PEP8/pylint cleanup

wwpdb/apps/ann_tasks_v2/correspnd/CorresPNDTemplate.py

@@ -513,7 +513,7 @@ def __doRender(self):
         myD["major_release"] = self.__letterTemplateMap["major_release"]
         myD["major_minor_addition"] = self.__letterTemplateMap["major_minor_addition"]
         myD["minor"] = self.__letterTemplateMap["minor"]
-        myD["minor_release"],is_repl_rel = self.__getRelaseInfo()
+        myD["minor_release"], is_repl_rel = self.__getRelaseInfo()
         if is_repl_rel:
             myD["major_release"] = self.__letterTemplateMap["release_repl_rel"]
         #
@@ -739,7 +739,7 @@ def __getRelaseInfo(self):
                 text += self.__letterTemplateMap["pre_release_no"]
             #
         #
-        return text,is_repl_rel
+        return text, is_repl_rel
 
     def __getTableContext(self, count):
         text = ""

wwpdb/apps/ann_tasks_v2/report/PdbxReport.py

@@ -191,6 +191,9 @@ def doReport(self, contentType="model"):
                 pdbxR = PdbxLinksReportIo(verbose=self.__verbose, log=self.__lfh)
             elif contentType == "em-map-info-report":
                 pdbxR = EmInfoReportIo(verbose=self.__verbose, log=self.__lfh)
+            else:
+                self.__lfh.write("+PdbxReport.doReport() - unknown contentType %s\n" % contentType)
+                return oD
 
             pdbxR.setFilePath(localPath, idCode=None)
             pdbxR.get()

wwpdb/apps/ann_tasks_v2/report/styles/PdbxEmExtensionCategoryStyle.py

@@ -16,8 +16,6 @@
 __email__ = "[email protected]"
 __license__ = "Apache 2.0"
 
-
-
 from mmcif_utils.style.PdbxCategoryStyleBase import PdbxCategoryStyleBase
 
 
@@ -107,7 +105,7 @@ class PdbxEmExtensionCategoryStyle(PdbxCategoryStyleBase):
             ('_em_entity_assembly.id', '%s', 'str', ''),
             ('_em_entity_assembly.assembly_id', '%s', 'str', ''),
             ('_em_entity_assembly.parent_id', '%s', 'str', ''),
-            #('_em_entity_assembly.chimera', '%s', 'str', ''),
+            # ('_em_entity_assembly.chimera', '%s', 'str', ''),
             ('_em_entity_assembly.source', '%s', 'str', ''),
             ('_em_entity_assembly.type', '%s', 'str', ''),
             ('_em_entity_assembly.name', '%s', 'str', ''),
@@ -290,13 +288,13 @@ class PdbxEmExtensionCategoryStyle(PdbxCategoryStyleBase):
             ('_em_3d_reconstruction.nominal_pixel_size', '%s', 'str', ''),
             ('_em_3d_reconstruction.actual_pixel_size', '%s', 'str', ''),
             ('_em_3d_reconstruction.num_particles', '%s', 'str', ''),
-            #('_em_3d_reconstruction.num_subtomograms', '%s', 'str', ''),
+            # ('_em_3d_reconstruction.num_subtomograms', '%s', 'str', ''),
             ('_em_3d_reconstruction.euler_angles_details', '%s', 'str', ''),
             ('_em_3d_reconstruction.num_class_averages', '%s', 'str', ''),
             ('_em_3d_reconstruction.software', '%s', 'str', ''),
             ('_em_3d_reconstruction.fsc_type', '%s', 'str', ''),
             ('_em_3d_reconstruction.image_processing_id', '%s', 'str', ''),
-            #('_em_3d_reconstruction.software_id_list', '%s', 'str', ''),
+            # ('_em_3d_reconstruction.software_id_list', '%s', 'str', ''),
             ('_em_3d_reconstruction.symmetry_type', '%s', 'str', ''),
         ],
         'em_3d_fitting': [
@@ -309,7 +307,7 @@ class PdbxEmExtensionCategoryStyle(PdbxCategoryStyleBase):
             ('_em_3d_fitting.overall_b_value', '%s', 'str', ''),
             ('_em_3d_fitting.ref_space', '%s', 'str', ''),
             ('_em_3d_fitting.ref_protocol', '%s', 'str', ''),
-            #('_em_3d_fitting.software_id_list', '%s', 'str', ''),
+            # ('_em_3d_fitting.software_id_list', '%s', 'str', ''),
         ],
         'em_3d_fitting_list': [
             ('_em_3d_fitting_list.id', '%s', 'str', ''),
@@ -588,7 +586,7 @@ class PdbxEmExtensionCategoryStyle(PdbxCategoryStyleBase):
             ('_em_tomography.imaging_id', '%s', 'str', ''),
         ],
         'em_image_recording': [
-            #('_em_image_recording.approximate_date', '%s', 'str', ''),
+            # ('_em_image_recording.approximate_date', '%s', 'str', ''),
             ('_em_image_recording.average_exposure_time', '%s', 'str', ''),
             ('_em_image_recording.avg_electron_dose_per_image', '%s', 'str', ''),
             ('_em_image_recording.details', '%s', 'str', ''),
@@ -656,7 +654,7 @@ class PdbxEmExtensionCategoryStyle(PdbxCategoryStyleBase):
             ('_em_ctf_correction.amplitude_correction_space', '%s', 'str', ''),
             ('_em_ctf_correction.correction_operation', '%s', 'str', ''),
             ('_em_ctf_correction.details', '%s', 'str', ''),
-            #('_em_ctf_correction.em_software_id', '%s', 'str', ''),
+            # ('_em_ctf_correction.em_software_id', '%s', 'str', ''),
             ('_em_ctf_correction.id', '%s', 'str', ''),
             ('_em_ctf_correction.phase_reversal', '%s', 'str', ''),
             ('_em_ctf_correction.phase_reversal_anisotropic', '%s', 'str', ''),
@@ -667,7 +665,7 @@ class PdbxEmExtensionCategoryStyle(PdbxCategoryStyleBase):
             ('_em_ctf_correction.amplitude_correction_space', '%s', 'str', ''),
             ('_em_ctf_correction.correction_operation', '%s', 'str', ''),
             ('_em_ctf_correction.details', '%s', 'str', ''),
-            #('_em_ctf_correction.em_software_id', '%s', 'str', ''),
+            # ('_em_ctf_correction.em_software_id', '%s', 'str', ''),
             ('_em_ctf_correction.id', '%s', 'str', ''),
             ('_em_ctf_correction.phase_reversal', '%s', 'str', ''),
             ('_em_ctf_correction.phase_reversal_anisotropic', '%s', 'str', ''),

wwpdb/apps/ann_tasks_v2/report/styles/PdbxIo.py

@@ -874,6 +874,7 @@ def update(self, catName, attributeName, value, iRow=0):
     def write(self, filePath):
         return self.writeFile(filePath)
 
+
 class EmInfoReportIo(PdbxStyleIoUtil):
     """Methods for reading EM information details."""
 

wwpdb/apps/ann_tasks_v2/webapp/CommonTasksWebAppWorker.py

@@ -2303,7 +2303,7 @@ def _renderCheckReports(self, entryId, fileSource="archive", instance=None, cont
                     versionId = "latest"
                 else:
                     versionId = "none"
-                
+
                 # Try to avoid fetch if not needed
                 downloadPath = du.getFilePath(entryId, contentType="model", formatType="pdbx", fileSource=fileSource, instance=instance, versionId=versionId)
                 if downloadPath is None or not os.path.exists(downloadPath):

wwpdb/apps/ann_tasks_v2/webapp/ReviewDataWebAppWorker.py

@@ -113,6 +113,7 @@ def _updateAndReportFileOps(self):
         rC = ResponseContent(reqObj=self._reqObj, verbose=self._verbose, log=self._lfh)
         rC.setReturnFormat("json")
 
+        contentType = contentFormat = partitionNumber = None
         if self._isFileUpload():
             # make a copy of the file in the session directory and set 'fileName'
             self._uploadFile()
@@ -149,6 +150,7 @@ def _updateAndReportFileOps(self):
             #
             pR = PdbxReport(reqObj=self._reqObj, verbose=self._verbose, log=self._lfh)
             aTagList.append(du.getAnchorTag())
+            downloadPath = du.getDownloadPath()
             layout = "multiaccordion"
             htmlList.extend(pR.makeTabularReport(filePath=downloadPath, contentType=contentType, idCode=idCode, layout=layout))
             if len(aTagList) > 0: