v1.3.8.19 (02/12/2019) (#273)

- bug fix: xce to read resolution at Mn(I)/sig(I) of 2.0 (and 1.5 if possible) from aimless log; now only reads either one or the other. Datasets table now only shows reso at 2.0 since 1.5 not always shown
- bug fix: read gda barcodes into DB and display in datasets table

ChangeLog.txt

@@ -1,3 +1,7 @@
+v1.3.8.19 (02/12/2019)
+- bug fix: xce to read resolution at Mn(I)/sig(I) of 2.0 (and 1.5 if possible) from aimless log; now only reads either one or the other. Datasets table now only shows reso at 2.0 since 1.5 not always shown
+- bug fix: read gda barcodes into DB and display in datasets table
+
 v1.3.8.18 (25/11/2019)
 - bug fix: added except statement in get_gda_barcodes to catch errors during parsing of multiple visits
 
@@ -99,20 +103,4 @@ v1.3.3 (19/02/2019)
 - bug fix: removed not supported 'group leader' and 'investigator' option from edit deposition data menu
 
 v1.3.2 (12/02/2019)
-- bug fix: removed reference to non-existent labels (prevented opening of pandda models/ maps)
-
-v1.3.1 (25/01/2019)
-- bug fix: support of new autoProc directory structure at DLS
-- bug fix: removal of non-existent DataProcessingProgram entries at DLS from collectionTable
-- bug fix: xce coot plugin: changed layout so that full window can be displayed on any screen
-
-v1.3 (16/01/2019)
-- bug fix: get space group from aimless log file if file contains output from other programs like unique
-- bug fix: change qsub command for dimple and restraints generation so that it works outside DLS
-- new feature: assign labels to datasets in xce-coot interface
-- bug fix: accomodate None value when querying DB for event map information
-- new feature: preparation of apo mmcif files containing SF's all all datasets used for pandda.analyse
-- improvement: refinement of pandda models enabled where ligand binding did not lead to any differences between bound-state and ground-state
-- bug fix: update data_rxxxxsf field in apo mmcif file
-- fix pandda button in settings tab
-- add XCE manual to help menu 
+- bug fix: removed reference to non-existent labels (prevented opening of 

XChemExplorer.py

@@ -3810,7 +3810,7 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict):
 
         column_name = ['Program',
                        'Resolution\nOverall',
-                       'Resolution\n[Mn<I/sig(I)> = 1.5]',
+                       'Resolution\n[Mn<I/sig(I)> = 2.0]',
                        'DataProcessing\nSpaceGroup',
                        'Mn<I/sig(I)>\nHigh',
                        'Rmerge\nLow',

gui_scripts/settings_preferences.py

@@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object):
 
     def settings(self, xce_object):
         # set XCE version
-        xce_object.xce_version = 'v1.3.8.18'
+        xce_object.xce_version = 'v1.3.8.19'
 
         # general settings
         xce_object.allowed_unitcell_difference_percent = 12
@@ -301,7 +301,7 @@ def tables(self, xce_object):
         #                                            - appears in create_widgets_for_autoprocessing_results_only()
 
         xce_object.datasets_summary_table_columns = ['Sample ID',
-                                                     'Resolution\n[Mn<I/sig(I)> = 1.5]',
+                                                     'Resolution\n[Mn<I/sig(I)> = 2.0]',
                                                      'DataProcessing\nSpaceGroup',
                                                      'DataProcessing\nRfree',
                                                      'SoakDB\nBarcode',

lib/XChemDB.py

@@ -748,6 +748,7 @@ def import_csv_file(self,csv_file):
         connect.commit()
 
     def update_data_source(self,sampleID,data_dict):
+        print 'here'
         data_dict['LastUpdated']=str(datetime.now().strftime("%Y-%m-%d %H:%M"))
         data_dict['LastUpdated_by']=getpass.getuser()
 

lib/XChemLog.py

@@ -26,7 +26,7 @@ def create_logfile(self,version):
             '     #                                                                     #\n'
             '     # Version: %s                                       #\n' %pasteVersion+
             '     #                                                                     #\n'
-            '     # Date: 25/11/2019                                                    #\n'
+            '     # Date: 02/12/2019                                                    #\n'
             '     #                                                                     #\n'
             '     # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK  #\n'
             '     #          [email protected]                                 #\n'

lib/XChemThread.py

@@ -1152,7 +1152,7 @@ def run(self):
         db=XChemDB.data_source(os.path.join(self.database_directory,self.data_source_file))
         database=os.path.join(self.database_directory,self.data_source_file)
 
-        print(self.sample_list)
+#        print(self.sample_list)
 
         for n,item in enumerate(self.sample_list):
 
@@ -2150,7 +2150,7 @@ def __init__(self,
         self.xce_logfile = xce_logfile
         self.Logfile = XChemLog.updateLog(xce_logfile)
 
-        self.db = XChemDB.data_source(os.path.join(database))
+        self.db = XChemDB.data_source(database)
         self.allSamples = self.db.collected_xtals_during_visit_for_scoring(visit)
 
         self.gdaLogInstructions = gdaLogInstructions
@@ -2178,9 +2178,10 @@ def run(self):
     def update_database(self,pinDict):
         self.Logfile.insert('updating database with pinDIs from GDA logfiles')
         for sample in pinDict:
-            dbDict = {'DataCollectionPinBarcode': pinDict[sample]}
-            self.db.update_data_source(sample,dbDict)
-
+            dbDict = {}
+            dbDict['DataCollectionPinBarcode'] = pinDict[sample]
+#            self.db.update_data_source(sample,dbDict)
+            self.db.update_specified_table(sample,dbDict,'collectionTable')
 
 
 class choose_autoprocessing_outcome(QtCore.QThread):
@@ -2215,7 +2216,7 @@ def __init__(self,
                     self.allSamples.append(e)
         else:
             self.allSamples = self.db.collected_xtals_during_visit_for_scoring(visit)
-        print 'here', self.allSamples
+#        print 'here', self.allSamples
 #        self.allSamples = self.db.collected_xtals_during_visit_for_scoring(visit,rescore)
 
 
@@ -2403,13 +2404,13 @@ def __init__(self,
 #        self.target = target
         self.processedDir =  processedDir
         self.visit,self.beamline = XChemMain.getVisitAndBeamline(self.processedDir)
-        print 'visit'
+#        print 'visit'
         self.projectDir = projectDir
         self.Logfile = XChemLog.updateLog(xce_logfile)
         self.target = target
         self.agamemnon = agamemnon
         if self.agamemnon:
-            print 'procDir',self.processedDir
+#            print 'procDir',self.processedDir
 #            if len(procDir.split('/')) >= 8:
 #                if procDir.split('/')[7] == 'agamemnon'
 #            quit()

lib/XChemUtils.py

@@ -588,6 +588,10 @@ def read_aimless_logfile(self,logfile):
         except IndexError:
             pass
 
+        resolution_at_15_sigma_line_overall_found=False
+        resolution_at_20_sigma_line_overall_found=False
+
+
 #
 #        print '=====>',self.aimless['DataCollectionRun'],logfile
 #
@@ -641,15 +645,18 @@ def read_aimless_logfile(self,logfile):
                 self.aimless['DataProcessingCChalfLow'] = line.split()[2]
                 self.aimless['DataProcessingCChalfHigh'] = line.split()[3]
             if line.startswith('Estimates of resolution limits: overall'):
-                resolution_at_sigma_line_overall_found=True
-            if resolution_at_sigma_line_overall_found:
+                resolution_at_15_sigma_line_overall_found=True
+                resolution_at_20_sigma_line_overall_found=True
+            if resolution_at_15_sigma_line_overall_found:
                 if 'from Mn(I/sd)' in line and len(line.split()) >= 7:
                     if '1.5' in line.split()[3]:
                         self.aimless['DataProcessingResolutionHigh15sigma']=line.split()[6][:-1]
-                        resolution_at_sigma_line_overall_found=False
+                        resolution_at_15_sigma_line_overall_found=False
+            if resolution_at_20_sigma_line_overall_found:
+                if 'from Mn(I/sd)' in line and len(line.split()) >= 7:
                     if '2.0' in line.split()[3]:
                         self.aimless['DataProcessingResolutionHigh20sigma']=line.split()[6][:-1]
-                        resolution_at_sigma_line_overall_found=False
+                        resolution_at_20_sigma_line_overall_found=False
             if (line.startswith('Average unit cell:') or line.startswith('  Unit cell parameters')) and len(line.split())==9:
                 tmp = [line.split()]
                 a = int(float(tmp[0][3]))