diff --git a/tox.ini b/tox.ini index a1e3156..e8ddd42 100644 --- a/tox.ini +++ b/tox.ini @@ -47,9 +47,6 @@ minversion = 3.4.0 skip_missing_interpreters = true skipsdist = false -[pytest] -python_files = "*PyTest.py" - [testenv] passenv = CONFIG_SUPPORT_TOKEN_ENV,OE_LICENSE allowlist_externals = echo @@ -80,7 +77,6 @@ commands = {envpython} -m unittest discover -v --start-directory {[local_settings]test_path_2} --pattern "{[local_settings]test_pattern}" {envpython} -m unittest discover -v --start-directory {[local_settings]test_path_3} --pattern "{[local_settings]test_pattern}" {envpython} -m unittest discover -v --start-directory {[local_settings]test_path_4} --pattern "{[local_settings]test_pattern}" - {envpython} -m pytest -v {[local_settings]test_path_1} --tb=short echo "Completed {envname}" # diff --git a/wwpdb/apps/ann_tasks_v2/pcm/PcmCCDEditorForm.py b/wwpdb/apps/ann_tasks_v2/pcm/PcmCCDEditorForm.py index ba40a6c..866de5b 100644 --- a/wwpdb/apps/ann_tasks_v2/pcm/PcmCCDEditorForm.py +++ b/wwpdb/apps/ann_tasks_v2/pcm/PcmCCDEditorForm.py @@ -12,6 +12,7 @@ from wwpdb.utils.dp.RcsbDpUtility import RcsbDpUtility from wwpdb.io.locator.PathInfo import PathInfo + class PcmCCDEditorForm(object): """ The CoordEditorForm class generates coordinate editor form. diff --git a/wwpdb/apps/ann_tasks_v2/utils/GetCovalentBond.py b/wwpdb/apps/ann_tasks_v2/utils/GetCovalentBond.py index 62853e0..b78db0b 100644 --- a/wwpdb/apps/ann_tasks_v2/utils/GetCovalentBond.py +++ b/wwpdb/apps/ann_tasks_v2/utils/GetCovalentBond.py @@ -127,20 +127,20 @@ def __processCloseContactContent(self, jsonObj): atom += "(" + tupL[5] + ")" # tablerow += "" + tupL[16] + "" + tupL[0] + "" + tupL[1] + "" + tupL[2] + tupL[3] + "" \ - + atom + "" + tupL[6] + "" + + atom + "" + tupL[6] + "" atom = tupL[11] if tupL[12]: atom += "(" + tupL[12] + ")" # tablerow += "" + tupL[7] + "" + tupL[8] + "" + tupL[9] + tupL[10] + "" + atom + "" \ - + tupL[13] + "" + tupL[14] + "" + + tupL[13] + "" + tupL[14] + "" # tupL[6] = tupL[6].replace("_", "-") tupL[13] = tupL[13].replace("_", "-") bond_id = "covalent_bond_" + str(count) # tablerow += "" + tupL[15] + '        ' + + '" value="' + "_".join(tupL[:16]) + '"/>' # tablerow += "\n" count += 1 diff --git a/wwpdb/apps/ann_tasks_v2/utils/PointSuite.py b/wwpdb/apps/ann_tasks_v2/utils/PointSuite.py index a9cd356..c4e9b69 100644 --- a/wwpdb/apps/ann_tasks_v2/utils/PointSuite.py +++ b/wwpdb/apps/ann_tasks_v2/utils/PointSuite.py @@ -14,16 +14,19 @@ __license__ = "Creative Commons Attribution 3.0 Unported" __version__ = "V0.07" -import json,os,sys,traceback +import os +import sys +import traceback from wwpdb.utils.dp.RcsbDpUtility import RcsbDpUtility try: from mmcif.io.IoAdapterCore import IoAdapterCore as IoAdapter -except: +except ImportError: from mmcif.io.IoAdapterPy import IoAdapterPy as IoAdapter # + class PointSuite(object): """ PointSuite class encapsulates running the programs defined in the suite. """ @@ -43,11 +46,11 @@ def __setup(self): def importMats(self, inputMatFilePath, logPath): """ Run PointSuite's "importmats" program """ - exportList = [ os.path.join(self.__sessionPath, "import.biomt"), os.path.join(self.__sessionPath, "import.cif"), \ - os.path.join(self.__sessionPath, "import.matrix") ] + exportList = [os.path.join(self.__sessionPath, "import.biomt"), os.path.join(self.__sessionPath, "import.cif"), + os.path.join(self.__sessionPath, "import.matrix")] # - allFileList = [ os.path.join(self.__sessionPath, "import.biomt"), os.path.join(self.__sessionPath, "import.cif"), \ - os.path.join(self.__sessionPath, "import.matrix"), logPath ] + allFileList = [os.path.join(self.__sessionPath, "import.biomt"), os.path.join(self.__sessionPath, "import.cif"), + os.path.join(self.__sessionPath, "import.matrix"), logPath] # for filePath in allFileList: if os.access(filePath, os.F_OK): @@ -75,7 +78,7 @@ def importMats(self, inputMatFilePath, logPath): tmpMatricesCifPath = os.path.join(self.__sessionPath, "tmp-import.cif") ofh = open(tmpMatricesCifPath, "w") ofh.write("data_matrices\n#\n%s\n" % data) - ofh.close() + ofh.close() # try: ioObj = IoAdapter() @@ -96,7 +99,7 @@ def findFrame(self, modelCifPath, biomtFilePath, logPath): """ frameCifPath = os.path.join(self.__sessionPath, "findframe.cif") # - for filePath in ( frameCifPath, logPath ): + for filePath in (frameCifPath, logPath): if os.access(filePath, os.F_OK): os.remove(filePath) # @@ -109,12 +112,12 @@ def findFrame(self, modelCifPath, biomtFilePath, logPath): dp.expLog(dstPath=logPath, appendMode=False) dp.cleanup() - def makeAssembly(self, modelCifPath, transmtFilePath, logPath): + def makeAssembly(self, modelCifPath, transmtFilePath, logPath): """ Run PointSuite's "makeassembly" program """ assemblyCifPath = os.path.join(self.__sessionPath, "assembly.cif") # - for filePath in ( assemblyCifPath, logPath ): + for filePath in (assemblyCifPath, logPath): if os.access(filePath, os.F_OK): os.remove(filePath) # @@ -132,7 +135,7 @@ def mergeAssemblyInfo(self, inModelCifPath, assemblyCifPath, outModelCifPath, lo """ modifiedAssemblyCifPath = os.path.join(self.__sessionPath, "assembly-with-data-block.cif") # - for filePath in ( outModelCifPath, modifiedAssemblyCifPath, logPath ): + for filePath in (outModelCifPath, modifiedAssemblyCifPath, logPath): if os.access(filePath, os.F_OK): os.remove(filePath) # @@ -146,7 +149,7 @@ def mergeAssemblyInfo(self, inModelCifPath, assemblyCifPath, outModelCifPath, lo # ofh = open(modifiedAssemblyCifPath, "w") ofh.write("data_assembly\n#\n%s\n" % data) - ofh.close() + ofh.close() # dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh) dp.imp(inModelCifPath) diff --git a/wwpdb/apps/ann_tasks_v2/webapp/CommonTasksWebAppWorker.py b/wwpdb/apps/ann_tasks_v2/webapp/CommonTasksWebAppWorker.py index 20d6159..1d02707 100644 --- a/wwpdb/apps/ann_tasks_v2/webapp/CommonTasksWebAppWorker.py +++ b/wwpdb/apps/ann_tasks_v2/webapp/CommonTasksWebAppWorker.py @@ -3743,7 +3743,7 @@ def _uploadBiomtFileOp(self): rC.setError(errMsg="No file uploaded") return rC # - originalUploadFileName = wuu.getUploadFileName(fileTag="file") + # originalUploadFileName = wuu.getUploadFileName(fileTag="file") # entryId = self._reqObj.getValue("entryid") entryFileName = self._reqObj.getValue("entryfilename") @@ -3760,8 +3760,8 @@ def _uploadBiomtFileOp(self): 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 ): + 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) # @@ -3781,7 +3781,7 @@ def _uploadBiomtFileOp(self): 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() @@ -3789,8 +3789,8 @@ def _uploadBiomtFileOp(self): # text = 'Uploaded "' + originalUploadFileName + '" file:\n' + data text = "" # - for fileTup in ( ( "import.biomt", importBiomtPath ), ( "import.cif", importCifPath ), \ - ( "import.matrix", importMatrixPath ), ( "assembly.cif", assemblyCifPath ) ): + 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 # @@ -3801,7 +3801,7 @@ def _uploadBiomtFileOp(self): if text: text += "\n\n" # - text += '"' + fileTup[0] + '" file:\n' + data + text += '"' + fileTup[0] + '" file:\n' + data # successfulFlag = False if os.access(assemblyCifPath, os.R_OK): @@ -3826,7 +3826,7 @@ def _uploadBiomtFileOp(self): rC.set("summary", summary_text) # log_text = "" - for filePath in ( importmatsLogPath, findframeLogPath, makeassemblyLogPath, mergeLogPath ): + for filePath in (importmatsLogPath, findframeLogPath, makeassemblyLogPath, mergeLogPath): if not os.access(filePath, os.F_OK): continue #