def testReadMapHeaderPygal(self): """ Test read map header -- export JSON packet and plot density distribution - """ 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.__testMapNormal) of = self.__testMapNormal + "_map-header-data_P1.json" dp.imp(inpPath) dp.op("annot-read-map-header") dp.expLog("annot-read-map-header.log") dp.exp(of) dp.cleanup() # mD = json.load(open(of, 'r')) logger.info("Map header keys: %r\n" % mD.keys()) logger.info("Map header: %r\n" % mD.items()) logger.info("Input header keys: %r\n" % mD['input_header'].keys()) logger.info("Output header keys: %r\n" % mD['output_header'].keys()) # x = mD['input_histogram_categories'] y = mD['input_histogram_values'] logy = [] for v in y: if float(v) <= 0.0: logy.append(math.log10(.1)) else: logy.append(math.log10(float(v))) # width = float(x[-1] - x[0]) / float(len(x)) #width = 2.0 logger.info("Starting plot len x %d len y %d \n" % (len(x), len(logy))) nL = int(len(x) / 10) # if False: bar_chart = pygal.Bar(x_label_rotation=20, show_minor_x_labels=False, style=LightColorizedStyle) bar_chart = pygal.Bar(x_label_rotation=20, show_minor_x_labels=False, style=LightGreenStyle) bar_chart.title = 'Map density distribution' bar_chart.x_labels = map(str, [int(t) for t in x]) bar_chart.x_labels_major = map(str, [int(t) for t in x[::nL]]) bar_chart.add('Voxels (log(10)', logy) plotFileName = "map-density-plot-pygal.svg" bar_chart.render_to_file(plotFileName) except Exception as e: logger.exception("Failing with %s" % str(e)) self.fail()
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 read_mtz_sf(self, pathin): """Reads MTZ structure factor file Return True on success, otherwise False """ logger.debug("Starting mtz read %s" % pathin) suffix = '-dir' prefix = 'rcsb-' if self.__tmppath is not None and os.path.isdir(self.__tmppath): workpath = tempfile.mkdtemp(suffix, prefix, self.__tmppath) else: workpath = tempfile.mkdtemp(suffix, prefix) diagfn = os.path.join(workpath, "sf-convert-diags.cif") ciffn = os.path.join(workpath, "sf-convert-datafile.cif") dmpfn = os.path.join(workpath, "sf-convert-mtzdmp.log") logfn = os.path.join(workpath, "sf-convert.log") dp = RcsbDpUtility(siteId=self.__siteid, tmpPath=self.__tmppath) dp.imp(pathin) dp.op('annot-sf-convert') dp.expLog(logfn) dp.expList(dstPathList=[ciffn, diagfn, dmpfn]) if os.path.exists(ciffn): ret = self.read_mmcif_sf(ciffn) else: ret = False if self.__cleanup: dp.cleanup() shutil.rmtree(workpath, ignore_errors=True) return ret
def rcsb2Pdbx(self, inpPath, outPath, stripFlag=False, stripEntityFlag=False): """ RCSB CIF -> PDBx conversion (Using the smaller application in the annotation package) """ try: dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh) dp.imp(inpPath) if stripFlag: if stripEntityFlag: dp.op("annot-rcsb2pdbx-strip-plus-entity") else: dp.op("annot-rcsb2pdbx-strip") else: dp.op("annot-rcsb2pdbx") logPath = os.path.join(self.__sessionPath, "annot-rcsb2pdbx.log") dp.expLog(logPath) dp.exp(outPath) if (not self.__debug): dp.cleanup() except: traceback.print_exc(file=self.__lfh) return False # return True
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 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 rcsbEps2Pdbx(self, inpPath, outPath, stripFlag=False, stripEntityFlag=False): """ RCSB CIFEPS -> PDBx conversion (This still requires using the full maxit application) """ try: dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh) dp.imp(inpPath) if stripFlag: if stripEntityFlag: dp.op("annot-rcsbeps2pdbx-strip-plus-entity") else: dp.op("annot-rcsbeps2pdbx-strip") else: dp.op("annot-cif2cif") logPath = os.path.join(self.__sessionPath, "annot-rcsbeps2pdbx.log") dp.expLog(logPath) dp.exp(outPath) if (not self.__debug): dp.cleanup() except: traceback.print_exc(file=self.__lfh) return False # return True
def __getLoadFile(self, sessionPath, listfile, sqlfile, logfile): fn = os.path.join(self.__sessionPath, listfile) mapping = self.__cIcommon.get_site_da_internal_schema_path() self.__lfh.write( "DbLoadUtil::__getLoadFile(): listfile %s sqlfile %s logfile %s\n" % (fn, sqlfile, logfile)) try: dp = RcsbDpUtility(tmpPath=sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh) dp.setDebugMode() dp.imp(fn) dp.addInput(name="mapping_file", value=mapping, type="file") dp.addInput(name="file_list", value=True) # This code handles model files dp.addInput(name="first_block", value=True) dp.op("db-loader") dp.expLog(logfile) dp.exp(sqlfile) dp.cleanup() return except: # noqa: E722 pylint: disable=bare-except self.__lfh.write( "DbLoadUtil::__getLoadFile(): failing, with exception.\n") traceback.print_exc(file=self.__lfh)
def testAnnotValidateListNmrTest(self): """ Test create validation report for the test list of example PDB ids (NMR examples) """ logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: count = 0 for pdbId in self.__testValidateNmrIdList: 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" 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") # adding explicit selection of steps -- # Alternate if count % 2 == 0: dp.addInput(name="step_list", value=" coreclust,chemicalshifts,writexml,writepdf ") count += 1 dp.imp(xyzPath) dp.addInput(name="cs_file_path", value=csPath) 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 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 testFixSpecialPosition(self): """ Test for fixing atoms on special position """ 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.__testFileValidateXyz) dp.imp(inpPath) dp.op("annot-dcc-fix-special-position") dp.expLog("special-position-fix.log") dp.exp("special-position-output-fix.log") # No output - none on special self.assertEqual(['missing'], dp.getResultPathList()) f = open('special-position-output-fix.log', 'r') lines = f.read() f.close() self.assertIn('No atoms sit on special position', lines) dp.cleanup() except Exception as e: logger.exception("Failing with %s" % str(e)) self.fail() # This case has atoms on special position that needs correction try: dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True) # # dp.setDebugMode(True) # inpPath = os.path.join(self.__testFilePath, self.__testSpecialPosition) dp.imp(inpPath) dp.op("annot-dcc-fix-special-position") dp.expLog("special-position-fix2.log") dp.exp("special-position-output-fix2.log") print(dp.getResultPathList()) # We expect output self.assertNotEqual(['missing'], dp.getResultPathList()) dp.expList(dstPathList=['special-position-out-fix2.cif']) # Check output - for differences... f = open('special-position-output-fix2.log', 'r') lines = f.read() f.close() self.assertIn('Error: Wrong occupancy of 1.00 for atom (O : id=D_HOH_1)', lines) dp.cleanup() except Exception as e: logger.exception("Failing with %s" % str(e)) self.fail()
def testSpecialPosition(self): """Test for atom on special position""" logger.info("\nStarting") try: dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True) # # dp.setDebugMode(True) # inpPath = os.path.join(self.__testFilePath, self.__testFileValidateXyz) dp.imp(inpPath) dp.op("annot-dcc-special-position") dp.expLog("special-position.log") dp.exp("special-position-output.log") f = open("special-position-output.log", "r") lines = f.read() f.close() self.assertIn("No atoms sit on special position", lines) dp.cleanup() except Exception as e: logger.exception("Failing with %s", str(e)) self.fail() # This case has atoms on special position that needs correction try: dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True) # # dp.setDebugMode(True) # inpPath = os.path.join(self.__testFilePath, self.__testSpecialPosition) dp.imp(inpPath) dp.op("annot-dcc-special-position") dp.expLog("special-position2.log") dp.exp("special-position-output2.log") f = open("special-position-output2.log", "r") lines = f.read() f.close() self.assertIn( "Error: Wrong occupancy of 1.00 for atom (O : id=D_HOH_1)", lines) dp.cleanup() except Exception as e: logger.exception("Failing with %s", str(e)) self.fail()
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 cif2Pdbx(self, inpPath, outPath): """CIF -> PDBx conversion (public subset with PDBid conversion)""" try: dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh) dp.imp(inpPath) dp.op("cif2pdbx-public") logPath = os.path.join(self.__sessionPath, "annot-cif2pdbx.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 testAnnotSecondaryStructure(self): """ Calculate secondary structure for a complicated case where pro-motif will fail. """ logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: of = "annot-ss-" + self.__testFileAnnotSS + ".gz" dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True) inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotSS) dp.imp(inpPath) dp.op("annot-secondary-structure") dp.expLog("annot-secondary-structure.log") dp.exp(of) dp.cleanup() except Exception as e: logger.exception("Failing with %s" % str(e)) self.fail()
def rcsb2PdbxWithPdbId(self, inpPath, outPath): """RCSB CIF -> PDBx conversion (converting to PDB ID entry/datablock id.)""" try: dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh) dp.imp(inpPath) dp.op("annot-rcsb2pdbx-withpdbid") logPath = os.path.join(self.__sessionPath, "annot-rcsb2pdbx.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 testAnnotValidation(self): """ Calculate geometrical validation - """ logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: of = "annot-validation-" + self.__testFileAnnotValidate + ".gz" dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True) inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotValidate) dp.imp(inpPath) dp.op("annot-validation") dp.expLog("annot-validation.log") dp.exp(of) dp.cleanup() except Exception as e: logger.exception("Failing with %s" % str(e)) self.fail()
def testAnnotLinkSSBond(self): """ Calculate link and ss-bond features - """ logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: of = "annot-link-" + self.__testFileAnnotLink + ".gz" dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True) inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotLink) dp.imp(inpPath) dp.op("annot-link-ssbond") dp.expLog("annot-link-ssbond.log") dp.exp(of) dp.cleanup() except Exception as e: logger.exception("Failing with %s" % str(e)) self.fail()
def convert_em_volume(self, in_em_volume, out_binary_volume, working_dir): logging.info("Converting EM maps to binary cif") logging.debug(working_dir) rdb = RcsbDpUtility(tmpPath=working_dir, siteId=self.__site_id, verbose=True) rdb.imp(in_em_volume) rdb.op("em-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 testAnnotRepositionSolventPlusDerived(self): """ Calculate distant solvent followed by computing key derived categories -- """ logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: of = "annot-reposition-add-derived-" + self.__testFileAnnotSolvent dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True) inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotSolvent) dp.imp(inpPath) dp.op("annot-reposition-solvent-add-derived") dp.expLog("annot-reposition-solvent-plus-derived.log") dp.exp(of) 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 cif2Pdb(self, inpPath, outPath): """CIF -> PDB conversion (Using the smaller application in the annotation package)""" try: dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh) dp.imp(inpPath) dp.op("annot-cif2pdb") logPath = os.path.join(self.__sessionPath, "annot-cif2pdb.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 testAnnotRcsb2PdbxStrip(self): """ RCSB CIF -> PDBx conversion (Using the smaller application in the annotation package) """ logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: of = "annot-rcsb2pdbx-strip-" + self.__testFileAnnotRcsb dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True) inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotRcsb) dp.imp(inpPath) dp.op("annot-rcsb2pdbx-strip") dp.expLog("annot-rcsb2pdbx-strip.log") dp.exp(of) dp.cleanup() except Exception as e: logger.exception("Failing with %s" % str(e)) self.fail()
def testAnnotBasePair(self): """Calculate base pairing""" logger.info("\nStarting") try: of = "annot-base-pair-" + self.__testFileAnnotNA + ".gz" dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True) inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotNA) dp.imp(inpPath) dp.op("annot-base-pair-info") dp.expLog("annot-base-pair.log") dp.exp(of) dp.cleanup() except Exception as e: logger.exception("Failing with %s", str(e)) self.fail()
def testAnnotUpdateDepositorAssembly(self): """ Update deposition provided assembly info into model (need better test example) """ logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name)) try: of = "annot-update-assembly-" + self.__testDepAssembly dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True) inpPath = os.path.join(self.__testFilePath, self.__testDepAssembly) dp.imp(inpPath) dp.op("annot-update-dep-assembly-info") dp.expLog("annot-update-dep-assembly.log") dp.exp(of) dp.cleanup() except Exception as e: logger.exception("Failing with %s" % str(e)) self.fail()
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 testAnnotRepositionSolvent(self): """Calculate distant solvent""" logger.info("\nStarting") try: of = "annot-reposition-" + self.__testFileAnnotSolvent dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True) inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotSolvent) dp.imp(inpPath) dp.op("annot-reposition-solvent") dp.expLog("annot-reposition-solvent.log") dp.exp(of) dp.cleanup() except Exception as e: logger.exception("Failing with %s", str(e)) self.fail()
def testAnnotCisPeptide(self): """Calculate cis-peptide linkages -""" logger.info("\nStarting") try: of = "annot-link-" + self.__testFileAnnotCisPeptide + ".gz" dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True) inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotCisPeptide) dp.imp(inpPath) dp.op("annot-cis-peptide") dp.expLog("annot-cis-peptide.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 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()