Examples with MiriamManager cbit.vcell.biomodel.meta.MiriamManager used on opensource projects

Example 11 with MiriamManager

use of cbit.vcell.biomodel.meta.MiriamManager in project vcell by virtualcell.

the class SpeciesPropertiesPanel method saveSelectedXRef.

public void saveSelectedXRef(final XRef selectedXRef, final MIRIAMQualifier miriamQualifier) {
    AsynchClientTask task1 = new AsynchClientTask("retrieving metadata", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            String urn = XRefToURN.createURN(selectedXRef.db(), selectedXRef.id());
            try {
                MiriamManager miriamManager = bioModel.getModel().getVcMetaData().getMiriamManager();
                MiriamResource resource = miriamManager.createMiriamResource(urn);
                String urnstr = resource.getMiriamURN();
                if (urnstr != null && urnstr.toLowerCase().contains("uniprot")) {
                    String prettyName = UniProtConstants.getNameFromID(urnstr);
                    if (prettyName != null) {
                        miriamManager.setPrettyName(resource, prettyName);
                    }
                }
                Set<MiriamResource> miriamResources = new HashSet<MiriamResource>();
                miriamResources.add(resource);
                miriamManager.addMiriamRefGroup(getSpeciesContext().getSpecies(), miriamQualifier, miriamResources);
                MiriamProviderServiceLocator providerLocator = new MiriamProviderServiceLocator();
                MiriamProvider provider = providerLocator.getMiriamWebServices();
                String pcLink = resource.getMiriamURN();
                if (pcLink != null && pcLink.length() > 0) {
                    String[] locations = provider.getLocations(pcLink);
                    if (locations != null) {
                        for (String url : locations) {
                            try {
                                miriamManager.addStoredCrossReferencedLink(resource, new URL(url));
                            } catch (MalformedURLException e) {
                                e.printStackTrace(System.out);
                            }
                        }
                    }
                }
            } catch (URNParseFailureException e) {
                e.printStackTrace();
                DialogUtils.showErrorDialog(SpeciesPropertiesPanel.this, e.getMessage());
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("displaying metadata", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            updatePCLink();
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 12 with MiriamManager

use of cbit.vcell.biomodel.meta.MiriamManager in project vcell by virtualcell.

the class AnnotationMapping method getRefInfo.

private HashMap<String, String> getRefInfo(BioModel bioModel, Identifiable identifiable) {
    HashMap<String, String> info = new HashMap<String, String>();
    VCMetaData vcMetaData = bioModel.getVCMetaData();
    MiriamManager miriamManager = vcMetaData.getMiriamManager();
    TreeMap<Identifiable, Map<MiriamRefGroup, MIRIAMQualifier>> miriamDescrHeir = miriamManager.getMiriamTreeMap();
    Map<MiriamRefGroup, MIRIAMQualifier> refGroupMap = miriamDescrHeir.get(identifiable);
    if (refGroupMap != null) {
        for (MiriamRefGroup refGroup : refGroupMap.keySet()) {
            MIRIAMQualifier qualifier = refGroupMap.get(refGroup);
            String[] quaTemp = qualifier.toString().split("/");
            String bioQualifier = quaTemp[quaTemp.length - 1];
            bioQualifier = bioQualifier.substring(0, bioQualifier.length() - 1);
            for (MiriamResource miriamResource : refGroup.getMiriamRefs()) {
                String refSource = miriamResource.getMiriamURN();
                String[] temp = refSource.split(":");
                String sourceInfo = temp[2] + ":" + bioQualifier;
                String refId = miriamResource.getIdentifier();
                info.put(refId, sourceInfo);
            // System.out.println(refId + "*********" + sourceInfo);
            }
        }
    }
    return info;
}

Example 13 with MiriamManager

use of cbit.vcell.biomodel.meta.MiriamManager in project vcell by virtualcell.

the class PathwayMapping method createMolecularTypeFromBioPaxObject.

// TODO: not in use
// public void createBioModelEntitiesFromBioPaxObjects(BioModel bioModel, Object[] selectedObjects) throws Exception
// {
// for(int i = 0; i < selectedObjects.length; i++) {
// if(selectedObjects[i] instanceof BioPaxObject) {
// BioPaxObject bioPaxObject = (BioPaxObject)selectedObjects[i];
// if(bioPaxObject instanceof PhysicalEntity && !(bioPaxObject instanceof Complex)) {
// createMolecularTypeFromBioPaxObject(bioModel, (PhysicalEntity)bioPaxObject);
// }
// } else if(selectedObjects[i] instanceof ConversionTableRow) {
// ConversionTableRow ctr = (ConversionTableRow)selectedObjects[i];
// if(ctr.getBioPaxObject() instanceof PhysicalEntity && !(ctr.getBioPaxObject() instanceof Complex)) {
// createMolecularTypeFromBioPaxObject(bioModel, (PhysicalEntity)ctr.getBioPaxObject());
// }
// }
// }
// 
// for(int i = 0; i < selectedObjects.length; i++) {
// if(selectedObjects[i] instanceof BioPaxObject) {
// BioPaxObject bioPaxObject = (BioPaxObject)selectedObjects[i];
// if(bioPaxObject instanceof PhysicalEntity) {
// createSpeciesContextFromBioPaxObject(bioModel, (PhysicalEntity)bioPaxObject);
// } else if(bioPaxObject instanceof Conversion) {
// createReactionStepsFromBioPaxObject(bioModel, (Conversion)bioPaxObject);
// }
// } else if(selectedObjects[i] instanceof ConversionTableRow) {
// ConversionTableRow ctr = (ConversionTableRow)selectedObjects[i];
// if(ctr.getBioPaxObject() instanceof PhysicalEntity) {
// createSpeciesContextFromTableRow(bioModel, (PhysicalEntity)ctr.getBioPaxObject(), ctr.stoich(), ctr.id(), ctr.location());
// } else if(ctr.getBioPaxObject() instanceof Conversion) {
// createReactionStepsFromTableRow(bioModel, (Conversion)ctr.getBioPaxObject(), ctr.stoich(), ctr.id(), ctr.location());
// }
// }
// }
// }
private MolecularType createMolecularTypeFromBioPaxObject(BioModel bioModel, PhysicalEntity bioPaxObject, boolean addSubunits) {
    String name;
    if (bioPaxObject.getName().size() == 0) {
        name = getSafetyName(bioPaxObject.getID());
    } else {
        name = getSafetyName(bioPaxObject.getName().get(0));
    }
    RbmModelContainer rbmmc = bioModel.getModel().getRbmModelContainer();
    if (rbmmc.getMolecularType(name) != null) {
        // already exists
        MolecularType mt = rbmmc.getMolecularType(name);
        // check whether it links to pathway object, create relationship object if not
        if (!bioModel.getRelationshipModel().isRelationship(mt, bioPaxObject)) {
            RelationshipObject ro = new RelationshipObject(mt, bioPaxObject);
            bioModel.getRelationshipModel().addRelationshipObject(ro);
        }
        return mt;
    }
    int numSubunits = 0;
    if (addSubunits) {
        for (String comment : bioPaxObject.getComments()) {
            numSubunits = StringUtils.countMatches(comment, "SUBUNIT:");
        }
    }
    MolecularType mt = new MolecularType(name, bioModel.getModel());
    try {
        for (int i = 0; i < numSubunits; i++) {
            MolecularComponent mc = new MolecularComponent("Subunit" + i);
            mt.addMolecularComponent(mc);
        }
        rbmmc.addMolecularType(mt, true);
        // we know for sure that a relationship can't exist, so we make one
        RelationshipObject ro = new RelationshipObject(mt, bioPaxObject);
        bioModel.getRelationshipModel().addRelationshipObject(ro);
    } catch (ModelException | PropertyVetoException e) {
        e.printStackTrace();
    }
    ArrayList<String> commentList = bioPaxObject.getComments();
    final String htmlStart = "<html><font face = \"Arial\"><font size =\"-2\">";
    final String htmlEnd = "</font></font></html>";
    if (commentList != null && !commentList.isEmpty()) {
        String comment = commentList.get(0);
        if (!comment.isEmpty()) {
            String text = FormatDetails(comment);
            mt.setComment(htmlStart + text + htmlEnd);
        }
    } else {
        mt.setComment("");
    }
    VCMetaData vcMetaData = bioModel.getVCMetaData();
    MiriamManager miriamManager = vcMetaData.getMiriamManager();
    MIRIAMQualifier qualifier = MIRIAMQualifier.MODEL_isDescribedBy;
    ArrayList<Xref> xrefList = bioPaxObject.getxRef();
    for (Xref xref : xrefList) {
        String url = xref.getURL();
        if (url == null || url.isEmpty()) {
            continue;
        }
        System.out.println(xref.getDb() + ": " + xref.getId());
        try {
            HashSet<MiriamResource> miriamResources = new HashSet<MiriamResource>();
            // http://www.ncbi.nlm.nih.gov/protein/NP_005429	unrecognized (not a valid DataType)
            // http://www.uniprot.org/uniprot/P17275			good
            // TODO: find a mechanism to store the unrecognized ones - they often do work
            MiriamResource mr = miriamManager.createMiriamResource(url);
            miriamResources.add(mr);
            miriamManager.addMiriamRefGroup(mt, qualifier, miriamResources);
        } catch (URNParseFailureException e) {
            e.printStackTrace();
        }
        System.out.println(xref.getDisplayName());
    }
    return mt;
}