def testChemicalShiftCoordinateCheck2Alt(self):
""" Test upload check of one CS file --- Using the wrong model to generate errors
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
dp.setDebugMode(flag=True)
inpPath = os.path.join(self.__testFilePath, self.__testConcatCS)
xyzPath = os.path.abspath(os.path.join(self.__testFilePath, self.__testFileNmrModelAlt))
outPath = "output-cs-file-concat-alt.cif"
chkPath = "cs-diag-atom-name-check-concat-alt.cif"
dp.imp(inpPath)
dp.addInput(name="coordinate_file_path", value=xyzPath)
dp.addInput(name="chemical_shifts_coord_check_file_path", value=chkPath)
dp.op("annot-chem-shifts-atom-name-check")
dp.expLog("annot-chem-shifts-atom-name-check-concat-alt.log")
dp.exp(outPath)
#
if os.access(chkPath, os.R_OK):
csr = PdbxChemShiftReport(inputPath=chkPath, verbose=self.__verbose, log=self.__lfh)
status = csr.getStatus()
logger.info("Status code: %s\n" % status)
warnings = csr.getWarnings()
logger.info("\n\nWarning count : %d\n %s\n" % (len(warnings), ('\n').join(warnings)))
#
errors = csr.getErrors()
logger.info("\n\nError count : %d\n %s\n" % (len(errors), ('\n').join(errors)))
#
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def mtz2Pdbx(self,
mtzFilePath,
outSfFilePath,
pdbxFilePath=None,
logFilePath=None,
diagsFilePath=None,
dumpFilePath=None,
timeout=120):
""" Convert input MTZ format to PDBx sf file.
"""
try:
diagfn = logFilePath if logFilePath is not None else "sf-convert-diags.cif"
dmpfn = dumpFilePath if dumpFilePath is not None else "sf-convert-mtzdmp.log"
#
dp = RcsbDpUtility(tmpPath=self.__sessionPath,
siteId=self.__siteId,
verbose=self.__verbose,
log=self.__lfh)
dp.imp(mtzFilePath)
dp.setTimeout(timeout)
if pdbxFilePath is not None:
dp.addInput(name="xyz_file_path", value=pdbxFilePath)
dp.op("annot-sf-convert")
dp.expLog(logFilePath)
dp.expList(dstPathList=[outSfFilePath, diagfn, dmpfn])
if (not self.__debug):
dp.cleanup()
return True
except:
self.__lfh.write(
"+DataFileAdapter.mtz2Pdbx() - failing for mtz file path %s output path %s\n"
% (mtzFilePath, outSfFilePath))
traceback.print_exc(file=self.__lfh)
return False
def testAnnotDccReport(self):
""" Test create DCC report -
"""
logger.info("\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
ofn = "dcc-report.cif"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
dp.setDebugMode()
xyzPath = os.path.join(self.__testFilePath,
self.__testFileValidateXyz)
sfPath = os.path.join(self.__testFilePath,
self.__testFileValidateSf)
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
dp.op("annot-dcc-report")
dp.expLog("dcc-report.log")
dp.exp(ofn)
# dp.expList(dstPathList=[ofpdf,ofxml])
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testPisaAssemblyDownloadModelPdb(self):
""" """
logger.info("\nStarting")
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
fPath = os.path.join(self.__testFilePath, self.__testFileCifPisa)
dp.imp(fPath)
dp.addInput(name="pisa_session_name", value="session_3re3_cif")
dp.op("pisa-analysis")
dp.expLog("pisa-anal-assembly-cif.log.gz")
dp.op("pisa-assembly-report-xml")
dp.exp("pisa-assembly-report-cif.xml")
dp.expLog("pisa-report-xml-cif.log.gz")
#
for assemId in ["1", "2", "3", "4", "5"]:
dp.addInput(name="pisa_assembly_id", value=assemId)
oFileName = "3rer-assembly-" + assemId + ".pdb.gz"
oLogName = "3rer-assembly-" + assemId + "-pdb.log.gz"
dp.op("pisa-assembly-coordinates-pdb")
dp.exp(oFileName)
dp.expLog(oLogName)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testChemicalShiftCoordinateCheck2(self):
"""Test upload check of one CS file --- Using a processed chemical shift file"""
logger.info("\nStarting")
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
dp.setDebugMode(flag=True)
inpPath = os.path.join(self.__testFilePath, self.__testConcatCS)
xyzPath = os.path.abspath(
os.path.join(self.__testFilePath, self.__testFileNmrModel))
outPath = "output-cs-file-concat.cif"
chkPath = "cs-diag-atom-name-check-concat.cif"
dp.imp(inpPath)
dp.addInput(name="coordinate_file_path", value=xyzPath)
dp.addInput(name="chemical_shifts_coord_check_file_path",
value=chkPath)
dp.op("annot-chem-shifts-atom-name-check")
dp.expLog("annot-chem-shifts-atom-name-check-concat.log")
dp.exp(outPath)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testAnnotSiteAndMerge(self):
"""Calculate site environment"""
logger.info("\nStarting")
try:
of = "annot-site-" + self.__testFileAnnotSite # +".gz"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
inpPath = os.path.join(self.__testFilePath,
self.__testFileAnnotSite)
dp.imp(inpPath)
dp.addInput(name="block_id", value=self.__testIdAnnotSite)
dp.op("annot-site")
dp.expLog("annot-site.log")
dp.exp(of)
inpPath = os.path.join(self.__testFilePath,
self.__testFileAnnotSite)
dp.imp(inpPath)
dp.addInput(name="site_info_file_path", value=of, type="file")
dp.op("annot-merge-struct-site")
dp.exp("annot-site-updated.cif.gz")
dp.expLog("annot-site-updated-cif.log.gz")
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def pdbx2Assemblies(self, idCode, inpFilePath, outPath=".", indexFilePath=None):
"""Create model assemby files from input PDBx model file."""
try:
pdbxPath = inpFilePath
logPath = os.path.join(self.__sessionPath, "pdbx-assembly.log")
# indexFilePath=os.path.join(self.__sessionPath,"pdbx-assembly-index.txt")
#
dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
dp.imp(pdbxPath)
if idCode is not None:
dp.addInput(name="deposition_data_set_id", value=idCode, type="param")
if indexFilePath is not None:
dp.addInput(name="index_file_path", value=indexFilePath, type="param")
dp.op("annot-gen-assem-pdbx")
dp.expLog(logPath)
pthList = dp.getResultPathList()
# wrkPath = dp.getWorkingDir()
for pth in pthList:
if os.access(pth, os.R_OK):
(_t, fn) = os.path.split(pth)
shutil.copyfile(pth, os.path.join(outPath, fn))
# if (not self.__debug):
# dp.cleanup()
#
if self.__verbose:
self.__lfh.write("+DataFileAdapter.pdbx2Assemblies() - input model file path: %s\n" % inpFilePath)
self.__lfh.write("+DataFileAdapter.pdbx2Assemblies() - assembly output paths: %r\n" % pthList)
return True
except: # noqa: E722 pylint: disable=bare-except
self.__lfh.write("+DataFileAdapter.pdbx2Assemblies() - failing for input file path %s output path %s\n" % (inpFilePath, outPath))
traceback.print_exc(file=self.__lfh)
return False
def testAnnotLigandMapCalc(self):
"""Test create density maps --"""
logger.info("\nStarting")
try:
for pdbId in ["3of4"]:
# of2fofc=pdbId+"_2fofc.map"
# offofc=pdbId+"_fofc.map"
testFileXyz = pdbId + ".cif"
testFileSf = pdbId + "-sf.cif"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
xyzPath = os.path.join(self.__testFilePath, testFileXyz)
sfPath = os.path.join(self.__testFilePath, testFileSf)
outMapPath = "."
outMapPathFull = os.path.abspath(outMapPath)
#
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
dp.addInput(name="output_map_file_path", value=outMapPathFull)
dp.op("annot-make-ligand-maps")
dp.expLog(pdbId + "-annot-make-ligand-maps.log")
# dp.expList(dstPathList=[of2fofc,offofc])
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testAnnotValidateListXrayTest(self):
"""Test create validation report for the test list of example PDB ids (NMR examples)"""
logger.info("\nStarting")
try:
for pdbId in self.__testValidateXrayIdList:
ofpdf = pdbId + "-valrpt.pdf"
ofxml = pdbId + "-valdata.xml"
offullpdf = pdbId + "-valrpt_full.pdf"
ofpng = pdbId + "-val-slider.png"
ofsvg = pdbId + "-val-slider.svg"
#
testFileValidateXyz = pdbId + ".cif"
testFileValidateSf = pdbId + "-sf.cif"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
# dp.setDebugMode(True)
xyzPath = os.path.abspath(
os.path.join(self.__testFilePath, testFileValidateXyz))
sfPath = os.path.abspath(
os.path.join(self.__testFilePath, testFileValidateSf))
# dp.addInput(name="request_annotation_context", value="yes")
dp.addInput(name="request_validation_mode", value="annotate")
# dp.addInput(name="request_validation_mode", value="server")
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
dp.op("annot-wwpdb-validate-all")
dp.expLog(pdbId + "-annot-validate-test.log")
dp.expList(dstPathList=[ofpdf, ofxml, offullpdf, ofpng, ofsvg])
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def test_AnnotMergeRemote(self):
""" Test of updating geometrical validation diagnostics -
"""
self.__lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
for pdbId in self.__testValidateXrayIdList:
self.__tmpPath = tempfile.mkdtemp(
dir=self.__siteWebAppsSessionsPath)
testFileValidateXyz = pdbId + ".cif"
xyzPath = os.path.abspath(
os.path.join(self.__testFilePath, testFileValidateXyz))
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
of = os.path.join(self.__tmpPath, "annot-merge-xyz-remote.cif")
dp.imp(xyzPath)
dp.addInput(name="new_coordinate_file_path", value=xyzPath)
dp.addInput(name="new_coordinate_format", value='cif')
# dp.setRunRemote()
ret = dp.op("annot-merge-xyz")
dp.expLog(
os.path.join(self.__tmpPath, "annot-merge-xyz-remote.log"))
dp.exp(of)
# dp.cleanup()
self.assertTrue(ret == 0)
self.assertTrue(os.path.exists(of))
def testPisaAssemblyDownloadModelPdb(self):
"""
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
fPath = os.path.join(self.__testFilePath, self.__testFileCifPisa)
dp.imp(fPath)
dp.addInput(name="pisa_session_name", value="session_3re3_cif")
dp.op("pisa-analysis")
dp.expLog("pisa-anal-assembly-cif.log.gz")
dp.op("pisa-assembly-report-xml")
dp.exp("pisa-assembly-report-cif.xml")
dp.expLog("pisa-report-xml-cif.log.gz")
#
for assemId in ['1', '2', '3', '4', '5']:
dp.addInput(name="pisa_assembly_id", value=assemId)
oFileName = '3rer-assembly-' + assemId + '.pdb.gz'
oLogName = '3rer-assembly-' + assemId + '-pdb.log.gz'
dp.op("pisa-assembly-coordinates-pdb")
dp.exp(oFileName)
dp.expLog(oLogName)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testAnnotOmitMapCalc(self):
""" Test create density maps --
"""
logger.info("\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
for pdbId in self.__testValidateIdList:
of2fofc = pdbId + "_map-omit-2fofc_P1.map"
offofc = pdbId + "_map-omit-fofc_P1.map"
testFileXyz = pdbId + ".cif"
testFileSf = pdbId + "-sf.cif"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
dp.setDebugMode()
xyzPath = os.path.join(self.__testFilePath, testFileXyz)
sfPath = os.path.join(self.__testFilePath, testFileSf)
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
dp.op("annot-make-maps")
dp.expLog(pdbId + "-annot-make-maps.log")
dp.expList(dstPathList=[of2fofc, offofc])
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testEm2EmSpider(self):
""" Test mapfix utility
"""
logger.info("\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
#
inpPath = os.path.join(self.__testFilePath, self.__testMapSpider)
of = self.__testMapSpider + "-spider-cnv.map"
dp.imp(inpPath)
pixelSize = 2.54
dp.addInput(name="pixel-spacing-x", value=pixelSize)
dp.addInput(name="pixel-spacing-y", value=pixelSize)
dp.addInput(name="pixel-spacing-z", value=pixelSize)
dp.op("em2em-spider")
dp.expLog("em2em-spider.log")
dp.exp(of)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testMapFixRemote(self):
""" Test mapfix utility
"""
self.__lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
#
inpPath = os.path.join(self.__testFilePath, self.__testMapNormal)
of = os.path.join(self.__tmpPath, self.__testMapNormal + "-fix.map")
dp.imp(inpPath)
pixelSize = 2.54
#dp.addInput(name="pixel-spacing-x", value=pixelSize)
#dp.addInput(name="pixel-spacing-y", value=pixelSize)
#dp.addInput(name="pixel-spacing-z", value=pixelSize)
dp.addInput(name="input_map_file_path", value=inpPath)
dp.addInput(name="output_map_file_path", value=of)
dp.addInput(name="label", value='test')
dp.addInput(name="voxel", value='{0} {0} {0}'.format(pixelSize))
# dp.setRunRemote()
ret = dp.op("deposit-update-map-header-in-place")
dp.expLog(os.path.join(self.__tmpPath, "mapfix-big.log"))
dp.exp(of)
# dp.cleanup()
self.assertTrue(ret == 0)
self.assertTrue(os.path.exists(of))
def testPisaAnalysisCif(self):
"""
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
cifPath = os.path.join(self.__testFilePath, self.__testFileCifPisa)
dp.imp(cifPath)
dp.addInput(name="pisa_session_name", value="session_test_cif")
dp.op("pisa-analysis")
dp.expLog("pisa-anal-cif.log.gz")
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testCifCheckExt(self):
""" """
logger.info("\nStarting")
try:
for name in ["deposit", "archive_current", "archive_next"]:
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
cifPath = os.path.join(self.__testFilePath, self.__testFileCif)
dp.imp(cifPath)
dp.addInput(name="dictionary", value=name)
dp.op("check-cif-ext")
dp.exp("check-cif-diags-%s.txt" % name)
dp.expLog("check-cif-%s.log" % name)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testPisaAnalysisPdb(self):
""" """
logger.info("\nStarting")
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
pdbPath = os.path.join(self.__testFilePath, self.__testFilePdbPisa)
dp.imp(pdbPath)
dp.addInput(name="pisa_session_name", value="session_3re3_pdb")
dp.op("pisa-analysis")
dp.expLog("pisa-anal-pdb.log.gz")
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def pdbx2nmrstar(self, inpPath, outPath, pdbId=None):
"""PDBx to NMRSTAR"""
try:
dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
dp.imp(inpPath)
if pdbId is not None:
dp.addInput(name="pdb_id", value=pdbId, type="param")
dp.op("annot-pdbx2nmrstar")
logPath = os.path.join(self.__sessionPath, "annot-pdbx2nmrstar.log")
dp.expLog(logPath)
dp.exp(outPath)
if not self.__debug:
dp.cleanup()
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
return False
#
return True
def testPisaAssemblyReportXmlPdb(self):
"""
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
fPath = os.path.join(self.__testFilePath, self.__testFilePdbPisa)
dp.imp(fPath)
dp.addInput(name="pisa_session_name", value="session_3re3_cif")
dp.op("pisa-analysis")
dp.expLog("pisa-anal-assembly-pdb.log.gz")
dp.op("pisa-assembly-report-xml")
dp.exp("pisa-assembly-report-pdb.xml")
dp.expLog("pisa-report-xml-pdb.log.gz")
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testAnnotSiteAlt(self):
""" Calculate site environment
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
of = "annot-site-" + self.__testIdAnnotSiteAlt + '.cif'
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotSiteAlt)
dp.imp(inpPath)
dp.addInput(name="block_id", value=self.__testIdAnnotSiteAlt)
dp.op("annot-site")
dp.expLog("annot-site.log")
dp.exp(of)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testAnnotSecondaryStructureWithTopology(self):
""" Calculate secondary structure with a supporting topology file.
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
of = "annot-ss-with-top-" + self.__testFileAnnotSS + ".gz"
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotSS)
dp.imp(inpPath)
topPath = os.path.abspath(os.path.join(self.__testFilePath, self.__testFileAnnotSSTop))
dp.addInput(name="ss_topology_file_path", value=topPath)
dp.op("annot-secondary-structure")
dp.expLog("annot-secondary-structure-w-top.log")
dp.exp(of)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testAnnotConsolidatedTasksWithTopology(self):
""" Calculate annotation tasks in a single step including supporting topology data.
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
of = "annot-consolidated-top-" + self.__testFileAnnotSS + ".gz"
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotSS)
dp.imp(inpPath)
topPath = os.path.abspath(os.path.join(self.__testFilePath, self.__testFileAnnotSSTop))
dp.addInput(name="ss_topology_file_path", value=topPath)
dp.op("annot-consolidated-tasks")
dp.expLog("annot-consolidated-w-top.log")
dp.exp(of)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testAnnotSiteRemote(self):
"""Calculate site environment"""
logger.debug("\nStarting")
of = os.path.join(self.__tmpPath,
"annot-site-" + self.__testFileAnnotSite)
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotSite)
dp.imp(inpPath)
dp.addInput(name="block_id", value=self.__testIdAnnotSite)
# dp.setRunRemote()
ret = dp.op("annot-site")
dp.expLog(os.path.join(self.__tmpPath, "annot-site.log"))
dp.exp(of)
# dp.cleanup()
self.assertTrue(ret == 0)
self.assertTrue(os.path.exists(of))
def testAnnotValidateListNmrTestRemote(self):
""" Test create validation report for the test list of example PDB ids (NMR examples)
"""
self.__lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
for pdbId in self.__testValidateNmrIdList:
self.__tmpPath = tempfile.mkdtemp(
dir=self.__siteWebAppsSessionsPath)
self.__lfh.write("\nStarting {} in {}\n".format(
pdbId, self.__tmpPath))
ofpdf = os.path.join(self.__tmpPath, pdbId + "-valrpt.pdf")
ofxml = os.path.join(self.__tmpPath, pdbId + "-valdata.xml")
offullpdf = os.path.join(self.__tmpPath,
pdbId + "-valrpt_full.pdf")
ofpng = os.path.join(self.__tmpPath, pdbId + "-val-slider.png")
ofsvg = os.path.join(self.__tmpPath, pdbId + "-val-slider.svg")
#
testFileValidateXyz = pdbId + ".cif"
testFileValidateCs = pdbId + "-cs.cif"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
xyzPath = os.path.abspath(
os.path.join(self.__testFilePath, testFileValidateXyz))
csPath = os.path.abspath(
os.path.join(self.__testFilePath, testFileValidateCs))
dp.addInput(name="request_annotation_context", value="yes")
dp.addInput(name='run_dir',
value=os.path.join(
self.__siteWebAppsSessionsPath,
"validation_%s" % random.randrange(9999999)))
# adding explicit selection of steps --
# Alternate
#dp.addInput(name="step_list", value=" coreclust,chemicalshifts,writexml,writepdf ")
dp.addInput(name='kind', value='nmr')
dp.imp(xyzPath)
dp.addInput(name="cs_file_path", value=csPath)
# dp.setRunRemote()
ret = dp.op("annot-wwpdb-validate-all")
dp.expLog(
os.path.join(self.__tmpPath,
pdbId + "-annot-validate-test.log"))
dp.expList(dstPathList=[ofpdf, ofxml, offullpdf, ofpng, ofsvg])
# dp.cleanup()
self.assertTrue(ret == 0)
self.assertTrue(os.path.exists(ofpdf))
self.assertTrue(os.path.exists(ofxml))
self.assertTrue(os.path.exists(offullpdf))
self.assertTrue(os.path.exists(ofpng))
self.assertTrue(os.path.exists(ofsvg))
def convert_xray_density_map(self, coord_file, in_2fofc_cif, in_fofc_cif,
out_binary_volume, working_dir):
logging.info("Converting X-ray maps to binary cif")
logging.debug(working_dir)
rdb = RcsbDpUtility(tmpPath=working_dir,
siteId=self.__site_id,
verbose=True)
rdb.imp(coord_file)
rdb.addInput(name="two_fofc_cif", value=in_2fofc_cif, type="file")
rdb.addInput(name="one_fofc_cif", value=in_fofc_cif, type="file")
rdb.op("xray-density-bcif")
rdb.exp(out_binary_volume)
rdb.cleanup()
if out_binary_volume:
if os.path.exists(out_binary_volume):
return True
return False
def __generateLoadDb(self, tmpPath, filePath, sql_file, logFile):
try:
dp = RcsbDpUtility(tmpPath=tmpPath,
siteId=self.__siteId,
verbose=self.__verbose,
log=self.__lfh)
dp.imp(filePath)
dp.addInput(name="mapping_file", value=self.__mapping, type="file")
# This code handles model files - first block
dp.addInput(name="first_block", value=True)
dp.op("db-loader")
dp.expLog(logFile)
dp.exp(sql_file)
dp.cleanup()
return
except: # noqa: E722 pylint: disable=bare-except
self.__lfh.write(
"DbLoadingApi::__generateLoadDb(): failing, with exception.\n")
traceback.print_exc(file=self.__lfh)
def testAnnotDccRsrReport(self):
""" Test create DCC report -
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
ofn = "dcc-rsr-report.cif"
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
xyzPath = os.path.join(self.__testFilePath, self.__testDccModelId + '.cif')
sfPath = os.path.join(self.__testFilePath, self.__testDccModelId + '-sf.cif')
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
dp.addInput(name="dcc_arguments", value=" -rsr -refmac ")
dp.op("annot-dcc-report")
dp.expLog("dcc-rsr-report.log")
dp.exp(ofn)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testAnnotPrdSearch(self):
""" Test case for PRD Search --
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
ofn = "prd-search-result.cif"
firstModelPath = os.path.abspath('firstmodel.cif')
logFilePath = os.path.abspath("prd-search-log.log")
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testFilePrdSearch)
dp.imp(inpPath)
dp.addInput(name='firstmodel', value=firstModelPath)
dp.addInput(name='logfile', value=logFilePath)
dp.op("prd-search")
dp.expLog("prd-search-execution.log")
dp.exp(ofn)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testCif2PdbxExt(self):
"""
"""
logger.info("\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
for name in ['archive_next', 'archive_current']:
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
cifPath = os.path.join(self.__testFilePath, self.__testFileCif)
dp.imp(cifPath)
dp.addInput(name='destination', value=name)
dp.op("cif2pdbx-ext")
dp.exp("cif2pdbx-ext-%s.cif" % name)
dp.expLog("cif2pdbx-%s.log" % name)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testPisaAssemblyMergeModelCif(self):
"""
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
fPath = os.path.join(self.__testFilePath, self.__testFileCifPisa)
assignPath = os.path.join(self.__testFilePath, "3rer_assembly_assign_P1.cif")
dp.imp(fPath)
dp.addInput(name="pisa_session_name", value="session_3re3-cif")
dp.op("pisa-analysis")
dp.op("pisa-assembly-report-xml")
dp.exp("pisa-assembly-report-cif.xml")
#
cifPath = os.path.join(self.__testFilePath, self.__testFileCifPisa)
dp.imp(cifPath)
#
# assignmentFile = self.__inputParamDict['pisa_assembly_assignment_file_path']
#
dp.addInput(name="pisa_assembly_file_path", value="pisa-assembly-report-cif.xml", type="file")
dp.addInput(name="pisa_assembly_assignment_file_path", value=assignPath, type="file")
dp.op("pisa-assembly-merge-cif")
dp.exp("3rer-updated.cif.gz")
dp.expLog("3rer-updated-cif.log.gz")
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
