merge

commit.py

@@ -90,7 +90,7 @@ def runTests():
   for fileI in os.listdir('pasta_eln/Tests'):
     if not fileI.endswith('.py'):
       continue
-    result = subprocess.run(['python3','-m','pasta_eln.Tests.'+fileI], stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=False)
+    result = subprocess.run(['python3','-m','pasta_eln.Tests.'+fileI[:-3]], stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=False)
     success = result.stdout.decode('utf-8').count('*** DONE WITH VERIFY ***')
     if success==1:
       success += result.stdout.decode('utf-8').count('**ERROR')
@@ -99,7 +99,7 @@ def runTests():
     else:
       successAll = False
       print("  FAILED: Python unit test "+fileI)
-      print("    run: 'python3 Tests/"+fileI+"' and check logFile")
+      print("    run: 'python3 -m pasta_eln.Tests."+fileI[:-3]+"' and check logFile")
   return
 
 

pasta_eln/backend.py

@@ -8,6 +8,10 @@
 from .miscTools import upIn, upOut, createDirName, generic_hash, camelCase
 from .handleDictionaries import ontology2Labels, fillDocBeforeCreate
 
+#TODO_P5 App freezes on loadKey
+#TODO_P5 unprocessed files should be have separate docType
+#TODO_P5 rerun extractors as batch
+
 class Backend(CLI_Mixin):
   """
   PYTHON BACKEND
@@ -287,6 +291,21 @@ def scanTree(self, **kwargs):
     startPath = Path(self.cwd)
     #prepare lists and start iterating
     inDB_all = self.db.getView('viewHierarchy/viewPaths')
+    #update content between DB and harddisk
+    for line in inDB_all:
+      if line['value'][1][0][0]=='x':
+        continue
+      doc = self.db.getDoc(line['id'])
+      if 'content' in doc:
+        path = self.basePath/line['key']
+        doc= {'-type':['procedure']}
+        self.useExtractors(path, '', doc)
+        self.db.updateDoc(doc, line['id'])
+    #TODO_P5: Basic functionality for V1
+    #V1: GUI content write-protected; assume one link and no conflicts
+    #V2: What happens if you change a file (procedure) on disk / database -> conflicts
+    #    Copy of procedure exists on harddisk: one entry in db and links; then change one, but not other, -branch should separate; can they reunite?
+
     pathsInDB_x    = [i['key'] for i in inDB_all if i['value'][1][0][0]=='x']  #all structure elements: task, subtasts
     pathsInDB_data = [i['key'] for i in inDB_all if i['value'][1][0][0]!='x']
     for root, dirs, files in os.walk(self.cwd, topdown=True):
@@ -307,7 +326,7 @@ def scanTree(self, **kwargs):
         if path in pathsInDB_x: #path already in database
           pathsInDB_x.remove(path)
           continue
-        _ = self.addData('x'+str(len(hierStack)), {'-name':dirName}, hierStack)
+        self.addData('x'+str(len(hierStack)), {'-name':dirName}, hierStack)
         newDir = Path(self.basePath)/self.db.getDoc(self.currentID)['-branch'][0]['path']
         (newDir/'.id_pastaELN.json').rename(Path(self.basePath)/root/dirName/'.id_pastaELN.json') #move index file into old folder
         newDir.rmdir()                     #remove created path
@@ -339,7 +358,10 @@ def scanTree(self, **kwargs):
           change = {'-branch': {'op':'d', 'oldpath':branch['path'], 'path':branch['path'], \
                                 'stack':branch['stack'] }}
           break
-      self.db.updateDoc(change, docID)
+      if change is None:
+        print('**ERROR Tried to remove orphan in database but could not', orphan)
+      else:
+        self.db.updateDoc(change, docID)
     if rerunScanTree:
       self.scanTree()
     return

pasta_eln/dialogConfig.py

@@ -11,7 +11,7 @@
 
 class Configuration(QDialog):
   """ Main class of entire config dialog """
-  def __init__(self, backend, startTap):
+  def __init__(self, backend, startTap=''):
     """
     Initialization
 

pasta_eln/dialogConfigGUI.py

@@ -30,7 +30,6 @@ def __init__(self, backend, callbackFinished):
       self.wD = self.addRowList('imageWidthDetails','Image width in details view', ['500','600','700','800'])
       self.wS = self.addRowList('sidebarWidth','Sidebar width', ['200','300','400'])
       self.log = self.addRowList('loggingLevel','Logging level (more->less)', ['DEBUG','INFO','WARNING','ERROR'])
-      self.nTC = self.addRowList('tableColumnsMax','Maximum number of table columns', ['8','16','32'])
       self.tabAppearanceL.addRow(TextButton('Save changes', self.saveData, None),
                                 TextButton('Restart PASTA-ELN', restart, None))
 
@@ -82,7 +81,6 @@ def saveData(self):
     self.backend.configuration['GUI']['imageWidthDetails'] = int(self.wD.currentText())
     self.backend.configuration['GUI']['sidebarWidth'] =  int(self.wS.currentText())
     self.backend.configuration['GUI']['loggingLevel'] = self.log.currentText()
-    self.backend.configuration['GUI']['tableColumnsMax'] = int(self.nTC.currentText())
     with open(Path.home()/'.pastaELN.json', 'w', encoding='utf-8') as fConf:
       fConf.write(json.dumps(self.backend.configuration,indent=2))
     restart()

pasta_eln/gui.py

@@ -11,6 +11,7 @@
 from .widgetSidebar import Sidebar
 from .widgetBody import Body
 from .dialogForm import Form
+from .dialogConfig import Configuration
 os.environ['QT_API'] = 'pyside6'
 
 # Subclass QMainWindow to customize your application's main window
@@ -28,10 +29,13 @@ def __init__(self):
 
     #Menubar
     menu = self.menuBar()
-    _ = menu.addMenu("&File")
+    menu.addMenu("&File")
     viewMenu = menu.addMenu("&View list")
-    _ = menu.addMenu("&System")
-    _ = menu.addMenu("&Help")
+    systemMenu = menu.addMenu("&System")
+    action = QAction('&Configuration',self)
+    action.triggered.connect(self.openConfigDialog)
+    systemMenu.addAction(action)
+    menu.addMenu("&Help")
 
     shortCuts = {'measurement':'m', 'sample':'s'}
     for docType, docLabel in self.comm.backend.db.dataLabels.items():
@@ -78,6 +82,14 @@ def viewMenu(self):
     self.comm.changeTable.emit(docType, '')
     return
 
+  def openConfigDialog(self):
+    """
+    open configuration dialog
+    """
+    configWindow = Configuration(self.comm.backend)
+    configWindow.exec()
+    return
+
 
 ##############
 ## Main function

pasta_eln/widgetDetails.py

@@ -1,9 +1,9 @@
 """ widget that shows the details of the items """
 import json
-from PySide6.QtWidgets import QScrollArea, QWidget, QVBoxLayout, QHBoxLayout, QLabel   # pylint: disable=no-name-in-module
+from PySide6.QtWidgets import QScrollArea, QWidget, QVBoxLayout, QHBoxLayout, QLabel, QMenu  # pylint: disable=no-name-in-module
 from PySide6.QtCore import Qt, Slot, QByteArray   # pylint: disable=no-name-in-module
 from PySide6.QtSvgWidgets import QSvgWidget       # pylint: disable=no-name-in-module
-from PySide6.QtGui import QPixmap, QImage         # pylint: disable=no-name-in-module
+from PySide6.QtGui import QPixmap, QImage, QAction# pylint: disable=no-name-in-module
 from .style import TextButton, Image, Label
 
 class Details(QScrollArea):
@@ -26,8 +26,9 @@ def __init__(self, comm):
     self.headerL = QHBoxLayout(headerW)
     self.mainL.addWidget(headerW)
     self.imageW = QWidget()
+    self.imageW.setContextMenuPolicy(Qt.CustomContextMenu)
+    self.imageW.customContextMenuRequested.connect(self.contextMenu)
     self.imageL = QVBoxLayout(self.imageW)
-    #TODO_P2 include extractor change
     self.mainL.addWidget(self.imageW)
     self.btnDetails = TextButton('Details', self.showArea, self.mainL, 'Details', 'Show / hide details', \
                                   checkable=True, hide=True)
@@ -51,6 +52,31 @@ def __init__(self, comm):
     self.mainL.addWidget(self.metaDatabaseW)
     self.mainL.addStretch(1)
 
+  def contextMenu(self, pos):
+    """
+    Create a context menu
+
+    Args:
+      pos (position): Position to create context menu at
+    """
+    context = QMenu(self)
+    mask   = '/'.join(self.doc['-type'][:3])
+    choices= {key:value for key,value in self.comm.backend.configuration['extractors'].items() if key.startswith(mask)}
+    for key,value in choices.items():
+      thisAction = QAction(value, self)
+      thisAction.setData(key)
+      thisAction.triggered.connect(self.changeExtractor)
+      context.addAction(thisAction)
+    context.exec(self.mapToGlobal(pos))
+    return
+
+  def changeExtractor(self):
+    """
+    What happens when user changes extractor
+    """
+    extractor = self.sender().data()
+    print(extractor)
+    return
 
   @Slot(str)
   def changeDetails(self, docID):