Examples with Collection org.sbolstandard.core2.Collection used on opensource projects

Example 11 with Collection

use of org.sbolstandard.core2.Collection in project libSBOLj by SynBioDex.

the class SBOLReader method parseCollectionV1.

/**
 * @param SBOLDoc
 * @param topLevel
 * @return
 * @throws SBOLConversionException
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>if an SBOL validation rule violation occurred in any of the following constructors or methods:
 * 	<ul>
 * 		<li>{@link URIcompliance#createCompliantURI(String, String, String, String, boolean)},</li>
 * 		<li>{@link Collection#Collection(URI)},</li>
 * 		<li>{@link Collection#setVersion(String)},</li>
 * 		<li>{@link Collection#setWasDerivedFrom(URI)},</li>
 * 		<li>{@link Collection#setDisplayId(String)},</li>
 * 		<li>{@link Collection#setMembers(Set)},</li>
 * 		<li>{@link Identified#setAnnotations(List)}, or</li>
 * 		<li>{@link SBOLDocument#addCollection(Collection)}; or</li>
 * 	</ul>
 * </li>
 * <li>the following SBOL validation rule was violated: 10202.</li>
 * </ul>
 */
private static Collection parseCollectionV1(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) throws SBOLValidationException, SBOLConversionException {
    URI identity = topLevel.getIdentity();
    URI persistentIdentity = null;
    String displayId = null;
    String name = null;
    String description = null;
    Set<URI> members = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    if (URIPrefix != null) {
        displayId = URIcompliance.findDisplayId(topLevel.getIdentity().toString());
        identity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, version, typesInURI);
        persistentIdentity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, "", typesInURI);
    }
    for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
        if (namedProperty.getName().equals(Sbol1Terms.Collection.displayId)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10204", topLevel.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            displayId = URIcompliance.fixDisplayId(displayId);
            if (URIPrefix != null) {
                identity = createCompliantURI(URIPrefix, TopLevel.COLLECTION, displayId, version, typesInURI);
                persistentIdentity = createCompliantURI(URIPrefix, TopLevel.COLLECTION, displayId, "", typesInURI);
            }
        } else if (namedProperty.getName().equals(Sbol1Terms.Collection.name)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10212", topLevel.getIdentity());
            }
            name = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol1Terms.Collection.description)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10213", topLevel.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol1Terms.Collection.component)) {
            if (namedProperty.getValue() instanceof Literal) {
                members.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else {
                members.add(parseDnaComponentV1(SBOLDoc, (NestedDocument<QName>) namedProperty.getValue()).getIdentity());
            }
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    // Collection c = SBOLDoc.createCollection(identity);
    Collection c = new Collection(identity);
    if (persistentIdentity != null) {
        c.setPersistentIdentity(persistentIdentity);
        c.setVersion(version);
    }
    if (identity != topLevel.getIdentity())
        c.addWasDerivedFrom(topLevel.getIdentity());
    if (displayId != null)
        c.setDisplayId(displayId);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    if (!members.isEmpty())
        c.setMembers(members);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    Collection oldC = SBOLDoc.getCollection(topLevel.getIdentity());
    if (oldC == null) {
        SBOLDoc.addCollection(c);
    } else {
        if (!c.equals(oldC)) {
            throw new SBOLValidationException("sbol-10202", c);
        }
    }
    return c;
}

Example 12 with Collection

use of org.sbolstandard.core2.Collection in project libSBOLj by SynBioDex.

the class SBOLDocument method updateReferences.

// TODO: need to update persistentIdentities too
private void updateReferences(URI originalIdentity, URI newIdentity) throws SBOLValidationException {
    for (TopLevel topLevel : getTopLevels()) {
        for (URI wasDerivedFrom : topLevel.getWasDerivedFroms()) {
            if (wasDerivedFrom.equals(originalIdentity)) {
                topLevel.removeWasDerivedFrom(originalIdentity);
                topLevel.addWasDerivedFrom(newIdentity);
            }
        }
        for (URI wasGeneratedBy : topLevel.getWasGeneratedBys()) {
            if (wasGeneratedBy.equals(originalIdentity)) {
                topLevel.removeWasGeneratedBy(originalIdentity);
                topLevel.addWasGeneratedBy(newIdentity);
            }
        }
        for (URI attachmentURI : topLevel.getAttachmentURIs()) {
            if (attachmentURI.equals(originalIdentity)) {
                topLevel.removeAttachment(originalIdentity);
                topLevel.addAttachment(newIdentity);
            }
        }
    }
    for (Collection collection : getCollections()) {
        for (URI memberURI : collection.getMemberURIs()) {
            if (memberURI.equals(originalIdentity)) {
                collection.removeMember(originalIdentity);
                collection.addMember(newIdentity);
            }
        }
        updateReferences(collection, originalIdentity, newIdentity);
    }
    for (ComponentDefinition componentDefinition : getComponentDefinitions()) {
        updateReferences(componentDefinition, originalIdentity, newIdentity);
        for (Component component : componentDefinition.getComponents()) {
            if (component.getDefinitionURI().equals(originalIdentity)) {
                component.setDefinition(newIdentity);
                for (MapsTo mapsTo : component.getMapsTos()) {
                    ComponentDefinition cd = getComponentDefinition(newIdentity);
                    if (cd != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(component, originalIdentity, newIdentity);
            for (MapsTo mapsTo : component.getMapsTos()) {
                updateReferences(mapsTo, originalIdentity, newIdentity);
            }
        }
        for (SequenceAnnotation sa : componentDefinition.getSequenceAnnotations()) {
            for (Location loc : sa.getLocations()) {
                updateReferences(loc, originalIdentity, newIdentity);
            }
            updateReferences(sa, originalIdentity, newIdentity);
        }
        for (SequenceConstraint sc : componentDefinition.getSequenceConstraints()) {
            updateReferences(sc, originalIdentity, newIdentity);
        }
        for (URI sequenceURI : componentDefinition.getSequenceURIs()) {
            if (sequenceURI.equals(originalIdentity)) {
                componentDefinition.removeSequence(originalIdentity);
                componentDefinition.addSequence(newIdentity);
            }
        }
    }
    for (ModuleDefinition moduleDefinition : getModuleDefinitions()) {
        updateReferences(moduleDefinition, originalIdentity, newIdentity);
        for (FunctionalComponent functionalComponent : moduleDefinition.getFunctionalComponents()) {
            if (functionalComponent.getDefinitionURI().equals(originalIdentity)) {
                functionalComponent.setDefinition(newIdentity);
                for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
                    ComponentDefinition cd = getComponentDefinition(newIdentity);
                    if (cd != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(functionalComponent, originalIdentity, newIdentity);
            for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
                updateReferences(mapsTo, originalIdentity, newIdentity);
            }
        }
        for (Module module : moduleDefinition.getModules()) {
            if (module.getDefinitionURI().equals(originalIdentity)) {
                module.setDefinition(newIdentity);
                for (MapsTo mapsTo : module.getMapsTos()) {
                    ModuleDefinition md = getModuleDefinition(newIdentity);
                    if (md != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(md.getPersistentIdentity().toString(), displayId, md.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(module, originalIdentity, newIdentity);
            for (MapsTo mapsTo : module.getMapsTos()) {
                updateReferences(mapsTo, originalIdentity, newIdentity);
            }
        }
        for (Interaction interaction : moduleDefinition.getInteractions()) {
            updateReferences(interaction, originalIdentity, newIdentity);
            for (Participation participation : interaction.getParticipations()) {
                updateReferences(participation, originalIdentity, newIdentity);
            }
        }
        for (URI modelURI : moduleDefinition.getModelURIs()) {
            if (modelURI.equals(originalIdentity)) {
                moduleDefinition.removeModel(originalIdentity);
                moduleDefinition.addModel(newIdentity);
            }
        }
    }
    for (Model model : getModels()) {
        updateReferences(model, originalIdentity, newIdentity);
    }
    for (Attachment attachment : getAttachments()) {
        updateReferences(attachment, originalIdentity, newIdentity);
    }
    for (Implementation implementation : getImplementations()) {
        if (implementation.isSetBuilt() && implementation.getBuiltURI().equals(originalIdentity)) {
            implementation.setBuilt(newIdentity);
        }
        updateReferences(implementation, originalIdentity, newIdentity);
    }
    for (Sequence sequence : getSequences()) {
        updateReferences(sequence, originalIdentity, newIdentity);
    }
    for (GenericTopLevel genericTopLevel : getGenericTopLevels()) {
        updateReferences(genericTopLevel, originalIdentity, newIdentity);
    }
    for (CombinatorialDerivation combinatorialDerivation : getCombinatorialDerivations()) {
        updateReferences(combinatorialDerivation, originalIdentity, newIdentity);
        if (combinatorialDerivation.getTemplateURI().equals(originalIdentity)) {
            combinatorialDerivation.setTemplate(newIdentity);
            ComponentDefinition cd = getComponentDefinition(newIdentity);
            if (cd != null) {
                for (VariableComponent variableComponent : combinatorialDerivation.getVariableComponents()) {
                    String displayId = URIcompliance.extractDisplayId(variableComponent.getVariableURI());
                    URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                    variableComponent.setVariable(newURI);
                }
            }
        }
        for (VariableComponent variableComponent : combinatorialDerivation.getVariableComponents()) {
            updateReferences(variableComponent, originalIdentity, newIdentity);
        }
    }
    for (Activity activity : getActivities()) {
        updateReferences(activity, originalIdentity, newIdentity);
        for (Association association : activity.getAssociations()) {
            if (association.getAgentURI().equals(originalIdentity)) {
                association.setAgent(newIdentity);
            }
            if (association.isSetPlan() && association.getPlanURI().equals(originalIdentity)) {
                association.setPlan(newIdentity);
            }
            updateReferences(association, originalIdentity, newIdentity);
        }
        for (Usage usage : activity.getUsages()) {
            if (usage.getEntityURI().equals(originalIdentity)) {
                usage.setEntity(newIdentity);
            }
            updateReferences(usage, originalIdentity, newIdentity);
        }
    }
    for (Agent agent : getAgents()) {
        updateReferences(agent, originalIdentity, newIdentity);
    }
    for (Plan plan : getPlans()) {
        updateReferences(plan, originalIdentity, newIdentity);
    }
}

Example 13 with Collection

use of org.sbolstandard.core2.Collection in project libSBOLj by SynBioDex.

the class SBOLDocument method removeTopLevel.

/**
 * Removes the given top-level from this SBOL document's list of top-levels.
 *
 * @param topLevel
 *            the top-level to be removed
 * @param instancesMap
 *            map of toplevel instances
 * @return {@code true} if the given top-level was successfully removed,
 *         {@code false} otherwise
 * @throws SBOLValidationException
 *             if the following SBOL validation rule was violated: 12103.
 */
private final <TL extends TopLevel> boolean removeTopLevel(TopLevel topLevel, Map<URI, TL> instancesMap) throws SBOLValidationException {
    if (complete) {
        for (Collection c : collections.values()) {
            if (c.containsMember(topLevel.getIdentity())) {
                throw new SBOLValidationException("sbol-12103", c);
            }
        }
    }
    Set<TopLevel> setToRemove = new HashSet<>();
    setToRemove.add(topLevel);
    boolean changed = instancesMap.values().removeAll(setToRemove);
    URI latestVersion = null;
    for (TL tl : instancesMap.values()) {
        if (topLevel.getPersistentIdentity().toString().equals(tl.getPersistentIdentity().toString())) {
            if (latestVersion == null) {
                latestVersion = tl.getIdentity();
            } else if (isFirstVersionNewer(extractVersion(tl.getIdentity()), extractVersion(latestVersion))) {
                latestVersion = tl.getIdentity();
            }
        }
    }
    if (latestVersion != null) {
        instancesMap.put(topLevel.getPersistentIdentity(), instancesMap.get(latestVersion));
    }
    return changed;
}

Example 14 with Collection

use of org.sbolstandard.core2.Collection in project libSBOLj by SynBioDex.

the class Collection method copy.

/* (non-Javadoc)
	 * @see org.sbolstandard.core2.abstract_classes.TopLevel#copy(java.lang.String, java.lang.String, java.lang.String)
	 */
/**
 * @throws SBOLValidationException if an SBOL validation rule violation occurred in any of the following methods:
 * <ul>
 * <li>{@link #deepCopy()},</li>
 * <li>{@link URIcompliance#createCompliantURI(String, String, String)},</li>
 * <li>{@link #setDisplayId(String)},</li>
 * <li>{@link #setVersion(String)},</li>
 * <li>{@link #setWasDerivedFrom(URI)}, or</li>
 * <li>{@link #setIdentity(URI)}.</li>
 * </ul>
 */
@Override
Collection copy(String URIprefix, String displayId, String version) throws SBOLValidationException {
    Collection cloned = this.deepCopy();
    cloned.setPersistentIdentity(createCompliantURI(URIprefix, displayId, ""));
    cloned.setDisplayId(displayId);
    cloned.setVersion(version);
    URI newIdentity = createCompliantURI(URIprefix, displayId, version);
    if (!this.getIdentity().equals(newIdentity)) {
        cloned.addWasDerivedFrom(this.getIdentity());
    } else {
        cloned.setWasDerivedFroms(this.getWasDerivedFroms());
    }
    cloned.setIdentity(newIdentity);
    return cloned;
}

Example 15 with Collection

use of org.sbolstandard.core2.Collection in project libSBOLj by SynBioDex.

the class SynBioHubFrontend method submit.

/**
 * Submit file to a new private collection on SynBioHub
 * @param id The submission identifier
 * @param version The submission version
 * @param name The submission name
 * @param description The submission description
 * @param citations The pubMedIds for this submission
 * @param overwrite_merge '0' prevent, '1' overwrite, '2' merge and prevent, '3' merge and overwrite
 * @param inputStream inputStream to submit to SynBioHub
 * @throws SynBioHubException if there was an error communicating with the SynBioHub
 */
private void submit(URI uri, String id, String version, String name, String description, String citations, String overwrite_merge, InputStream inputStream) throws SynBioHubException {
    if (user.equals("")) {
        Exception e = new Exception("Must be logged in to submit.");
        throw new SynBioHubException(e);
    }
    String url = backendUrl + "/submit";
    HttpPost request = new HttpPost(url);
    request.setHeader("X-authorization", user);
    request.setHeader("Accept", "text/plain");
    MultipartEntityBuilder params = MultipartEntityBuilder.create();
    /* example for setting a HttpMultipartMode */
    params.setMode(HttpMultipartMode.BROWSER_COMPATIBLE);
    if (uri == null) {
        params.addTextBody("id", id);
        params.addTextBody("version", version);
        params.addTextBody("name", name);
        params.addTextBody("description", description);
        params.addTextBody("citations", citations);
        params.addTextBody("collectionChoices", "");
    } else {
        params.addTextBody("rootCollections", uri.toString());
    }
    params.addTextBody("overwrite_merge", overwrite_merge);
    params.addTextBody("user", user);
    if (inputStream != null) {
        params.addBinaryBody("file", inputStream, ContentType.DEFAULT_BINARY, "file");
    } else {
        params.addTextBody("file", "");
    }
    try {
        request.setEntity(params.build());
        HttpResponse response = client.execute(request);
        checkResponseCode(response);
    } catch (Exception e) {
        // e.printStackTrace();
        throw new SynBioHubException(e);
    } finally {
        request.releaseConnection();
    }
}