fix: xml validation (DEV-1360)

knora/dsp_tools.py

@@ -48,30 +48,29 @@ def program(user_args: list[str]) -> None:
     subparsers = parser.add_subparsers(title='Subcommands', description='Valid subcommands are', help='sub-command help')
 
     # create
-    parser_create = subparsers.add_parser('create', help='Upload an ontology and/or list(s) from a JSON file to the '
-                                               'DaSCH Service Platform')
+    parser_create = subparsers.add_parser('create', help='Upload a project and/or list(s) from a JSON project file to '
+                                               'the DaSCH Service Platform')
     parser_create.set_defaults(action='create')
     parser_create.add_argument('-s', '--server', type=str, default=default_localhost, help=url_text)
     parser_create.add_argument('-u', '--user', default=default_user, help=username_text)
     parser_create.add_argument('-p', '--password', default=default_pw, help=password_text)
-    parser_create.add_argument('-V', '--validate-only', action='store_true', help='Do only validation of JSON, no '
-                                    'upload of the ontology')
+    parser_create.add_argument('-V', '--validate-only', action='store_true', help='Only validate the project against '
+                               'the JSON schema, without uploading it')
     parser_create.add_argument('-l', '--lists-only', action='store_true', help='Upload only the list(s)')
     parser_create.add_argument('-v', '--verbose', action='store_true', help=verbose_text)
     parser_create.add_argument('-d', '--dump', action='store_true', help='dump test files for DSP-API requests')
-    parser_create.add_argument('datamodelfile', help='path to data model file')
+    parser_create.add_argument('projectfile', help='path to a JSON project file')
 
     # get
-    parser_get = subparsers.add_parser('get', help='Get the ontology (data model) of a project from the DaSCH Service '
-                                                   'Platform.')
+    parser_get = subparsers.add_parser('get', help='Get a project from the DaSCH Service Platform.')
     parser_get.set_defaults(action='get')
     parser_get.add_argument('-u', '--user', default=default_user, help=username_text)
     parser_get.add_argument('-p', '--password', default=default_pw, help=password_text)
     parser_get.add_argument('-s', '--server', type=str, default=default_localhost, help=url_text)
     parser_get.add_argument('-P', '--project', type=str, help='Shortcode, shortname or iri of project', required=True)
     parser_get.add_argument('-v', '--verbose', action='store_true', help=verbose_text)
-    parser_get.add_argument('datamodelfile', help='Path to the file the ontology should be written to',
-                            default='onto.json')
+    parser_get.add_argument('projectfile', help='Path to the file the project should be written to',
+                            default='project.json')
 
     # xmlupload
     parser_upload = subparsers.add_parser('xmlupload', help='Upload data from an XML file to the DaSCH Service Platform.')
@@ -101,7 +100,7 @@ def program(user_args: list[str]) -> None:
 
     # excel2resources
     parser_excel_resources = subparsers.add_parser('excel2resources', help='Create a JSON file from an Excel file '
-                                                        'containing resources for a DSP ontology. ')
+                                                   'containing resources for a DSP ontology. ')
     parser_excel_resources.set_defaults(action='excel2resources')
     parser_excel_resources.add_argument('excelfile', help='Path to the Excel file containing the resources',
                                         default='resources.xlsx')
@@ -147,35 +146,37 @@ def program(user_args: list[str]) -> None:
     if args.action == 'create':
         if args.lists_only:
             if args.validate_only:
-                validate_lists_section_with_schema(path_to_json_project_file=args.datamodelfile)
+                validate_lists_section_with_schema(path_to_json_project_file=args.projectfile)
+                print('"Lists" section of the JSON project file is syntactically correct and passed validation.')
+                exit(0)
             else:
-                create_lists(input_file=args.datamodelfile,
+                create_lists(input_file=args.projectfile,
                              server=args.server,
                              user=args.user,
                              password=args.password,
                              dump=args.dump)
         else:
-            if args.validate_only and validate_project(args.datamodelfile):
-                print('Data model is syntactically correct and passed validation.')
+            if args.validate_only:
+                validate_project(args.projectfile)
+                print('JSON project file is syntactically correct and passed validation.')
                 exit(0)
             else:
-                create_project(input_file=args.datamodelfile,
+                create_project(input_file=args.projectfile,
                                server=args.server,
                                user_mail=args.user,
                                password=args.password,
                                verbose=args.verbose,
                                dump=args.dump if args.dump else False)
     elif args.action == 'get':
         get_ontology(project_identifier=args.project,
-                     outfile=args.datamodelfile,
+                     outfile=args.projectfile,
                      server=args.server,
                      user=args.user,
                      password=args.password,
                      verbose=args.verbose)
     elif args.action == 'xmlupload':
         if args.validate:
-            validate_xml_against_schema(input_file=args.xmlfile,
-                                        schema_file="knora/dsplib/schemas/data.xsd")
+            validate_xml_against_schema(input_file=args.xmlfile)
         else:
             xml_upload(input_file=args.xmlfile,
                        server=args.server,
@@ -187,13 +188,13 @@ def program(user_args: list[str]) -> None:
                        incremental=args.incremental)
     elif args.action == 'excel2lists':
         excel2lists(excelfolder=args.excelfolder,
-                    outfile=args.outfile)
+                    path_to_output_file=args.outfile)
     elif args.action == 'excel2resources':
         excel2resources(excelfile=args.excelfile,
-                        outfile=args.outfile)
+                        path_to_output_file=args.outfile)
     elif args.action == 'excel2properties':
         excel2properties(excelfile=args.excelfile,
-                         outfile=args.outfile)
+                         path_to_output_file=args.outfile)
     elif args.action == 'id2iri':
         id_to_iri(xml_file=args.xmlfile,
                   json_file=args.jsonfile,

knora/dsplib/utils/onto_create_lists.py

@@ -71,10 +71,15 @@ def create_lists(
     dump: bool = False
 ) -> Tuple[dict[str, Any], bool]:
     """
-    This method uploads the "lists" section of a JSON project definition file to a DSP server. If the JSON project file
-    is still unparsed, this method parses it, expands the Excel sheets that are referenced, and validates it.
+    This method uploads the "lists" section of a JSON project definition file to a DSP server. The project must already
+    exist on the DSP server.
+
+    If the JSON project file is passed as "input_file", this method parses it, expands the Excel sheets that are
+    referenced, and validates it. If it is passed as "project_definition", these preliminary steps are not necessary.
+
     The "lists" section of the parsed project definition is then uploaded to the DSP server. If a list with the same
     name is already existing in this project on the DSP server, this list is skipped.
+
     Returns a tuple consisting of a dict and a bool. The dict contains the IRIs of the created list nodes. If there are
     no lists in the project definition, an empty dictionary is returned. The bool indicates if everything went smoothly
     during the process. If a warning or error occurred (e.g. one of the lists already exists, or one of the nodes could

knora/dsplib/utils/shared.py

@@ -2,6 +2,7 @@
 import unicodedata
 import pandas as pd
 import regex
+import os
 from lxml import etree
 from requests import RequestException
 from datetime import datetime
@@ -87,17 +88,18 @@ def try_network_action(
     raise BaseError(failure_msg)
 
 
-def validate_xml_against_schema(input_file: str, schema_file: str) -> bool:
+def validate_xml_against_schema(input_file: str) -> bool:
     """
     Validates an XML file against an XSD schema
 
     Args:
         input_file: the XML file to be validated
-        schema_file: the schema against which the XML file should be validated
 
     Returns:
         True if the XML file is valid. Otherwise, a BaseError with a detailed error log is raised
     """
+    current_dir = os.path.dirname(os.path.realpath(__file__))
+    schema_file = os.path.join(current_dir, "../schemas/data.xsd")
     xmlschema = etree.XMLSchema(etree.parse(schema_file))
     doc = etree.parse(input_file)
 

knora/dsplib/utils/xml_upload.py

@@ -241,10 +241,8 @@ def xml_upload(input_file: str, server: str, user: str, password: str, imgdir: s
     """
 
     # Validate the input XML file
-    current_dir = os.path.dirname(os.path.realpath(__file__))
-    schema_file = os.path.join(current_dir, '../schemas/data.xsd')
     try:
-        validate_xml_against_schema(input_file, schema_file)
+        validate_xml_against_schema(input_file)
     except BaseError as err:
         print(f"=====================================\n"
               f"{err.message}")