Esempio n. 1
0
 private void readCentralDirectoryEntry(final Map<ZipEntry, NameAndComment> noUTF8Flag)
     throws IOException {
   this.archive.readFully(this.CFH_BUF);
   int off = 0;
   final OffsetEntry offset = new OffsetEntry();
   final Entry ze = new Entry(offset);
   final int versionMadeBy = ZipShort.getValue(this.CFH_BUF, off);
   off += 2;
   ze.setPlatform(versionMadeBy >> 8 & 0xF);
   off += 2;
   final GeneralPurposeBit gpFlag = GeneralPurposeBit.parse(this.CFH_BUF, off);
   final boolean hasUTF8Flag = gpFlag.usesUTF8ForNames();
   final ZipEncoding entryEncoding =
       hasUTF8Flag ? ZipEncodingHelper.UTF8_ZIP_ENCODING : this.zipEncoding;
   ze.setGeneralPurposeBit(gpFlag);
   off += 2;
   ze.setMethod(ZipShort.getValue(this.CFH_BUF, off));
   off += 2;
   final long time = ZipUtil.dosToJavaTime(ZipLong.getValue(this.CFH_BUF, off));
   ze.setTime(time);
   off += 4;
   ze.setCrc(ZipLong.getValue(this.CFH_BUF, off));
   off += 4;
   ze.setCompressedSize(ZipLong.getValue(this.CFH_BUF, off));
   off += 4;
   ze.setSize(ZipLong.getValue(this.CFH_BUF, off));
   off += 4;
   final int fileNameLen = ZipShort.getValue(this.CFH_BUF, off);
   off += 2;
   final int extraLen = ZipShort.getValue(this.CFH_BUF, off);
   off += 2;
   final int commentLen = ZipShort.getValue(this.CFH_BUF, off);
   off += 2;
   final int diskStart = ZipShort.getValue(this.CFH_BUF, off);
   off += 2;
   ze.setInternalAttributes(ZipShort.getValue(this.CFH_BUF, off));
   off += 2;
   ze.setExternalAttributes(ZipLong.getValue(this.CFH_BUF, off));
   off += 4;
   final byte[] fileName = new byte[fileNameLen];
   this.archive.readFully(fileName);
   ze.setName(entryEncoding.decode(fileName), fileName);
   offset.headerOffset = ZipLong.getValue(this.CFH_BUF, off);
   this.entries.add(ze);
   final byte[] cdExtraData = new byte[extraLen];
   this.archive.readFully(cdExtraData);
   ze.setCentralDirectoryExtra(cdExtraData);
   this.setSizesAndOffsetFromZip64Extra(ze, offset, diskStart);
   final byte[] comment = new byte[commentLen];
   this.archive.readFully(comment);
   ze.setComment(entryEncoding.decode(comment));
   if (!hasUTF8Flag && this.useUnicodeExtraFields) {
     noUTF8Flag.put(ze, new NameAndComment(fileName, comment));
   }
 }
Esempio n. 2
0
  /**
   * Updates the entry based on the field that is specified. Mainly created for use by the bulk
   * import auto update
   *
   * @param entry entry to be updated
   * @param plasmid should be set if updating strain with plasmid
   * @param value value to be set
   * @param field to set
   * @return updated entry array containing both entry and plasmid. if plasmid is null only entry is
   *     returned
   */
  public static Entry[] infoToEntryForField(
      Entry entry, Entry plasmid, String value, EntryField field) {
    switch (field) {
      case PI:
        {
          entry.setPrincipalInvestigator(value);
          if (plasmid != null) plasmid.setPrincipalInvestigator(value);
          break;
        }

      case PI_EMAIL:
        {
          entry.setPrincipalInvestigatorEmail(value);
          break;
        }

      case FUNDING_SOURCE:
        {
          entry.setFundingSource(value);
          if (plasmid != null) plasmid.setFundingSource(value);
          break;
        }

      case IP:
        entry.setIntellectualProperty(value);
        if (plasmid != null) plasmid.setIntellectualProperty(value);
        break;

      case BIO_SAFETY_LEVEL:
        Integer level = BioSafetyOption.intValue(value);
        if (level == null) {
          if (value.contains("1")) level = 1;
          else if (value.contains("2")) level = 2;
          else break;
        }
        entry.setBioSafetyLevel(level);
        if (plasmid != null) {
          plasmid.setBioSafetyLevel(level);
        }
        break;

      case NAME:
        entry.setName(value);
        break;

      case ALIAS:
        entry.setAlias(value);
        break;

      case KEYWORDS:
        entry.setKeywords(value);
        break;

      case SUMMARY:
        entry.setShortDescription(value);
        break;

      case NOTES:
        entry.setLongDescription(value);
        break;

      case REFERENCES:
        entry.setReferences(value);
        break;

      case LINKS:
        HashSet<Link> links = new HashSet<>();
        Link link = new Link();
        link.setLink(value);
        link.setEntry(entry);
        links.add(link);
        entry.setLinks(links);
        break;

      case STATUS:
        entry.setStatus(value);
        if (plasmid != null) plasmid.setStatus(value);
        break;

      case SELECTION_MARKERS:
        HashSet<SelectionMarker> markers = new HashSet<>();
        SelectionMarker marker = new SelectionMarker(value, entry);
        markers.add(marker);
        entry.setSelectionMarkers(markers);
        break;

      case PARENTAL_STRAIN:
      case GENOTYPE_OR_PHENOTYPE:
      case PLASMIDS:
        entry = infoToStrainForField(entry, value, field);
        break;

      case BACKBONE:
      case ORIGIN_OF_REPLICATION:
      case CIRCULAR:
      case PROMOTERS:
      case REPLICATES_IN:
        entry = infoToPlasmidForField(entry, value, field);
        break;

      case HOMOZYGOSITY:
      case ECOTYPE:
      case HARVEST_DATE:
      case GENERATION:
      case SENT_TO_ABRC:
      case PLANT_TYPE:
      case PARENTS:
        entry = infoToSeedForField(entry, value, field);
        break;
      default:
        break;
    }
    if (plasmid == null) return new Entry[] {entry};

    return new Entry[] {entry, plasmid};
  }
Esempio n. 3
0
  private static Entry setCommon(Entry entry, PartData info) {
    if (entry == null || info == null) return null;

    if (info.getName() != null) entry.setName(info.getName());

    if (info.getSelectionMarkers() != null) {
      Set<SelectionMarker> markers = getSelectionMarkers(info.getSelectionMarkers(), entry);
      entry.setSelectionMarkers(markers);
    }

    if (info.getReferences() != null) entry.setReferences(info.getReferences());

    if (StringUtils.isBlank(entry.getPartNumber())) entry.setPartNumber(info.getPartId());

    Date currentTime = new Date();
    if (entry.getCreationTime() == null) entry.setCreationTime(currentTime);

    entry.setModificationTime(currentTime);

    if (info.getOwnerEmail() != null) {
      entry.setOwnerEmail(info.getOwnerEmail());
    }

    if (info.getOwner() != null) entry.setOwner(info.getOwner());

    if (info.getCreatorEmail() != null) {
      entry.setCreatorEmail(info.getCreatorEmail());
    }

    if (info.getCreator() != null) entry.setCreator(info.getCreator());

    if (info.getStatus() == null) {
      if (StringUtils.isBlank(entry.getStatus())) entry.setStatus("");
    } else entry.setStatus(info.getStatus());

    if (info.getAlias() != null) entry.setAlias(info.getAlias());

    if (info.getBioSafetyLevel() == null) {
      if (entry.getBioSafetyLevel() == null) entry.setBioSafetyLevel(0);
    } else entry.setBioSafetyLevel(info.getBioSafetyLevel());

    if (info.getShortDescription() != null) entry.setShortDescription(info.getShortDescription());
    if (info.getLongDescription() != null) entry.setLongDescription(info.getLongDescription());
    if (info.getIntellectualProperty() != null)
      entry.setIntellectualProperty(info.getIntellectualProperty());

    Set<Link> links = getLinks(info.getLinks(), entry);
    entry.setLinks(links);

    Visibility visibility = info.getVisibility();
    if (visibility != null) entry.setVisibility(visibility.getValue());

    // checking for null instead of blank since it could be cleared
    if (info.getFundingSource() != null) entry.setFundingSource(info.getFundingSource());
    if (info.getPrincipalInvestigator() != null)
      entry.setPrincipalInvestigator(info.getPrincipalInvestigator());
    if (info.getPrincipalInvestigatorEmail() != null)
      entry.setPrincipalInvestigatorEmail(info.getPrincipalInvestigatorEmail());

    if (info.getKeywords() != null) entry.setKeywords(info.getKeywords());

    // parameters
    List<Parameter> parameters = getParameters(info.getCustomFields(), entry);
    entry.setParameters(parameters);
    return entry;
  }