Merge pull request #189 from PASTA-ELN/sb_smallerBugs

Repair smaller bugs that I found

pasta_eln/GUI/form.py

@@ -433,37 +433,18 @@ def execute(self, command:list[Any]) -> None:
       # ---- if docType changed: save; no further save to db required ----
       if hasattr(self, 'docTypeComboBox') and self.docTypeComboBox.currentData() != '':
         self.doc['-type'] = [self.docTypeComboBox.currentData()]
-        if '_ids' in self.doc: #group update
-          self.doc = {k:v for k,v in self.doc.items() if v} # filter out empty items
-          for docID in self.doc.pop('_ids'):
-            doc = self.db.getDoc(docID)
-            doc.update( self.doc )
-            self.db.remove(doc['_id'])
-            del doc['_id']
-            del doc['_rev']
-            doc = fillDocBeforeCreate(doc, self.docTypeComboBox.currentData())
-            self.db.saveDoc(doc)
-        else:                  #single or sequential update
-          self.db.remove(self.doc['_id'])
-          del self.doc['_id']
-          del self.doc['_rev']
-          self.doc = fillDocBeforeCreate(self.doc, self.docTypeComboBox.currentData())
-          self.db.saveDoc(self.doc)
-      # ---- all other changes ----
-      else:
-        if '_ids' in self.doc: #group update
-          if '-name' in self.doc:
-            del self.doc['-name']
-          ids = self.doc.pop('_ids')
-          self.doc = {i:j for i,j in self.doc.items() if j!=''}
-          for docID in ids:
-            doc = self.db.getDoc(docID)
-            doc.update( self.doc )
-            self.comm.backend.editData(doc)
-        elif '_id' in self.doc:                                   #default update on item
-          self.comm.backend.editData(self.doc)
-        else:                                                     #create new dataset
-          self.comm.backend.addData(self.doc['-type'][0], copy.deepcopy(self.doc), newProjID)
+      if '_ids' in self.doc:                              # group update
+        if '-name' in self.doc:
+          del self.doc['-name']
+        self.doc = {k:v for k,v in self.doc.items() if v} # filter out empty items
+        for docID in self.doc.pop('_ids'):
+          doc = self.db.getDoc(docID)
+          doc.update( self.doc )
+          self.comm.backend.editData(doc)
+      elif '_id' in self.doc:                             # default update on item
+        self.comm.backend.editData(self.doc)
+      else:                                               # create new dataset
+        self.comm.backend.addData(self.doc['-type'][0], copy.deepcopy(self.doc), newProjID)
       #!!! NO updates / redraw here since one does not know from where form came
       # e.g. sequential edit cannot have redraw here
       if command[0] is Command.FORM_SAVE_NEXT:

pasta_eln/GUI/project.py

@@ -339,10 +339,10 @@ def modelChanged(self, item:QStandardItem) -> None:
     item.setData(item.data() | {'hierStack': '/'.join(stackNew+[docID])})
     # change siblings
     for line in siblingsOld:
-      db.updateBranch(docID=line['id'], branch=line['value'][3], child=line['value'][0]-1)
+      db.updateBranch(  docID=line['id'], branch=line['value'][4], child=line['value'][0]-1)
     for line in siblingsNew:
       if line['id']!=docID:
-        db.updateBranch(docID=line['id'], branch=line['value'][3], child=line['value'][0]+1)
+        db.updateBranch(docID=line['id'], branch=line['value'][4], child=line['value'][0]+1)
     return
 
 

pasta_eln/GUI/projectTreeView.py

@@ -32,7 +32,8 @@ def contextMenuEvent(self, p:QPoint) -> None:
     Args:
       p (QPoint): point of clicking
     """
-    folder = self.currentIndex().data().split('/')[-1][0]=='x'
+    item = self.model().itemFromIndex(self.currentIndex())
+    folder = item.data()['hierStack'].split('/')[-1][0]=='x'
     context = QMenu(self)
     if folder:
       Action('Add child folder',                   self, [Command.ADD_CHILD],      context)
@@ -69,6 +70,7 @@ def execute(self, command:list[Any]) -> None:
       child = QStandardItem('/'.join(hierStack+[docID]))
       child.setFlags(Qt.ItemIsEnabled | Qt.ItemIsSelectable | Qt.ItemIsDragEnabled | Qt.ItemIsDropEnabled) # type: ignore
       item.appendRow(child)
+      self.comm.changeProject.emit('','') #refresh project
       #appendRow is not 100% correct:
       # - better: insertRow before the first non-folder, depending on the child number
       #   -> get highest non 9999 childNumber
@@ -87,6 +89,7 @@ def execute(self, command:list[Any]) -> None:
       child = QStandardItem('/'.join(hierStack+[docID]))
       child.setFlags(Qt.ItemIsEnabled | Qt.ItemIsSelectable | Qt.ItemIsDragEnabled | Qt.ItemIsDropEnabled) # type: ignore
       parent.appendRow(child)
+      self.comm.changeProject.emit('','') #refresh project
       #++ TODO appendRow is not 100% correct: see above
     elif command[0] is Command.DELETE:
       ret = QMessageBox.critical(self, 'Warning', 'Are you sure you want to delete this data?',\
@@ -158,7 +161,9 @@ def tree2Clicked(self) -> None:
     docID = item.data()['hierStack'].split('/')[-1]
     doc   = self.comm.backend.db.getDoc(docID)
     self.comm.formDoc.emit(doc)
-    item  = self.model().itemFromIndex(self.currentIndex())
+    docNew = self.comm.backend.db.getDoc(docID)
+    item.setText(docNew['-name'])
+    item.setData(item.data() | {"docType":docNew['-type'], "gui":docNew['-gui']})
     item.emitDataChanged()  #force redraw (resizing and repainting) of this item only
     return
 

pasta_eln/database.py

@@ -1,15 +1,16 @@
 """ Class for interaction with couchDB """
-import traceback, logging, time, json, os, re
+import traceback, logging, time, json, os, re, base64, io
 from typing import Any, Optional, Union
 from pathlib import Path
 from anytree import Node
 from anytree.search import find_by_attr
+from PIL import Image
 from cloudant.client import CouchDB
 from cloudant.replicator import Replicator
 from PySide6.QtWidgets import QProgressBar  # pylint: disable=no-name-in-module
 from .fixedStringsJson import defaultDataHierarchy, defaultDataHierarchyNode
 from .handleDictionaries import dataHierarchy_pre_to_V4
-from .miscTools import tracebackString, DummyProgressBar
+from .miscTools import tracebackString, DummyProgressBar, outputString
 
 class Database:
   """
@@ -422,8 +423,7 @@ def updateBranch(self, docID:str, branch:int, child:int, stack:Optional[list[str
           oldJsonContent = json.load(fIn)
           oldDocID = oldJsonContent['_id']
       if path is not None and (self.basePath/path).exists() and docID!=oldDocID:
-        print(f'**ERROR** Target folder already exist: {path}. Try to create a new path name')
-        logging.error('Target folder already exist: %s. Try to create a new path name', path)
+        logging.info('Target folder already exist: %s. I will try to create a new path name', path)
       while path is not None and (self.basePath/path).exists() and docID!=oldDocID:
         if re.search(r"_\d+$", path) is None:
           path += '_1'
@@ -798,18 +798,15 @@ def checkDB(self, outputStyle:str='text', repair:bool=False, minimal:bool=False)
     Returns:
         str: output
     """
-    import base64, io
-    from PIL import Image
-    from .miscTools import outputString
     outstring = ''
     if outputStyle=='html':
       outstring += '<div align="right">'
     outstring+= outputString(outputStyle,'h2','LEGEND')
     if not minimal:
       outstring+= outputString(outputStyle,'ok','Green: perfect and as intended')
       outstring+= outputString(outputStyle,'okish', 'Blue: ok-ish, can happen: empty files for testing, strange path for measurements')
-    outstring+= outputString(outputStyle,'unsure','Pink: unsure if bug or desired (e.g. move step to random path-name)')
-    outstring+= outputString(outputStyle,'warning','Yellow: WARNING should not happen (e.g. procedures without project)')
+    outstring+= outputString(outputStyle,'unsure', 'Dark magenta: unsure if bug or desired (e.g. move step to random path-name)')
+    outstring+= outputString(outputStyle,'warning','Orange-red: WARNING should not happen (e.g. procedures without project)')
     outstring+= outputString(outputStyle,'error',  'Red: FAILURE and ERROR: NOT ALLOWED AT ANY TIME')
     if outputStyle=='html':
       outstring += '</div>'
@@ -910,12 +907,12 @@ def checkDB(self, outputStyle:str='text', repair:bool=False, minimal:bool=False)
         #doc-type specific tests
         if '-type' in doc and doc['-type'][0] == 'sample':
           if 'qrCode' not in doc:
-            outstring+= outputString(outputStyle,'error',f"dch09: qrCode not in sample {doc['_id']}")
+            outstring+= outputString(outputStyle,'warning',f"dch09: qrCode not in sample {doc['_id']}")
         elif '-type' in doc and doc['-type'][0] == 'measurement':
           if 'shasum' not in doc:
-            outstring+= outputString(outputStyle,'error',f"dch10: shasum not in measurement {doc['_id']}")
+            outstring+= outputString(outputStyle,'warning',f"dch10: shasum not in measurement {doc['_id']}")
           if 'image' not in doc:
-            outstring+= outputString(outputStyle,'error',f"dch11: image not in measurement {doc['_id']}")
+            outstring+= outputString(outputStyle,'warning',f"dch11: image not in measurement {doc['_id']}")
           else:
             if doc['image'].startswith('data:image'):  #for jpg and png
               try:
@@ -943,7 +940,7 @@ def checkDB(self, outputStyle:str='text', repair:bool=False, minimal:bool=False)
     shasumKeys = []
     for item in view:
       if item['key']=='':
-        outstring+= outputString(outputStyle,'error', f"measurement without shasum: {item['id']} {item['value']}")
+        outstring+= outputString(outputStyle,'warning', f"measurement without shasum: {item['id']} {item['value']}")
       else:
         if item['key'] in shasumKeys:
           key = item['key'] or '- empty string -'

pasta_eln/miscTools.py

@@ -59,7 +59,7 @@ def outputString(fmt:str='print', level:str='info', message:str='') -> str:
   if 'text' in fmt:
     return txtOutput
   if fmt=='html':
-    colors = {'info':'black','error':'red','warning':'orange','ok':'green','okish':'blue','unsure':'magenta'}
+    colors = {'info':'black','error':'red','warning':'orangered','ok':'green','okish':'blue','unsure':'darkmagenta'}
     if level[0]=='h':
       return f'<{level}>{message}</{level}>'
     if level not in colors: