Examples with NextProtException org.nextprot.api.commons.exception.NextProtException used on opensource projects

Example 56 with NextProtException

use of org.nextprot.api.commons.exception.NextProtException in project nextprot-api by calipho-sib.

the class RdfHelpController method helpFullInfo.

/*

	@RequestMapping("/rdf/help/type/{rdfType}/values")
	@ResponseBody
	public List<String> helpFullInfoValues(@PathVariable("rdfType") String rdfType, Model model) {
		try {
			return this.service.getRdfTypeValues(rdfType);
		} catch (Exception e) {
			throw new NextProtException(e.getMessage());
		}
	}

	@RequestMapping("/rdf/help/visgraphp")
	public String visgraphp(Model model) {

		Map<String, RdfTypeInfo> map = new HashMap<String, RdfTypeInfo>();
		List<String> names = new ArrayList<String>();

		for (RdfTypeInfo rti : this.service.getRdfTypeFullInfoList()) {
			map.put(rti.getTypeName(), rti);
			names.add(rti.getTypeName());
		}

		model.addAttribute("visutils", new VisUtils());
		model.addAttribute("map", map);
		model.addAttribute("names", names);

		return "visgraphp";
	}

	@RequestMapping("/rdf/help/visgraph")
	public String visgraph(Model model) {

		Map<String, RdfTypeInfo> map = new HashMap<String, RdfTypeInfo>();
		List<String> names = new ArrayList<String>();

		for (RdfTypeInfo rti : this.service.getRdfTypeFullInfoList()) {
			map.put(rti.getTypeName(), rti);
			if (!rti.getTypeName().startsWith(":Isoform") && !rti.getTypeName().startsWith(":Evidence")) {
				names.add(rti.getTypeName());
			} else
				System.out.println("Skipped for" + rti);
		}

		model.addAttribute("visutils", new VisUtils());
		model.addAttribute("map", map);
		model.addAttribute("names", names);

		return "visgraph";
	}

	// Example http://localhost:8080/nextprot-api/rdf/help/visgraph/:Entry,:Gene
	@RequestMapping("/rdf/help/visgraph/{rdfType}")
	public String visgraph(@PathVariable("rdfType") String rdfType, Model model) {

		Map<String, RdfTypeInfo> map = new HashMap<String, RdfTypeInfo>();
		for (RdfTypeInfo rti : this.service.getRdfTypeFullInfoList()) {
			map.put(rti.getTypeName(), rti);
		}

		model.addAttribute("visutils", new VisUtils());
		model.addAttribute("map", map);
		model.addAttribute("names", Arrays.asList(rdfType.split(",")));

		return "visgraph";
	}

	// Example http://localhost:8080/nextprot-api/rdf/help/visgraph/:Entry,:Gene
	@RequestMapping("/rdf/help/visgraphp/{rdfType}")
	public String visgraphp(@PathVariable("rdfType") String rdfType, Model model) {

		Map<String, RdfTypeInfo> map = new HashMap<String, RdfTypeInfo>();
		for (RdfTypeInfo rti : this.service.getRdfTypeFullInfoList()) {
			map.put(rti.getTypeName(), rti);
		}

		model.addAttribute("visutils", new VisUtils());
		model.addAttribute("map", map);
		model.addAttribute("names", Arrays.asList(rdfType.split(",")));

		return "visgraphp";
	}

	public static class VisUtils {
		private int n = 6666;
		Set<Integer> ids = new TreeSet<Integer>();
		Map<String, Integer> mapIds = new HashMap<String, Integer>();
		
		public void addId(int id) {
			ids.add(id);
		}

		public Integer getMaxDepth(RdfTypeInfo rti) {
			int max = 0;
			for (String p : rti.getPathToOrigin()) {
				max = Math.max(max, getDepth(p));
			}
			return max;
		}

		public Integer getTripleId(TripleInfo t) {
			String key = t.getSubjectType() + "" + t.getPredicate();
			if (!mapIds.containsKey(key)) {
				mapIds.put(key, n++);
			}
			return mapIds.get(key);
		}

		public Integer getNodeId(String currentNode, String relativePath, String _path) {
			System.out.println("CN:" + currentNode + " RP:" + relativePath + " P:" + _path);

			String path = _path.replace("/", "");

			if (currentNode.equals("Entry"))
				return getPathId(currentNode);

			if (currentNode.equals("isoform")) {
				String afterNode = path.replace(relativePath, "").replace(currentNode, "");
				int ni = afterNode.indexOf(":");
				int nextIndex = afterNode.indexOf(":", ni+1);
				if(nextIndex == -1) {
					nextIndex = ni;
				}
				if(ni == -1) {
					nextIndex = 0;
				}

				
				System.out.println("AN" + afterNode + " ANS" + afterNode.substring(nextIndex));
				return getPathId(currentNode + afterNode.substring(nextIndex));
			}
			
			String currentAndAfterNode = path.replace(relativePath, "");
			System.out.println(currentAndAfterNode + getPathId(currentAndAfterNode));
			System.out.println();
			return getPathId(currentAndAfterNode);
		}

		public Integer getPathId(String path) {
			if (!mapIds.containsKey(path)) {
				mapIds.put(path, n++);
			}
			return mapIds.get(path);
		}

		public boolean isLast(String path, String absolutePath) {
			return path.replace("/", "").equals(absolutePath);
		}

		public Integer getEdgeId(Integer id1, Integer id2) {
			String s = id1.toString() + id2.toString();
			return Integer.valueOf(s);
		}

		public Integer getDepth(String p) {
			return p.split(":").length;
		}

		public String getSimplePath(String path) {
			int n = StringUtils.reverse(path).indexOf(":");
			if (n == -1)
				return "Entry";
			return path.substring(path.length() - n);
		}

		public List<String> getPathArray(String path) {
			String s = path.replace("?entry ", "");
			String ss[] = s.split("/");
			List<String> r = new ArrayList<String>();
			String current = "?entry";
			current += " ";
			r.add(current);
			for (String p : ss) {
				current += p;
				r.add(current);
			}
			return r;
		}

		public boolean contains(int id) {
			return ids.contains(id);
		}
		
		private Set<String> edges = new TreeSet<String>();
		public String getEdge (Integer from, Integer to, String label){
			String key = null;
			if(from < to){
				key = from + "" + to;
			}else key = to + "" + from;
			
			if(edges.contains(key)){
				return "";
			}else {
				edges.add(key);
				return "edges.push({from: " + from + ", to: " + to + ", label: '" + label + "'});";
			}
		
		}
		
	}
	
	
	/**
	 * Full info of a single rdf:type
	 * 
	 * @param rdfType
	 * @param model
	 * @return
	 */
// we want this undocumented   @ApiMethod(path = "/rdf/help/type/{rdfType}", verb = ApiVerb.GET, description = "Gets a description and properties of a rdf type", produces = { MediaType.APPLICATION_JSON_VALUE })
@RequestMapping("/rdf/help/type/{rdfType}")
@ResponseBody
public RdfTypeInfo helpFullInfo(@PathVariable("rdfType") String rdfType, Model model) {
    try {
        RdfTypeInfo typ;
        typ = this.service.getRdfTypeFullInfo(rdfType);
        model.addAttribute("result", typ);
        return typ;
    } catch (Exception e) {
        e.printStackTrace();
        throw new NextProtException(e.getMessage());
    }
}

Example 57 with NextProtException

use of org.nextprot.api.commons.exception.NextProtException in project nextprot-api by calipho-sib.

the class SparqlServiceImpl method sparqlSelect.

@Override
public SparqlResult sparqlSelect(String sparql, String sparqlEndpointUrl, int timeout, String queryTitle, String testId, ResultsFormat format) {
    SparqlResult result = null;
    try {
        QueryExecution qExec = QueryExecutionFactory.sparqlService(sparqlEndpointUrl, sparql);
        qExec.setTimeout(timeout);
        ResultSet rs = qExec.execSelect();
        result = SparqlUtils.convertResultToFormat(rs, format);
        qExec.close();
    } catch (QueryParseException qe) {
        String msg = ExceptionUtils.fixLineNumberInErrorMessage(qe.getLocalizedMessage());
        throw new NextProtException("Malformed SPARQL: " + msg);
    }
    return result;
}

Example 58 with NextProtException

use of org.nextprot.api.commons.exception.NextProtException in project nextprot-api by calipho-sib.

the class ChromosomeReportController method exportChromosomeEntryCountByProteinEvidenceFile.

@ApiMethod(path = "/chromosome-report/export/hpp/entry-count-by-pe", verb = ApiVerb.GET, description = "Export number of entries grouped by protein existence for all chromosomes", produces = { NextprotMediaType.TSV_MEDIATYPE_VALUE })
@RequestMapping(value = "/chromosome-report/export/hpp/entry-count-by-pe", method = { RequestMethod.GET })
public void exportChromosomeEntryCountByProteinEvidenceFile(HttpServletResponse response) {
    try (OutputStream os = response.getOutputStream()) {
        response.setHeader("Content-Disposition", "attachment; filename=\"count-of-pe12345-by-chromosome.tsv\"");
        chromosomeReportExportService.exportHPPChromosomeEntryReportCountByProteinExistence(os);
    } catch (IOException e) {
        throw new NextProtException(e.getMessage() + ": cannot export entry count by protein existence for all chromosomes");
    }
}

Example 59 with NextProtException

use of org.nextprot.api.commons.exception.NextProtException in project nextprot-api by calipho-sib.

the class ChromosomeReportController method exportHPPChromosomeEntriesReportFile.

@ApiMethod(path = "/chromosome-report/export/hpp/{chromosome}", verb = ApiVerb.GET, description = "Export informations of neXtProt entries located on a given chromosome by accession", produces = { MediaType.TEXT_PLAIN_VALUE, NextprotMediaType.TSV_MEDIATYPE_VALUE })
@RequestMapping(value = "/chromosome-report/export/hpp/{chromosome}", method = { RequestMethod.GET })
public void exportHPPChromosomeEntriesReportFile(@ApiPathParam(name = "chromosome", description = "The chromosome number or name (X,Y..)", allowedvalues = { "Y" }) @PathVariable("chromosome") String chromosome, HttpServletRequest request, HttpServletResponse response) {
    NextprotMediaType mediaType = NextprotMediaType.valueOf(request);
    try (OutputStream os = response.getOutputStream()) {
        String filename = "HPP_chromosome_" + chromosome + "." + mediaType.getExtension();
        response.setHeader("Content-Disposition", "attachment; filename=\"" + filename + "\"");
        chromosomeReportExportService.exportHPPChromosomeEntryReport(chromosome, NextprotMediaType.valueOf(request), os);
    } catch (IOException e) {
        throw new NextProtException(e.getMessage() + ": cannot export HPP chromosome " + chromosome + " as " + mediaType);
    }
}

Example 60 with NextProtException

use of org.nextprot.api.commons.exception.NextProtException in project nextprot-api by calipho-sib.

the class TerminologyDaoImpl method findTerminologyByAccession.

@Override
// SHOULD USE findTermByAccessionAndTerminology
@Cacheable("terminology-by-accession")
public CvTerm findTerminologyByAccession(String accession) {
    Set<String> acs = new HashSet<>();
    acs.add(accession);
    SqlParameterSource params = new MapSqlParameterSource("accessions", acs);
    List<CvTerm> terms = new NamedParameterJdbcTemplate(dsLocator.getDataSource()).query(sqlDictionary.getSQLQuery("terminology-by-acs"), params, new DbTermRowMapper());
    if (terms.size() == 0)
        return null;
    else if (terms.size() > 1) {
        throw new NextProtException("Found " + terms.size() + " terms that corresponds to the same accession. Use the method findTerminologyByAccessionForTerminology (accession, terminology) instead");
    }
    return terms.get(0);
}