[med-svn] [Git][med-team/microbegps][master] Follow more hints of Dmitry Shachnev <mitya57 at debian.org>
Andreas Tille
gitlab at salsa.debian.org
Fri Sep 6 14:03:11 BST 2019
Andreas Tille pushed to branch master at Debian Med / microbegps
Commits:
232b707f by Andreas Tille at 2019-09-06T13:02:48Z
Follow more hints of Dmitry Shachnev <mitya57 at debian.org>
- - - - -
1 changed file:
- debian/patches/PyQt5.patch
Changes:
=====================================
debian/patches/PyQt5.patch
=====================================
@@ -315,6 +315,114 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
gridLayout.setColumnStretch(0,2)
gridLayout.setColumnStretch(1,2)
gridLayout.addWidget(recipeLbl,0,0)
+@@ -343,7 +343,7 @@ class Pipeline(QtGui.QWidget):
+ try:
+ target_table,read_table = gps.read_sam_files_no_pysam(directory,status_reporter)
+ except Exception as e:
+- self.failed.emit(e.message)
++ self.failed.emit(str(e))
+ raise
+ else:
+ self.done.emit(target_table,read_table)
+@@ -389,7 +389,7 @@ class Pipeline(QtGui.QWidget):
+ pr=printer)
+ gps.calculate_mapping_statistics(p.target_table)
+ except Exception as e:
+- self.failed.emit(e.message)
++ self.failed.emit(str(e))
+ raise
+ else:
+ self.done.emit()
+@@ -441,7 +441,7 @@ class Pipeline(QtGui.QWidget):
+ else:
+ ref_table = gps.get_reference_table(p.target_table,p.read_table)
+ except Exception as e:
+- self.failed.emit(e.message)
++ self.failed.emit(str(e))
+ raise
+ else:
+ self.done.emit(ref_table)
+@@ -488,7 +488,7 @@ class Pipeline(QtGui.QWidget):
+ gps.filter_ref_table(p.ref_table,p.read_table,custom_filt1,printer)
+ #GpsTools.calculate_valcov(p.ref_table,printer)
+ except Exception as e:
+- self.failed.emit(e.message)
++ self.failed.emit(str(e))
+ raise
+ else:
+ self.done.emit()
+@@ -549,7 +549,7 @@ class Pipeline(QtGui.QWidget):
+ group_dict = gps.create_groups_dc(usr_mat,all_mat,n2i,p.sharedFractionUSR.value(),status=printer)
+ candidates = gps.enrich_groups(group_dict,p.ref_table,p.read_table,i2n)
+ except Exception as e:
+- self.failed.emit(e.message)
++ self.failed.emit(str(e))
+ raise
+ else:
+ self.done.emit(candidates)
+@@ -591,7 +591,7 @@ class Pipeline(QtGui.QWidget):
+ p.mainWindow.visualize(p.candidates,p.ref_table,p.read_table)
+ p.mainWindow.settings_pipeline = p.get_settings()
+ except Exception as e:
+- self.failed.emit(e.message)
++ self.failed.emit(str(e))
+ raise
+ else:
+ self.done.emit()
+@@ -646,7 +646,7 @@ class Pipeline(QtGui.QWidget):
+ try:
+ target_table,read_table = gps.read_sam_files_no_pysam(directory,self.status.emit)
+ except Exception as e:
+- self.failed.emit(0,e.message)
++ self.failed.emit(0,str(e))
+ raise
+ else:
+ self.done.emit(0)
+@@ -664,7 +664,7 @@ class Pipeline(QtGui.QWidget):
+ pr=p.pr)
+ gps.calculate_mapping_statistics(target_table)
+ except Exception as e:
+- self.failed.emit(1,e.message)
++ self.failed.emit(1,str(e))
+ raise
+ else:
+ self.done.emit(1)
+@@ -686,7 +686,7 @@ class Pipeline(QtGui.QWidget):
+ else:
+ ref_table = gps.get_reference_table(target_table,read_table)
+ except Exception as e:
+- self.failed.emit(2,e.message)
++ self.failed.emit(2,str(e))
+ raise
+ else:
+ self.done.emit(2)
+@@ -703,7 +703,7 @@ class Pipeline(QtGui.QWidget):
+ return True
+ gps.filter_ref_table(ref_table,read_table,custom_filt1,p.pr)
+ except Exception as e:
+- self.failed.emit(3,e.message)
++ self.failed.emit(3,str(e))
+ raise
+ else:
+ self.done.emit(3)
+@@ -730,7 +730,7 @@ class Pipeline(QtGui.QWidget):
+ group_dict = gps.create_groups_dc(usr_mat,all_mat,n2i,p.sharedFractionUSR.value(),status=p.pr)
+ candidates = gps.enrich_groups(group_dict,ref_table,read_table,i2n)
+ except Exception as e:
+- self.failed.emit(4,e.message)
++ self.failed.emit(4,str(e))
+ raise
+ else:
+ self.done.emit(4)
+@@ -742,7 +742,7 @@ class Pipeline(QtGui.QWidget):
+ p.mainWindow.visualize(candidates,ref_table,read_table)
+ p.mainWindow.settings_pipeline = p.get_settings()
+ except Exception as e:
+- self.failed.emit(5,e.message)
++ self.failed.emit(5,str(e))
+ raise
+ else:
+ self.done.emit(5)
@@ -805,14 +805,14 @@ class Pipeline(QtGui.QWidget):
self.stepsDone = min(step-1,self.stepsDone)
@@ -350,6 +458,15 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
def __init__(self):
super(GPSAnalyzer, self).__init__()
self.initUI()
+@@ -889,7 +889,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ mod = importer.find_module(mod_name).load_module(mod_name)
+ modules_d[mod_name] = mod.GPSModule(self)
+ except Exception as e:
+- self.pr('<b><font color="DarkRed">Failed loading module %s</font></b><br>Message: <i>%s</i>'%(mod_name,e.message))
++ self.pr('<b><font color="DarkRed">Failed loading module %s</font></b><br>Message: <i>%s</i>'%(mod_name,str(e)))
+ self.modules = modules_d
+ if len(self.modules) > 0:
+ self.pr('Loaded modules: <i>%s</i>'%(', '.join(iter(self.modules.keys()))))
@@ -898,22 +898,22 @@ class GPSAnalyzer(QtGui.QMainWindow):
self.pipelineGui = Pipeline(self)
@@ -703,6 +820,24 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
self.phyloTreeWidget.expandItem(self.taxid_to_item[taxid])
self.taxid_to_item[taxid].setText(1,'%i'%N_reads)
self.phyloTreeWidget.resizeColumnToContents(0)
+@@ -1570,7 +1570,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ #nodes,ranks = taxonomy.parse_nodes_dmp(gzip.open('data/taxonomy/nodes.dmp.gz','r'))
+ nodes,ranks = taxonomy.parse_nodes_dmp(pkg_resources.resource_stream('microbegps','data/taxonomy/nodes.dmp'))
+ except Exception as e:
+- self.failed.emit('<b><font color="DarkRed">Error loading NCBI taxonomy!</font></b><br>Message: <i>'+e.message+'</i>')
++ self.failed.emit('<b><font color="DarkRed">Error loading NCBI taxonomy!</font></b><br>Message: <i>'+str(e)+'</i>')
+ raise
+ else:
+ self.done.emit(nodes,ranks)
+@@ -1584,7 +1584,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ #target = taxonomy.parse_names_dmp(gzip.open('data/taxonomy/names.dmp.gz','r'))
+ target = taxonomy.parse_names_dmp(pkg_resources.resource_stream('microbegps','data/taxonomy/names.dmp'))
+ except Exception as e:
+- self.failed.emit('<b><font color="DarkRed">Error loading NCBI names!</font></b><br>Message: <i>'+e.message+'</i>')
++ self.failed.emit('<b><font color="DarkRed">Error loading NCBI names!</font></b><br>Message: <i>'+str(e)+'</i>')
+ raise
+ else:
+ self.done.emit(target)
@@ -1613,7 +1613,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
self.pipelineGui.show()
@@ -712,6 +847,15 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
if len(fname):
if not fname.endswith('.gpsa'):
if not '.' in fname:
+@@ -1631,7 +1631,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ 'settings_analyzer':self.settings_analyzer}
+ pickle.dump(s_data,open(fname,'wb'),protocol=-1)
+ except Exception as e:
+- self.pr('Error while saving file: '+e.message)
++ self.pr('Error while saving file: '+str(e))
+ raise
+ else:
+ self.pr("Finished saving data.")
@@ -1641,7 +1641,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
@@ -721,7 +865,16 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
fname = str(dialog.getOpenFileName(caption='Load Data',filter="GPS Analyzer Files (*.gpsa);;All Files (*.*)",parent=self))
if len(fname):
self.pr("Loading data from file "+fname)
-@@ -1676,7 +1676,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+@@ -1659,7 +1659,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ settings_pipeline = settings.get('settings_pipeline',dict())
+ settings_analyzer = settings.get('settings_analyzer',dict())
+ except Exception as e:
+- self.pr('Error while loading file: '+e.message)
++ self.pr('Error while loading file: '+str(e))
+ raise
+ else:
+ self.treeView.clear()
+@@ -1676,17 +1676,17 @@ class GPSAnalyzer(QtGui.QMainWindow):
""" Export the whole tree to files that can be loaded with iTOL.
http://itol.embl.de/upload.cgi"""
try:
@@ -729,8 +882,11 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
+ outdir = str(QtWidgets.QFileDialog().getExistingDirectory(caption='Select iTOL output directory',parent=self))
taxonomy.candidates_to_LCA_tree(self.sgroups,self.taxonomy_nodes,self.taxonomy_names,outdir)
except Exception as e:
- self.pr('Error while saving iTOL files: '+e.message)
-@@ -1686,7 +1686,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+- self.pr('Error while saving iTOL files: '+e.message)
++ self.pr('Error while saving iTOL files: '+str(e))
+ raise
+
+
def export_graphic(self):
""" export the current content of the figure to file. Use the DPI
quality specified in exportFigureQuality """
@@ -860,3 +1016,41 @@ Last-Update: Fri, 06 Sep 2019 10:26:15 +0200
- self.GPS.tree_item_clicked_handler(self.GPS.treeView.currentItem(),0)
\ No newline at end of file
+ self.GPS.tree_item_clicked_handler(self.GPS.treeView.currentItem(),0)
+--- a/microbegps/taxonomy.py
++++ b/microbegps/taxonomy.py
+@@ -12,7 +12,7 @@ def parse_nodes_dmp(node_file):
+ nodes = dict()
+ ranks = dict()
+ for line in node_file:
+- fields = line.rstrip('\t|\n').split('\t|\t')
++ fields = line.decode('utf-8').rstrip('\t|\n').split('\t|\t')
+ if len(fields) < 4:
+ print('skipped line',line)
+ continue
+@@ -28,7 +28,7 @@ def parse_names_dmp(names_file):
+ """ """
+ taxid_to_name = dict()
+ for line in names_file:
+- fields = line.rstrip('\t|\n').split('\t|\t')
++ fields = line.decode('utf-8').rstrip('\t|\n').split('\t|\t')
+ if len(fields) != 4:
+ print('skipped line',line)
+ continue
+@@ -45,7 +45,7 @@ def parse_catalog(catalog_file):
+ """ """
+ gi_to_taxid = dict()
+ for line in catalog_file:
+- fields = line.rstrip().split('\t')
++ fields = line.decode('utf-8').rstrip().split('\t')
+ gi = fields[3]
+ taxid = int(fields[0])
+ gi_to_taxid[gi] = taxid
+@@ -58,7 +58,7 @@ def gis_to_taxid_and_name(gis, catalog):
+ gi_to_taxid = dict()
+ gi_to_name = dict()
+ for line in catalog:
+- fields = line.rstrip().split('\t')
++ fields = line.decode('utf-8').rstrip().split('\t')
+ gi = fields[3]
+ taxid = int(fields[0])
+ name = fields[1]
View it on GitLab: https://salsa.debian.org/med-team/microbegps/commit/232b707fc3decced598626be60d820989bcba133
--
View it on GitLab: https://salsa.debian.org/med-team/microbegps/commit/232b707fc3decced598626be60d820989bcba133
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190906/d5d51fb7/attachment-0001.html>
More information about the debian-med-commit
mailing list