manual merge fix

gui/elabUpload.py

@@ -221,7 +221,7 @@ class elabUpload(QWidget, Ui_tabELNData):
                 self.elnUploadButton.setCursor(QtGui.QCursor(QtCore.Qt.ArrowCursor))
     
         except Exception as e:
-            logging.info("ElabUpload UploadData: "+repr(error))
+            logging.info("ElabUpload UploadData: "+repr(e))
             self.errorLabel.setText(repr(e))
             self.elnUploadButton.setEnabled(True)
             self.elnUploadButton.setCursor(QtGui.QCursor(QtCore.Qt.ArrowCursor))
@@ -265,7 +265,7 @@ class Worker(QObject):
             self.progress.emit(3)
             self.finished.emit()
         except Exception as e:
-            logging.info("ElabUpload data upload and annotation worker: "+repr(error))
+            logging.info("ElabUpload data upload and annotation worker: "+repr(e))
             print(repr(e))
 
         self.annotateElab()

gui/irodsBrowser.py

@@ -284,9 +284,15 @@ class irodsBrowser(QWidget, Ui_tabBrowser):
         self.__clearErrorLabel()
         self.__clearViewTabs()
 
+<<<<<<< HEAD
         self.metadataTable.setRowCount(0);
         self.aclTable.setRowCount(0);
         self.resourceTable.setRowCount(0);
+=======
+        self.widget.metadataTable.setRowCount(0)
+        self.widget.aclTable.setRowCount(0)
+        self.widget.resourceTable.setRowCount(0)
+>>>>>>> master
         
         col = index.column()
         row = index.row()
@@ -413,8 +419,13 @@ class irodsBrowser(QWidget, Ui_tabBrowser):
                 self.errorLabel.setText(
                     "IRODS NETWORK ERROR: No Connection, please check network")
             except Exception as error:
+<<<<<<< HEAD
                 print("ERROR upload :", fileSelect[0], "failed; \n\t", repr(error))
                 self.errorLabel.setText(repr(error))
+=======
+                print("ERROR download :", parent+'/'+objName, "failed; \n\t", repr(error))
+                self.widget.errorLabel.setText(repr(error))
+>>>>>>> master
 
 
     #@QtCore.pyqtSlot(QtCore.QModelIndex)

gui/irodsDataCompression.py

@@ -142,10 +142,15 @@ class irodsDataCompression(QWidget, Ui_tabDataCompression):
     def dataCreateExtractFinished(self, success, message, operation):
         self.setCursor(QtGui.QCursor(QtCore.Qt.ArrowCursor))
         self.enableButtons(True)
+        stdout, stderr = message
         if success and operation == "create":
             idx, source = self.collectionTreeModel.get_checked()
+<<<<<<< HEAD
             stdout, stderr = message
             self.createStatusLabel.setText("STATUS: Created " + str(stdout))
+=======
+            self.widget.createStatusLabel.setText("STATUS: Created " + str(stdout))
+>>>>>>> master
             parentIdx = self.collectionTreeModel.getParentIdx(idx)
             self.collectionTreeModel.refreshSubTree(parentIdx)
         elif not success and operation == "create":

gui/irodsSearch.py

@@ -4,7 +4,11 @@ from PyQt5.uic import loadUi
 import os
 
 from utils.utils import getDownloadDir
+<<<<<<< HEAD
 from gui.ui_files.searchDialog import Ui_searchDialog
+=======
+import logging
+>>>>>>> master
 
 class irodsSearch(QDialog, Ui_searchDialog):
     def __init__(self, ic, collTable):

gui/irodsTicketLogin.py

@@ -43,10 +43,17 @@ class irodsTicketLogin(QWidget, Ui_tabTicketAccess):
 
 
     def irodsSession(self):
+<<<<<<< HEAD
         self.infoLabel.clear()
         host = self.serverEdit.text()
         path = self.pathEdit.text()
         token = self.ticketEdit.text()
+=======
+        self.widget.infoLabel.clear()
+        host = self.widget.serverEdit.text().strip()
+        path = self.widget.pathEdit.text().strip()
+        token = self.widget.ticketEdit.text().strip()
+>>>>>>> master
 
         try:
             self.ic = irodsConnectorAnonymous(host, token, path)

irods-iBridgesCli.py

@@ -47,7 +47,7 @@ def getConfig(path):
 def connectIRODS(config):
 
     #icommands present and irods_environment file present and user wants to use standard envFile
-    standardEnv = os.path.expanduser('~' +os.sep+'.irods/irods_environment.json')
+    standardEnv = os.path.expanduser('~' +os.sep+'.irods'+os.sep+'irods_environment.json')
     if os.path.exists(standardEnv) and \
             (config['iRODS']['irodsenv'] == '' or config['iRODS']['irodsenv'] == standardEnv):
         try:
@@ -68,7 +68,7 @@ def connectIRODS(config):
         print(BLUE+"INFO: Data up and download by python API."+DEFAULT)
 
     else:
-        raise FileNotFoundError('Environment file not found: '+ envFile)
+        raise FileNotFoundError('Environment file not found e.g. '+ standardEnv)
 
     return ic
 

utils/irodsConnector.py

 from irods.session import iRODSSession
 from irods.access import iRODSAccess
 from irods.ticket import Ticket
-from irods.exception import CATALOG_ALREADY_HAS_ITEM_BY_THAT_NAME, CAT_NO_ACCESS_PERMISSION 
-from irods.exception import CAT_SUCCESS_BUT_WITH_NO_INFO, CAT_INVALID_ARGUMENT, CAT_INVALID_USER, CAT_INVALID_AUTHENTICATION
+from irods.exception import CATALOG_ALREADY_HAS_ITEM_BY_THAT_NAME, \
+                            CAT_NO_ACCESS_PERMISSION, CAT_SUCCESS_BUT_WITH_NO_INFO, \
+                            CAT_INVALID_ARGUMENT, CAT_INVALID_USER, CAT_INVALID_AUTHENTICATION,\
+                            NO_RULE_OR_MSI_FUNCTION_FOUND_ERR
+
 from irods.exception import CollectionDoesNotExist
 from irods.connection import PlainTextPAMPasswordError
 from irods.models import Collection, DataObject, Resource, ResourceMeta, CollectionMeta, DataObjectMeta
@@ -719,8 +722,13 @@ class irodsConnector():
             '*value': '"attr_value"'
         }
         """
-        rule = Rule(self.session, ruleFile, params=params, output=output)
-        out = rule.execute()
+        try:
+            rule = Rule(self.session, ruleFile, params=params, output=output)
+            out = rule.execute()
+        except Exception as e:
+            logging.info('RULE EXECUTION ERROR', exc_info=True)
+            return [], [repr(e)]
+
         stdout = []
         stderr = []
         if len(out.MsParam_PI) > 0:
@@ -730,7 +738,7 @@ class irodsConnector():
                 stderr = [o.decode() 
                     for o in (out.MsParam_PI[0].inOutStruct.stderrBuf.buf.strip(b'\x00')).split(b'\n')]
             except AttributeError:
-                #logging.info('RULE EXECUTION ERROR: '+str(stdout+stderr), exc_info=True)
+                logging.info('RULE EXECUTION ERROR: '+str(stdout+stderr), exc_info=True)
                 return stdout, stderr
         
         return stdout, stderr