Small changes

pasta_eln/inputOutput.py

@@ -59,7 +59,7 @@ def importELN(backend:Backend, elnFileName:str, projID:str) -> tuple[str,dict[st
   Args:
     backend (backend): backend
     elnFileName (str): name of file
-    projID (str): project to import data into. If '', create a new project (only available for PastaELN)
+    projID (str): project to import data into.
 
   Returns:
     str: success message, statistics
@@ -86,10 +86,10 @@ def importELN(backend:Backend, elnFileName:str, projID:str) -> tuple[str,dict[st
         publisherNode = [i for i in graph if i["@id"]==rocrateNode['sdPublisher']['@id']][0]
       elnName = publisherNode['name']
     logging.info('Import %s', elnName)
-    if not projID and elnName!='PASTA ELN':
+    if not projID:
       return "FAILURE: YOU CANNOT IMPORT AS PROJECT IF NON PASTA-ELN FILE",{}
-    if projID:
-      backend.changeHierarchy(projID)
+    backend.changeHierarchy(projID)
+    childrenStack = [0]
     mainNode    = [i for i in graph if i["@id"]=="./"][0]
     # clean subchildren from mainNode: see https://github.com/TheELNConsortium/TheELNFileFormat/issues/98
     parentNodes = {i['@id'] for i in mainNode['hasPart']}
@@ -235,6 +235,8 @@ def processPart(part:dict[str,str]) -> int:
           docType = ''
       if docType=='x0':
         backend.hierStack = []
+      childrenStack[-1] += 1
+      doc['childNum'] = childrenStack[-1]
       # print(f'Want to add doc:{doc} with type:{docType} and cwd:{backend.cwd}')
       try:
         docID = backend.addData(docType, doc)['id']
@@ -245,6 +247,7 @@ def processPart(part:dict[str,str]) -> int:
         docID = None
       if docID[0]=='x':
         backend.changeHierarchy(docID)
+        childrenStack.append(0)
         with open(backend.basePath/backend.cwd/'.id_pastaELN.json','w', encoding='utf-8') as f:  #local path, update in any case
           f.write(json.dumps(backend.db.getDoc(docID)))
         # children, aka recursive part
@@ -253,6 +256,7 @@ def processPart(part:dict[str,str]) -> int:
             continue
           addedDocs += processPart(child)
         backend.changeHierarchy(None)
+        childrenStack.pop()
       return addedDocs
 
     ######################

pasta_eln/sqlite.py

@@ -195,19 +195,24 @@ def getDoc(self, docID:str) -> dict[str,Any]:
     self.cursor.execute(f"SELECT * FROM branches WHERE id == '{docID}'")
     for dataI in self.cursor.fetchall():
       doc['branch'].append({'stack': dataI[2].split('/')[:-1],
-                             'child': dataI[3],
-                             'path':  None if dataI[4] == '*' else dataI[4],
-                             'show':   [i=='T' for i in dataI[5]]})
+                            'child': dataI[3],
+                            'path':  None if dataI[4] == '*' else dataI[4],
+                            'show':   [i=='T' for i in dataI[5]]})
     cmd = "SELECT properties.key, properties.value, properties.unit, propDefinitions.long, propDefinitions.IRI, " \
           "definitions.unit, definitions.query, definitions.IRI FROM properties LEFT JOIN propDefinitions USING(key) "\
           "LEFT JOIN definitions ON properties.key = (definitions.class || '.' || definitions.name) "\
           f"WHERE properties.id == '{docID}'"
+    # Big assumption in "LEFT JOIN definitions ON properties.key = (definitions.class || '.' || definitions.name)"
+    #   with 'docType' missing
+    # -> each property ".status" has the same meaning for all docTypes
+    # -> if it has the same meaning, it is only stored once??
     self.cursor.execute(cmd)
     res = self.cursor.fetchall()
-    metadataFlat:dict[str, tuple[str,str,str,str]] = {i[0]:(i[1],
-                          ('' if i[2] is None else i[2])+('' if i[5] is None else i[5]),
-                          ('' if i[3] is None else i[3])+('' if i[6] is None else i[6]),
-                          ('' if i[4] is None else i[4])+('' if i[7] is None else i[7])) for i in res}
+    metadataFlat:dict[str, tuple[str,str,str,str]]  = {i[0]:(    i[1],                      #value
+                          ('' if i[2] is None else i[2]) or ('' if i[5] is None else i[5]), #unit
+                          ('' if i[3] is None else i[3]) or ('' if i[6] is None else i[6]), #long
+                          ('' if i[4] is None else i[4]) or ('' if i[7] is None else i[7])  #IRI
+                          ) for i in res}
     doc |= hierarchy(metadataFlat)
     return doc
 
@@ -305,6 +310,8 @@ def insertMetadata(data:dict[str,Any], parentKeys:str) -> None:
       return
     # properties
     metaDoc = {k:v for k,v in doc.items() if k not in KEY_ORDER}
+    # remove the (unit, long, IRI) of the ones that are already in data hierarchy
+    #    create a test case for this
     insertMetadata(metaDoc, '')
     # save changes
     self.connection.commit()

tests/test_90_ImportOthers.py

@@ -50,9 +50,14 @@ def test_simple(qtbot):
             }
   urlBase = 'https://github.com/SteffenBrinckmann/TheELNFileFormat/raw/refs/heads/new_PastaELN/examples/'
   # 'https://github.com/TheELNConsortium/TheELNFileFormat/raw/refs/heads/master/examples/'
+  localDir= '/home/xyz/Repositories/TheELNConsortium/TheELNFileFormat/examples/'
+  local = False
   for eln, pathName in allELNs.items():
-    elnFileName = f'{tempDir}/{eln}'
-    request.urlretrieve(f'{urlBase}{pathName}', elnFileName)
+    if local:
+      elnFileName = f'{localDir}/{pathName}'
+    else:
+      elnFileName = f'{tempDir}/{eln}'
+      request.urlretrieve(f'{urlBase}{pathName}', elnFileName)
     print(f'\nStart with {eln}')
     projName = f'{eln[:-4]} Import'
     backend.addData('x0', {'name': projName})