Examples with BioModelReferenceRep cbit.vcell.modeldb.BioModelReferenceRep used on opensource projects

Example 1 with BioModelReferenceRep

use of cbit.vcell.modeldb.BioModelReferenceRep in project vcell by virtualcell.

the class PublicationServerResource method handleForm.

@Post
public Representation handleForm(Representation entity) {
    try {
        String myHost = getHostRef().getHostDomain();
        String allowedPublicationHost = PropertyLoader.getProperty(PropertyLoader.vcellPublicationHost, "");
        if (!allowedPublicationHost.equals(myHost)) {
            throw new PermissionException("Host '" + myHost + "' not allowed to edit publications");
        }
        Form form = new Form(entity);
        VCellApiApplication application = ((VCellApiApplication) getApplication());
        User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.ignoreInvalidCredentials);
        if (vcellUser == null) {
            throw new PermissionException("must be authenticated to edit publication info");
        }
        // The form contains input with names "user" and "password"
        String pubop = form.getFirstValue("pubop");
        // String password = form.getFirstValue("password");
        Map<String, Object> dataModel = new HashMap<String, Object>();
        if (pubop == null) {
            return new StringRepresentation(("value of publication 'operation' cannot be null"));
        } else if (pubop.equals("editNew")) {
            PublicationRepresentation value = new PublicationRepresentation();
            value.pubKey = AUTOMATICALLY_GENERATED;
            dataModel.put("publicationRepr", value);
        } else if (pubop.equals("editWithKey")) {
            Object pubidObj = getRequestAttributes().get(VCellApiApplication.PUBLICATIONID);
            PublicationRepresentation publication = getPublicationRepresentation(((VCellApiApplication) getApplication()).getRestDatabaseService(), vcellUser, new KeyValue(pubidObj.toString()));
            dataModel.put("publicationRepr", publication);
        } else if (pubop.equals("applyEdit")) {
            SimpleDateFormat sdf = new java.text.SimpleDateFormat("MM/dd/yyyy", java.util.Locale.US);
            // PublicationRepresentation publication = getPublicationRepresentation(((VCellApiApplication)getApplication()).getRestDatabaseService(),vcellUser,new KeyValue(form.getFirstValue("pubid")));
            String[] authors = StringUtils.split(form.getFirstValue("authors"), ";");
            for (int i = 0; i < authors.length; i++) {
                authors[i] = authors[i].trim();
            }
            String thePubID = form.getFirstValue("pubId");
            BioModelReferenceRep[] bioModelReferenceReps = (BioModelReferenceRep[]) convertToReferenceRep(form.getFirstValue("biomodelReferences"), BioModelReferenceRep.class);
            MathModelReferenceRep[] mathModelReferenceReps = (MathModelReferenceRep[]) convertToReferenceRep(form.getFirstValue("mathmodelReferences"), MathModelReferenceRep.class);
            PublicationRep publicationRep = new PublicationRep((thePubID == null || thePubID.equals(AUTOMATICALLY_GENERATED) ? null : new KeyValue(Integer.valueOf(thePubID).toString())), form.getFirstValue("title"), authors, (form.getFirstValue("year") == null || form.getFirstValue("year").trim().length() == 0 ? null : Integer.valueOf(form.getFirstValue("year"))), form.getFirstValue("citation"), form.getFirstValue("pubmedid"), form.getFirstValue("doi"), form.getFirstValue("endnoteid"), form.getFirstValue("url"), bioModelReferenceReps, mathModelReferenceReps, form.getFirstValue("wittid"), (form.getFirstValue("pubdate") == null || form.getFirstValue("pubdate").trim().length() == 0 ? null : sdf.parse(form.getFirstValue("pubdate"))));
            KeyValue savedOrEditedPubID = ((VCellApiApplication) getApplication()).getRestDatabaseService().savePublicationRep(publicationRep, vcellUser);
            // String address = getRequest().getClientInfo().getAddress();
            // int port = getRequest().getClientInfo().getPort();
            StringRepresentation s = getPubInfoHtml(myHost, savedOrEditedPubID);
            return s;
        } else if (pubop.equals("makepublic")) {
            String[] bmKeys = form.getValuesArray("bmpublic");
            KeyValue[] publishTheseBiomodels = new KeyValue[(bmKeys == null ? 0 : bmKeys.length)];
            for (int i = 0; i < publishTheseBiomodels.length; i++) {
                publishTheseBiomodels[i] = new KeyValue(bmKeys[i]);
            }
            String[] mmKeys = form.getValuesArray("mmpublic");
            KeyValue[] publishTheseMathmodels = new KeyValue[(mmKeys == null ? 0 : mmKeys.length)];
            for (int i = 0; i < publishTheseMathmodels.length; i++) {
                publishTheseMathmodels[i] = new KeyValue(mmKeys[i]);
            }
            if (publishTheseBiomodels.length > 0 || publishTheseMathmodels.length > 0) {
                ((VCellApiApplication) getApplication()).getRestDatabaseService().publishDirectly(publishTheseBiomodels, publishTheseMathmodels, vcellUser);
            }
            Object pubidObj = getRequestAttributes().get(VCellApiApplication.PUBLICATIONID);
            StringRepresentation s = getPubInfoHtml(myHost, new KeyValue(pubidObj.toString()));
            return s;
        } else {
            return new StringRepresentation(("value of pubop=" + pubop + " not expected").toCharArray());
        }
        Configuration templateConfiguration = application.getTemplateConfiguration();
        Representation myRepresentation = new ClientResource(LocalReference.createClapReference("/newpublication.ftl")).get();
        TemplateRepresentation templateRepresentation = new TemplateRepresentation(myRepresentation, templateConfiguration, dataModel, MediaType.TEXT_HTML);
        return templateRepresentation;
    } catch (Exception e) {
        return new StringRepresentation(e.getClass().getName() + " " + e.getMessage());
    }
}