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));
}
}
/**
* 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};
}
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;
}