def processBmrbNmrGridArchiveLink(urlLocation, saveDir, homeDir,
finalFileName):
data = getDataFromHttp(urlLocation)
zipFileName = 'file.zip'
zipFile = os.path.join(saveDir, zipFileName)
zipOut = open(zipFile, 'w')
zipOut.write(data)
zipOut.close()
os.chdir(saveDir)
os.spawnlp(os.P_WAIT, 'nice', 'nice', '-19', 'unzip', zipFileName)
os.chdir(homeDir)
os.remove(zipFile)
removeFiles = ['readme.html', 'main.css', 'index.csv']
for removeFile in removeFiles:
removeFilePath = os.path.join(saveDir, removeFile)
if os.path.exists(removeFilePath):
os.remove(removeFilePath)
files = os.listdir(saveDir)
for fileName in files:
if fileName[:5] == 'block' and fileName[-4:] == '.str':
os.rename(os.path.join(saveDir, fileName),
os.path.join(saveDir, finalFileName))
def getBmrbNmrGridJointCoordinateFile(pdbCode, forceGet=False):
"""
Get NMR restraints grid NMR-STAR file joined with coordinate info from mmCIF file
"""
pdbDir = os.path.join(nmrGridDataDir, pdbCode)
if not os.path.exists(pdbDir):
os.mkdir(pdbDir)
nmrStarFile = "joinedCoord.str.gz"
if not os.path.exists(os.path.join(pdbDir, nmrStarFile)) or forceGet:
origDir = os.getcwd()
# Location zipped file
urlLocation = "%s/%s/%s" % (bmrbJoinedCoordUrl, pdbCode, nmrStarFile)
data = getDataFromHttp(urlLocation)
localFile = os.path.join(pdbDir, nmrStarFile)
localOut = open(localFile, 'w')
localOut.write(data)
localOut.close()
Popen(['gunzip', '-f', localFile])
os.chdir(origDir)
return True
def getCasdNmrProjects(saveDataDir=None, forceWrite=False):
projectInfo = getCasdNmrProjectInfo()
# Get the files
if not saveDataDir:
saveDataDir = casdNmrDataDir
for (projectName, dataFile, pdbCodes) in projectInfo:
if dataFile[0] == '/':
dataUrl = os.path.join(eNmrUrl, dataFile[1:])
else:
dataUrl = dataFile
(path, fileName) = os.path.split(dataFile)
localDataFilePath = os.path.join(saveDataDir, fileName)
if forceWrite or not os.path.exists(localDataFilePath):
print " Downloading CASD-NMR project %s..." % fileName
dataLines = getDataFromHttp(dataUrl)
if os.path.exists(localDataFilePath):
os.remove(localDataFilePath)
fout = open(localDataFilePath, 'w')
fout.write(dataLines)
fout.close()
def updateFiles(self):
self.getPickleFile("nrgCingPdbCodes")
newNrgCingPdbCodes = getCingCcpnTgzFileList()
pdbCodes = newNrgCingPdbCodes.keys()
pdbCodes.sort()
for pdbCode in pdbCodes:
print pdbCode
downloadTgz = False
(date,pdbCodeDirectory,downloadUrl) = newNrgCingPdbCodes[pdbCode]
if not self.nrgCingPdbCodes.has_key(pdbCode):
downloadTgz = True
elif self.nrgCingPdbCodes[pdbCode][0] != date:
# Date change...
print " Date change on NRG-CING file for %s..." % (pdbCode)
downloadTgz = True
#
# Create directories and check if file exists, also download if not (could be earlier script problem)
#
saveDir = os.path.join(self.archiveDir,pdbCodeDirectory)
if not os.path.exists(saveDir):
os.mkdir(saveDir)
savePath = os.path.join(saveDir,"%s.tgz" % pdbCode)
if not os.path.exists(savePath):
downloadTgz = True
#
# Now download and update
#
if downloadTgz:
print " Downloading..."
data = getDataFromHttp(downloadUrl)
if os.path.exists(savePath):
os.remove(savePath)
fout = open(savePath,'w')
fout.write(data)
fout.close()
# Update pickled information and save... bit slower this but safer
self.nrgCingPdbCodes[pdbCode] = newNrgCingPdbCodes[pdbCode]
self.createPickleFile("nrgCingPdbCodes")
def cingProjectDownload(self, outputDir):
#
# Put in CCPN project as default. Always usea time-stamped directory name.
#
if not outputDir:
outputDir = self.ccpnProject.findFirstRepository(
name='userData').url.path
outputDir = os.path.join(outputDir, 'cing',
self.getFileTimeString())
#
# Make sure output dir exists
#
if not os.path.exists(outputDir):
os.makedirs(outputDir)
#
# Get the CING project name - safer in case changed on server side
#
projectPage = self.cingRequest("ProjectName")
pyDict = eval(projectPage)
projectName = pyDict['Result']
#
# Now download the file - first wait a bit just in case
#
time.sleep(20)
cingZipFile = "%s_CING_report.zip" % projectName
cingZipFileHttp = os.path.join(self.cingDownload, self.userId,
self.accessKey, cingZipFile)
# Try to re-download if not found.
outputData = None
while (not outputData or outputData.count("Not Found")):
time.sleep(20)
outputData = getDataFromHttp(cingZipFileHttp)
#
# And write it out...
#
self.cingZipFileOut = joinPath(outputDir, cingZipFile)
fout = open(self.cingZipFileOut, 'w')
fout.write(outputData)
fout.close()
def getBmrbEntry(bmrbId, skipCodes=None, forceGet=False):
if skipCodes and bmrbId in skipCodes:
return False
bmrbFile = "%s.str" % bmrbId
newBmrbFile = os.path.join(bmrbArchiveDataDir, bmrbFile)
if not forceGet and os.path.exists(newBmrbFile):
return True
#
# Download
#
print "Downloading %s..." % bmrbFile
bmrbFileLink = '%s%s' % (bmrbArchiveUrlLocation, bmrbId)
data = getDataFromHttp(bmrbFileLink)
#
# Exit if no data
#
if not data:
print " Download failed!"
return False
#
# Write the new file
#
if not os.path.exists(bmrbArchiveDataDir):
os.mkdir(bmrbArchiveDataDir)
fout = open(os.path.join(newBmrbFile), 'w')
fout.write(data)
fout.close()
return True
def getBmrbNmrGridCompletenessInfo(pdbCode, forceWrite=False):
"""
Read info on completeness check for.a PDB entry at the BMRB...
"""
fileName = 'completeness.str'
pdbDir = os.path.join(nmrGridDataDir, pdbCode)
finalFileName = os.path.join(pdbDir, fileName)
if forceWrite or not os.path.exists(finalFileName):
finalFileName = None
if not finalFileName:
urlLocation = '%s?db_username=wattos1&format=distance&pdb_id=%s&request_type=block_set&subtype=completeness&type=check' % (
nmrGridServletUrl, pdbCode)
data = getDataFromHttp(urlLocation)
dataLines = data.split("\n")
for dataLine in dataLines:
if mrArchiveLinkPatt.search(dataLine):
mrLinkSearch = mrLinkPatt.search(dataLine)
if mrLinkSearch:
archiveLink = "%s?%s" % (nmrGridServletUrl,
mrLinkSearch.group(1))
if not os.path.exists(pdbDir):
os.mkdir(pdbDir)
processBmrbNmrGridArchiveLink(archiveLink, pdbDir,
nmrGridDataDir, fileName)
finalFileName = os.path.join(pdbDir, fileName)
break
else:
print " Error: no link for completeness data for %s!" % pdbCode
return finalFileName