Ejemplo n.º 1
0
  @Test
  public void testOrderEntitiesByPrimaryKeys() {
    final List<Persistable> entities = new ArrayList<Persistable>();
    final Persistable persistable1 = control.createMock(Persistable.class);
    final Persistable persistable2 = control.createMock(Persistable.class);
    final Persistable persistable3 = control.createMock(Persistable.class);
    CollectionUtils.addAll(entities, persistable1, persistable2, persistable3);

    final String pk1 = new String("pk1");
    final String pk2 = new String("pk2");
    final String pk3 = new String("pk3");
    expect(persistable1.getPrimaryKey()).andReturn(pk1);
    expect(persistable2.getPrimaryKey()).andReturn(pk2);
    expect(persistable3.getPrimaryKey()).andReturn(pk3);

    final List<String> primaryKeys = new LinkedList<String>();
    CollectionUtils.addAll(primaryKeys, pk1, pk3, pk2);

    control.replay();
    final List<Persistable> orderedList =
        DaoUtils.orderEntitiesByPrimaryKeys(entities, primaryKeys);
    control.verify();

    assertEquals(orderedList.get(0), persistable1);
    assertEquals(orderedList.get(1), persistable3);
    assertEquals(orderedList.get(2), persistable2);
  }
Ejemplo n.º 2
0
  private void applySubsetRule(Map<String, List<Integer>> candidateDomVerMap) {
    List<String> removeKeyList = new ArrayList<String>();
    Set<String> keySet = candidateDomVerMap.keySet();
    for (String key1 : keySet) {
      byte[] keyArr1 = AlgorithmUtil.stringToBinaryArray(key1);
      List<Integer> keyList1 = AlgorithmUtil.binaryArrayToList(keyArr1);
      for (String key2 : keySet) {
        if (key1 != key2) {
          byte[] keyArr2 = AlgorithmUtil.stringToBinaryArray(key2);
          List<Integer> keyList2 = AlgorithmUtil.binaryArrayToList(keyArr2);

          if (CollectionUtils.isSubCollection(keyList1, keyList2)) {
            AlgorithmUtil.addElementToList(removeKeyList, key1);
          } else if (CollectionUtils.isSubCollection(keyList2, keyList1)) {
            AlgorithmUtil.addElementToList(removeKeyList, key2);
          } else {
            continue;
          }
        }
      }
    }

    for (String key : removeKeyList) {
      candidateDomVerMap.remove(key);
    }
  }
Ejemplo n.º 3
0
  /**
   * Will copy into this Person, the details from the input Person.
   *
   * @param rs - The Person from which the details to be copied from.
   */
  public void sync(final ResearchStaff rs) {
    super.sync(rs);
    setNciIdentifier(rs.getNciIdentifier());
    if (getAddress() != null) {
      getAddress().sync(rs.getAddress());
    } else {
      setAddress(rs.getAddress());
    }

    // sync the site researchstaffs
    CollectionUtils.forAllDo(
        getSiteResearchStaffs(),
        new Closure<SiteResearchStaff>() {
          public void execute(SiteResearchStaff srs) {
            SiteResearchStaff otherSRS = rs.findSiteResearchStaff(srs);
            srs.sync(otherSRS);
          }
        });

    // add new site researchstaff if needed
    for (SiteResearchStaff srs : rs.getSiteResearchStaffs()) {
      SiteResearchStaff availableSRS = findSiteResearchStaff(srs);
      if (availableSRS == null) addSiteResearchStaff(srs);
    }
  }
Ejemplo n.º 4
0
  /**
   * Méthode en charge de mettre à jour les lignes de stock à partir des mouvements de stock de type
   * Sortie. La mise à jour concerne la quantité.
   *
   * @param essai Essai.
   * @param pharmacie Pharmacie.
   * @param produit Produit.
   * @param conditionnement Conditionnement.
   * @param mapLines Map des lignes de stock à mettre à jour.
   */
  private void updateFromMvtTypeSortie(
      final MvtStockSearchCriteria critSortie, final Map<String, LigneStock> mapLines) {
    // Récupération des mouvements de type Sortie qui concernant l'essai, la
    // pharmacie, le
    // produit et le conditionnement
    critSortie.setTypesMouvement(TypeMvtStock.ALL_SORTIES);
    critSortie.setActiveOrder("datePeremption");

    final List<MvtStock> sorties = this.mvtStockService.getAll(critSortie);

    // on ne traite pas ici les dispensations globales car elles ne sortent
    // pas du stocks.
    CollectionUtils.filter(
        sorties,
        new Predicate<MvtStock>() {
          @Override
          public boolean evaluate(final MvtStock object) {
            return !object.getType().equals(TypeMvtStock.DOTATION);
          }
        });

    for (final MvtStock mvtStock : sorties) {
      final String key = this.getKeyMvtStock(mvtStock, false);
      if (mapLines.containsKey(key)) {
        final LigneStock ligneStock = mapLines.get(key);
        this.log.debug("Key: " + key + " objec: " + ligneStock);
        // Mise à jour de la quantité réelle en stock
        ligneStock.setQteGlobalStock(ligneStock.getQteGlobalStock() - mvtStock.getQuantite());
      } else {
        this.log.error("Aucun Mvt d'entrée correspondant à la sortie - idMvt " + mvtStock.getId());
      }
    }
  }
 @Override
 public boolean evaluate(ConceptAnnotation annotation) {
   if (stycodeset.size() == 0) {
     return true;
   } else {
     Set<String> stycodes = JsonUtils.stringToMap(annotation.getStycodes()).keySet();
     return (CollectionUtils.intersection(stycodeset, stycodes).size() > 0);
   }
 }
Ejemplo n.º 6
0
  private void initLignesStockDispensationNominative(final Sortie sortie) {
    final MvtStock mvt = sortie.getMvtSortie();

    final List<LigneStock> lignesStock =
        this.getAllLignesStock(
            mvt.getEssai(), mvt.getPharmacie(), mvt.getProduit(), mvt.getConditionnement(), false);

    // Filtre des stocks en quarantaine.
    org.apache.commons.collections15.CollectionUtils.filter(
        lignesStock, new NotPredicate<LigneStock>(new LigneStockEnQuarantainePredicate()));

    sortie.setLignesStock(lignesStock);
  }
Ejemplo n.º 7
0
 /**
  * get a vertex from a list.
  *
  * <p>priority: 1. vertices in considerableCandidateVertices4DS; 2. vertices in vertex cover 3.
  * the highest degree one ;
  *
  * @param verList
  * @return
  */
 private Integer getVertexFromCandiateMap(List<Integer> verList) {
   List<Integer> interConsider =
       (List<Integer>) CollectionUtils.intersection(verList, considerableCandidateVertices4DS);
   if (interConsider != null && !interConsider.isEmpty()) {
     return interConsider.get(0);
   }
   interConsider = (List<Integer>) CollectionUtils.intersection(verList, vertexCover);
   if (interConsider != null && !interConsider.isEmpty()) {
     return interConsider.get(0);
   }
   // List<VertexDegree> vdList =
   // AlgorithmUtil.sortVertexAccordingToDegreeInclude(this.g, verList);
   // return vdList.get(0).getVertex();
   IPriorityOrder<Integer, String> pocb = new DegreeDesc<Integer, String>();
   List<Integer> allVList =
       pocb.getOrderedVertexList(new PriorityBean<Integer, String>(g, null, null));
   for (Integer v : allVList) {
     if (verList.contains(v)) {
       return v;
     }
   }
   return null;
 }
Ejemplo n.º 8
0
  /** {@inheritDoc} */
  @Override
  public List<LigneStock> getAllLignesStock(
      final Essai essai,
      final Pharmacie pharmacie,
      final Produit produit,
      final Conditionnement conditionnement,
      final Boolean dotations) {
    final MvtStockSearchCriteria criteria = new MvtStockSearchCriteria();
    criteria.setEssai(essai);
    criteria.setPharmacie(pharmacie);
    criteria.setProduit(produit);
    criteria.setConditionnement(conditionnement);
    final List<LigneStock> resultWithNullStock = super.getAll(criteria);

    for (final LigneStock ligneStock : resultWithNullStock) {
      ligneStock.setDotation(dotations);
    }

    return new ArrayList<LigneStock>(
        CollectionUtils.select(resultWithNullStock, new LigneStockNonEpuisePredicate()));
  }
Ejemplo n.º 9
0
 @Override
 public PartitionSet getWritePartitions(EstimationThresholds t) {
   return new PartitionSet(CollectionUtils.subtract(this.partitions, this.readonly));
 }
Ejemplo n.º 10
0
  private void getCandidateDomVerMap() throws ExceedLongMaxException {
    candidateDomVerMap = new LinkedHashMap<String, List<Integer>>();

    // the vertex cover's complement set will be an independent set
    Collection<Integer> vertices = g.getVertices();
    Collection<Integer> independentSet = CollectionUtils.subtract(vertices, vertexCover);

    /*
     * the vertex cover size will be the parameter k used in the fpt
     * algorithm
     */
    int vertexCoverSize = vertexCover.size();
    byte[] comparedRuler = new byte[vertexCoverSize];
    Arrays.fill(comparedRuler, AlgorithmUtil.MARKED);

    for (Integer isv : independentSet) {
      Collection<Integer> neighOfIsv = g.getNeighbors(isv);
      byte ruler[] = new byte[vertexCoverSize];
      // initilze the array with 0
      Arrays.fill(ruler, AlgorithmUtil.UNMARKED);
      for (Integer neig : neighOfIsv) {
        /*
         * the position of the dominate vertex in the vertex cover will
         * set 1
         */
        int pos = vertexCover.indexOf(neig);
        if (pos != -1) {
          ruler[pos] = AlgorithmUtil.MARKED;
        }
      }

      // if (Arrays.equals(comparedRuler, ruler)) {
      // log.debug(isv + " dominates all vc");
      // }

      String rulerStr = AlgorithmUtil.arrayToString(ruler);

      List<Integer> candidateDomVerSet = candidateDomVerMap.get(rulerStr);

      if (candidateDomVerSet == null) {
        candidateDomVerSet = new ArrayList<Integer>();
      }
      // candidateDomVerSet.add(isv);
      AlgorithmUtil.addElementToList(candidateDomVerSet, isv);
      candidateDomVerMap.put(rulerStr, candidateDomVerSet);
    }

    /*
     * because the vertices in the vertex cover can also dominate other
     * vertices in the vertex cover,they are also considered
     */
    for (Integer vcv : vertexCover) {
      Collection<Integer> neighOfVcv = g.getNeighbors(vcv);

      byte ruler[] = new byte[vertexCoverSize];
      Arrays.fill(ruler, AlgorithmUtil.UNMARKED);

      // the vertex can dominated by itself
      int pos = vertexCover.indexOf(vcv);
      ruler[pos] = AlgorithmUtil.MARKED;

      for (Integer neig : neighOfVcv) {
        /*
         * the position of the dominate vertex in the vertex cover will
         * set 1
         *
         * a neighbour of the vertex is likely not to be in the vertex
         * cover
         */
        pos = vertexCover.indexOf(neig);
        if (pos != -1) {
          ruler[pos] = AlgorithmUtil.MARKED;
        }
      }

      // if (Arrays.equals(comparedRuler, ruler)) {
      // log.debug(vcv + " dominates all vc");
      // }
      String rulerStr = AlgorithmUtil.arrayToString(ruler);

      List<Integer> candidateDomVerSet = candidateDomVerMap.get(rulerStr);

      if (candidateDomVerSet == null) {
        candidateDomVerSet = new ArrayList<Integer>();
      }
      // candidateDomVerSet.add(vcv);
      AlgorithmUtil.addElementToList(candidateDomVerSet, vcv);
      candidateDomVerMap.put(rulerStr, candidateDomVerSet);
    }

    applySubsetRule(candidateDomVerMap);
  }
Ejemplo n.º 11
0
  @RequestMapping(value = "/map.html")
  public ModelAndView map(
      @RequestParam(value = "q1", required = false) String q1,
      @RequestParam(value = "q2", required = false) String q2,
      @RequestParam(value = "q3", required = false) String q3,
      @RequestParam(value = "if", required = false, defaultValue = UimaUtils.MIMETYPE_STRING)
          String inputFormat,
      @RequestParam(value = "of", required = true, defaultValue = "html") String outputFormat,
      @RequestParam(value = "ofs", required = false, defaultValue = "pretty")
          String outputFormatStyle,
      @RequestParam(value = "sgf", required = false) String[] styGroupFilter,
      @RequestParam(value = "scf", required = false) String[] styCodeFilter) {

    ModelAndView mav = new ModelAndView();
    mav.addObject("operation", "map");
    // validate parameters (at least one of o, q, u or t must
    // be supplied, otherwise show the input form
    mav.addObject("q1", StringUtils.isEmpty(q1) ? "" : q1);
    mav.addObject("q2", StringUtils.isEmpty(q2) ? "" : q2);
    mav.addObject("q3", StringUtils.isEmpty(q3) ? "" : q3);
    String q =
        StringUtils.isNotEmpty(q1)
            ? q1
            : StringUtils.isNotEmpty(q2) ? q2 : StringUtils.isNotEmpty(q3) ? q3 : null;
    if (StringUtils.isEmpty(q)) {
      setViewName(mav, outputFormat, outputFormatStyle);
      return mav;
    }
    try {
      if (NumberUtils.isNumber(q) && StringUtils.length(q) == 7) {
        return show(Integer.valueOf(q));
      } else {
        // show list of concepts
        String text = q;
        if ((q.startsWith("http://") && UimaUtils.MIMETYPE_HTML.equals(inputFormat))) {
          URL u = new URL(q);
          BufferedReader br = new BufferedReader(new InputStreamReader(u.openStream()));
          StringBuilder tbuf = new StringBuilder();
          String line = null;
          while ((line = br.readLine()) != null) {
            tbuf.append(line).append("\n");
          }
          br.close();
          text = tbuf.toString();
        }
        List<ConceptAnnotation> annotations = new ArrayList<ConceptAnnotation>();
        long startTs = System.currentTimeMillis();
        JCas jcas = UimaUtils.runAE(conceptMappingAE, text, inputFormat, null);
        FSIndex fsindex = jcas.getAnnotationIndex(ConceptAnnotation.type);
        for (Iterator<ConceptAnnotation> it = fsindex.iterator(); it.hasNext(); ) {
          ConceptAnnotation annotation = it.next();
          annotations.add(annotation);
        }
        CollectionUtils.filter(annotations, new StyGroupPredicate(styGroupFilter));
        CollectionUtils.filter(annotations, new StyCodePredicate(styCodeFilter));
        annotations = filterSubsumedConcepts(q, annotations);
        if (annotations.size() == 0) {
          mav.addObject("error", "No concepts found");
        } else {
          mav.addObject("text", text);
          mav.addObject("annotations", annotations);
          long endTs = System.currentTimeMillis();
          mav.addObject("elapsed", new Long(endTs - startTs));
        }
        setViewName(mav, outputFormat, outputFormatStyle);
      }
    } catch (Exception e) {
      mav.addObject("error", e.getMessage());
      setViewName(mav, outputFormat, outputFormatStyle);
    }
    return mav;
  }