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added _uploadBiomtFileOp() and copying PCM missing data csv file
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Ezra Peisach committed Aug 28, 2024
1 parent b775592 commit 6d19b37
Showing 1 changed file with 101 additions and 1 deletion.
102 changes: 101 additions & 1 deletion wwpdb/apps/ann_tasks_v2/webapp/CommonTasksWebAppWorker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,8 @@
# 13-Jan-2017 ep add _specialPositionUpdateOp
# 05-Oct-2017 zf add _loadEntityInfoOp(), _loadSymopInfoOp()
# 12-Feb-2018 ep add reqacctypes to data returned from _entryInfoOp()
# 09-Aug-2024 zf add _uploadBiomtFileOp()
# 26-Aug-2024 zf add copying PCM missing data csv file
##
"""
Common annotation tasks.
Expand Down Expand Up @@ -135,6 +137,7 @@
from wwpdb.apps.ann_tasks_v2.transformCoord.TransformCoord import TransformCoord
from wwpdb.apps.ann_tasks_v2.utils.MergeXyz import MergeXyz
from wwpdb.apps.ann_tasks_v2.utils.PdbFile import PdbFile
from wwpdb.apps.ann_tasks_v2.utils.PointSuite import PointSuite
from wwpdb.apps.ann_tasks_v2.utils.SessionDownloadUtils import SessionDownloadUtils
from wwpdb.apps.ann_tasks_v2.utils.TaskSessionState import TaskSessionState

Expand Down Expand Up @@ -1659,15 +1662,19 @@ def _importFromWF(self, identifier, fileSource="wf-archive", instanceWf="", getM
#
pth = de.copyToSession(contentType="xml-check-report", formatType="txt", version="latest", partitionNumber=1)
#
# PCM missing data csv file
#
pth = de.copyToSession(contentType="pcm-missing-data", formatType="csv", version="latest", partitionNumber=1)
#
# Handle maps if input option is set --
#
if getMaps:
pth = de.copyToSession(contentType="map-2fofc", formatType="map", version="latest", partitionNumber=1)
pth = de.copyToSession(contentType="map-fofc", formatType="map", version="latest", partitionNumber=1)
pth = de.copyToSession(contentType="map-omit-2fofc", formatType="map", version="latest", partitionNumber=1)
pth = de.copyToSession(contentType="map-omit-fofc", formatType="map", version="latest", partitionNumber=1)
de.copyDirToSession(dirName="np-cc-maps")
de.copyDirToSession(dirName="np-cc-omit-maps")

#
# SF file
#
Expand Down Expand Up @@ -3721,6 +3728,99 @@ def _uploadFileOp(self):

return rC

def _uploadBiomtFileOp(self):
""" """
if self._verbose:
self._lfh.write("+CommonTasksWebAppWorker._uploadBiomtFileOp() starting\n")

self._getSession(useContext=True)
rC = ResponseContent(reqObj=self._reqObj, verbose=self._verbose, log=self._lfh)
rC.setReturnFormat("json")

wuu = WebUploadUtils(reqObj=self._reqObj, verbose=self._verbose, log=self._lfh)
if not wuu.isFileUpload():
rC.setError(errMsg="No file uploaded")
return rC
#
originalUploadFileName = wuu.getUploadFileName(fileTag="file")
#
entryId = self._reqObj.getValue("entryid")
entryFileName = self._reqObj.getValue("entryfilename")
#
sessionInputFilePath = os.path.join(self._sessionPath, entryId + "-biomt.txt")
importBiomtPath = os.path.join(self._sessionPath, "import.biomt")
importCifPath = os.path.join(self._sessionPath, "import.cif")
importMatrixPath = os.path.join(self._sessionPath, "import.matrix")
frameCifPath = os.path.join(self._sessionPath, "findframe.cif")
transmtCifPath = os.path.join(self._sessionPath, "makextrans.cif")
assemblyCifPath = os.path.join(self._sessionPath, "assembly.cif")
updatedModelCifPath = os.path.join(self._sessionPath, entryId + "-updated.cif")
importmatsLogPath = os.path.join(self._sessionPath, "importmats.log")
findframeLogPath = os.path.join(self._sessionPath, "findframe.log")
makeassemblyLogPath = os.path.join(self._sessionPath, "makeassembly.log")
mergeLogPath = os.path.join(self._sessionPath, "merge.log")
for filePath in ( sessionInputFilePath, importBiomtPath, importCifPath, importMatrixPath, frameCifPath, transmtCifPath, \
assemblyCifPath, updatedModelCifPath, importmatsLogPath, findframeLogPath, makeassemblyLogPath, mergeLogPath):
if os.access(filePath, os.F_OK):
os.remove(filePath)
#
#
uploadFileName = wuu.copyToSession(fileTag="file", sessionFileName=entryId + "-biomt.txt")
if (uploadFileName is not None) and (len(uploadFileName) > 0):
if os.access(sessionInputFilePath, os.R_OK):
pts = PointSuite(reqObj=self._reqObj, verbose=self._verbose, log=self._lfh)
pts.importMats(sessionInputFilePath, importmatsLogPath)
#
if os.access(importBiomtPath, os.R_OK):
pts.findFrame(os.path.join(self._sessionPath, entryFileName), importBiomtPath, findframeLogPath)
#
if os.access(frameCifPath, os.R_OK):
shutil.copyfile(frameCifPath, transmtCifPath)
#
if os.access(transmtCifPath, os.R_OK):
pts.makeAssembly(os.path.join(self._sessionPath, entryFileName), transmtCifPath, makeassemblyLogPath)
#
#
ifh = open(sessionInputFilePath, "r")
data = ifh.read()
ifh.close()
#
text = 'Uploaded "' + originalUploadFileName + '" file:\n' + data
#
for fileTup in ( ( "import.biomt", importBiomtPath ), ( "import.cif", importCifPath ), \
( "import.matrix", importMatrixPath ), ( "assembly.cif", assemblyCifPath ) ):
if not os.access(fileTup[1], os.R_OK):
continue
#
ifh = open(fileTup[1], "r")
data = ifh.read()
ifh.close()
#
text += '\n\n"' + fileTup[0] + '" file:\n' + data
#
rC.setText(text)
#
if os.access(assemblyCifPath, os.R_OK):
pts.mergeAssemblyInfo(os.path.join(self._sessionPath, entryFileName), assemblyCifPath, updatedModelCifPath, mergeLogPath)
if os.access(updatedModelCifPath, os.R_OK):
rC.set("model_url", os.path.join("/sessions", str(self._sessionId), entryId + "-updated.cif"))
molstarDisplayDict = self.__molstarDisplay(entryId)
if ("molStar-maps" in molstarDisplayDict) and molstarDisplayDict["molStar-maps"]:
rC.set("molstar_maps", molstarDisplayDict["molStar-maps"], asJson=True)
#
#
#
#rC.setError(errMsg="Uploading file failed")
return rC
else:
rC.setError(errMsg="Uploading file failed")
return rC
#
else:
rC.setError(errMsg="Uploading file failed")
return rC
#

def _launchFromIdcodeOp(self):
"""Standalone launch from Idcode input callback method --
Expand Down

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