
                loadRelationshipRows(modMap, relationshipMap, input.getInputStream(relationshipsFile));
            } catch (NullPointerException e) {
                log.error(message, e);
                throw new ImportException(message, e);
            } catch (IOException e) {
                log.error(message, e);
                throw new ImportException(message, e);
            }


            // Load concrete domains refsets
            log.info("Read concrete domains reference set info");
            for (String filename : input.getConcreteDomainRefsetFiles()) {
                try {
                    loadReferenceSet(input, filename, modMap, cdMap, IRefsetFactory.CD);
                } catch (ArrayIndexOutOfBoundsException e) {
                    final String msg = "Error loading concrete domains reference set: " + filename +
                            ". Possibly has wrong number of columns.";

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        private final Queue<ImportEntry> entries = new LinkedList<ImportEntry>();
        @SuppressWarnings("unused")
        private final IProgressMonitor monitor;


        private void processNext() throws ImportException {
            RF2Input in = inputs.remove();


            // 1. Load module dependencies
            log.info("Loading module dependencies");
            IModuleDependencyRefset mdr = loadModuleDependencies(in);

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        // for this import entry
        Map<String, RelationshipRow> relationshipMap = new HashMap<String, RelationshipRow>();


        Map<String, RefsetRow> cdMap = new HashMap<String, RefsetRow>();


        RF2Input input = (RF2Input) entry.getInput();


        InputType inputType = input.getInputType();
        Set<String> conceptsFiles = input.getConceptsFiles();
        log.info("Reading concepts info: " + conceptsFiles.size());
        for(String conceptsFile : conceptsFiles) {
            final String message = "Unable to load concepts file. " +
                    "Please check your input configuration file. " +
                    "(input type = "+inputType+", file="+conceptsFile+")";
            try {
                loadConceptRows(modMap, conceptMap, input.getInputStream(conceptsFile));
            } catch (NullPointerException e) {
                log.error(message, e);
                throw new ImportException(message, e);
            } catch (IOException e) {
                log.error(message, e);
                throw new ImportException(message, e);
            }
        }


        // Load relationships
        Set<String> relationshipsFiles = input.getStatedRelationshipsFiles();
        if(relationshipsFiles == null || relationshipsFiles.isEmpty()) {
            relationshipsFiles = input.getRelationshipsFiles();
            log.info("Reading inferred relationships info: " + relationshipsFiles.size());
        } else {
            log.info("Reading stated relationships info: " + relationshipsFiles.size());
        }


        if(relationshipsFiles == null || relationshipsFiles.isEmpty()) {
            throw new ImportException("No relationships files was specified.");
        }


        for(String relationshipsFile : relationshipsFiles) {
            final String message = "Unable to load relationships file. Please check your input configuration " +
                    "file. (input type = " + inputType+", file=" + relationshipsFile+")";
            try {
                loadRelationshipRows(modMap, relationshipMap, input.getInputStream(relationshipsFile));
            } catch (NullPointerException e) {
                log.error(message, e);
                throw new ImportException(message, e);
            } catch (IOException e) {
                log.error(message, e);
                throw new ImportException(message, e);
            }


            // Load concrete domains refsets
            final Set<String> concreteDomainRefsetFiles = input.getConcreteDomainRefsetFiles();
            log.info("Reading concrete domains reference set info: " + concreteDomainRefsetFiles.size());
            for (String filename : concreteDomainRefsetFiles) {
                try {
                    loadReferenceSet(input, filename, modMap, cdMap, IRefsetFactory.CD);
                } catch (ArrayIndexOutOfBoundsException e) {

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        private final Queue<ImportEntry> entries = new LinkedList<ImportEntry>();
        @SuppressWarnings("unused")
        private final IProgressMonitor monitor;


        private void processNext() throws ImportException {
            RF2Input in = inputs.remove();


            // 1. Load module dependencies
            log.info("Loading module dependencies");
            IModuleDependencyRefset mdr = loadModuleDependencies(in);

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Related Classes of au.csiro.ontology.input.RF2Input

au.csiro.ontology.importer.rf2.RF2Importer

au.csiro.ontology.importer.rf2.RF2Importer$OntologyInterator

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