Examples of org.openbel.framework.common.index.Index

Package org.openbel.framework.common.index

Examples of org.openbel.framework.common.index.Index

org.openbel.framework.common.index.Index
Index encapsulates the information in a Resource Index file. @author Anthony Bargnesi <abargnesi@selventa.com>

                indexFile = resolvedResource.getCacheResourceCopy();
            }


            final ResourceIndex ri = ResourceIndex.INSTANCE;
            ri.loadIndex(indexFile);
            final Index index = ri.getIndex();




            final List<ResourceLocation> nsr = index.getNamespaceResources();
            final Map<String, NamespaceHeader> hvals;
            if (hasItems(nsr)) {
                hvals = new LinkedHashMap<String, NamespaceHeader>(index
                        .getNamespaceResources().size());
                for (ResourceLocation rl : index.getNamespaceResources()) {
                    String loc = rl.getResourceLocation();
                    ResolvedResource nsResource = c.resolveResource(
                            ResourceType.NAMESPACES, loc);
                    NamespaceHeader header = p.parseNamespace(loc,
                            nsResource.getCacheResourceCopy());

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            reportable.error("Unable to load index");
            reportable.error("Reason: " + e.getMessage());
            bail(GENERAL_FAILURE);
        }


        Index index = ResourceIndex.INSTANCE.getIndex();
        cacheMgrService.updateResourceIndexInCache(index);
    }

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        beginStage(PHASE3_STAGE1_HDR, "1", NUM_PHASES);


        final StringBuilder bldr = new StringBuilder();


        // Load the pfam resource from the resource index.
        Index resourceIndex = ResourceIndex.INSTANCE.getIndex();
        ResourceLocation pfResource = resourceIndex.getProteinFamilyResource();


        if (pfResource == null || pfResource.getResourceLocation() == null) {
            getPhaseConfiguration().setInjectProteinFamilies(false);
            stageError("Resource location for protein family is not set in " +
                    "resource index, disabling protein family expansion.");

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        beginStage(PHASE3_STAGE2_HDR, "2", NUM_PHASES);


        final StringBuilder bldr = new StringBuilder();


        // Load the named complexes resource from the resource index.
        Index resourceIndex = ResourceIndex.INSTANCE.getIndex();
        ResourceLocation ncResource = resourceIndex.getNamedComplexesResource();


        if (ncResource == null || ncResource.getResourceLocation() == null) {
            getPhaseConfiguration().setInjectNamedComplexes(false);
            stageError("Resource location for named complexes is not set " +
                    "in resource index, disabling named complex expansion.");

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        beginStage(PHASE3_STAGE3_HDR, "3", NUM_PHASES);


        final StringBuilder bldr = new StringBuilder();


        // Load the gene scaffolding resource from the resource index.
        Index resourceIndex = ResourceIndex.INSTANCE.getIndex();
        ResourceLocation gsResource =
                resourceIndex.getGeneScaffoldingResource();


        if (gsResource == null || gsResource.getResourceLocation() == null) {
            getPhaseConfiguration().setInjectGeneScaffolding(false);
            bldr.append("Resource location for gene scaffolding is not set ");
            bldr.append("in resource index, disabling gene scaffolding ");

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        }


        // create output directory for orthologized proto network
        artifactPath = createDirectoryArtifact(outputDirectory, DIR_ARTIFACT);


        final Index index = ResourceIndex.INSTANCE.getIndex();
        final Set<ResourceLocation> resources = index.getOrthologyResources();
        if (noItems(resources)) {
            final StringBuilder bldr = new StringBuilder();
            bldr.append("No orthology documents included.");
            markEndStage(bldr);
            stageOutput(bldr.toString());

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        return pn;
    }


    private void runPhaseThree(final ProtoNetwork orthoPn)
            throws ProtoNetworkError {
        final Index resourceIndex = ResourceIndex.INSTANCE.getIndex();
        final ResourceLocation pfResource = resourceIndex
                .getProteinFamilyResource();


        final Document pfdoc = readResource(pfResource);
        p3.pruneFamilies(false, pfdoc, orthoPn);
        p3.inferFamilies(pfdoc, orthoPn);
        final ProtoNetwork pfpn = p3.compile(pfdoc);
        p3.merge(orthoPn, pfpn);


        final ResourceLocation ncResource = resourceIndex
                .getNamedComplexesResource();
        final Document ncdoc = readResource(ncResource);
        p3.pruneComplexes(false, ncdoc, orthoPn);
        final ProtoNetwork ncpn = p3.compile(ncdoc);
        p3.merge(orthoPn, ncpn);


        final ResourceLocation gsResource = resourceIndex
                .getGeneScaffoldingResource();
        final Document gsdoc = readResource(gsResource);
        p3.pruneGene(gsdoc, orthoPn);
        final ProtoNetwork gspn = p3.compile(gsdoc);
        p3.merge(orthoPn, gspn);

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            throws EquivalenceMapResolutionFailure {


        Set<EquivalenceDataIndex> equivalenceDataIndexSet =
                new HashSet<EquivalenceDataIndex>();


        Index resourceIndex = ResourceIndex.INSTANCE.getIndex();


        if (hasItems(resourceIndex.getEquivalenceResources())) {
            for (Equivalence eqResource : resourceIndex
                    .getEquivalenceResources()) {
                String eqLocation = eqResource.getResourceLocation();
                try {
                    ResolvedResource resolved = cache.resolveResource(
                            ResourceType.EQUIVALENCES,

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Related Classes of org.openbel.framework.common.index.Index

org.openbel.framework.api.Namespaces

org.openbel.framework.compiler.PhaseTwoImpl

org.openbel.framework.tools.CacheManager

org.openbel.framework.tools.PhaseThreeApplication

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