Merge branch 'f-fix-zip-files' into 'dev'

Fix zip file export

See merge request !146

.gitlab-ci.yml

@@ -66,12 +66,12 @@ test-server-side-scripting:
 # Build a docker image in which tests for this repository can run
 build-testenv:
   tags: [ cached-dind ]
-  image: docker:19.03
+  image: docker:27.3.1
   stage: setup
   timeout: 3 h
-  only:
-    - web
-    - schedules
+  # only:
+  #   - web
+  #   - schedules
   script: 
     - cd test/docker
     - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $CI_REGISTRY

CHANGELOG.md

@@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed ###
 
+- [#254](https://gitlab.com/linkahead/linkahead-webui/-/issues/254) "Download files referenced in the table" failed
+
 ### Security ###
 
 ### Documentation ###

src/server_side_scripting/ext_file_download/zip_files.py

@@ -32,7 +32,7 @@ from zipfile import ZipFile
 
 import linkahead as db
 import pandas as pd
-from linkaheadadvancedtools.serverside import helper
+from caosadvancedtools.serverside import helper
 from linkahead import LinkAheadException, ConsistencyError, EntityDoesNotExistError
 
 
@@ -71,9 +71,7 @@ def collect_files_in_zip(ids, table):
         # download and add all files
         for file_id in ids:
             try:
-                tmp = db.execute_query("FIND FILE WITH ID={a:}".format(
-                    a=file_id),
-                    unique=True)
+                tmp = db.get_entity_by_id(file_id, role="FILE")
             except EntityDoesNotExistError as e:
                 # TODO
                 # Current behavior: script terminates with error if just one
@@ -81,14 +79,14 @@ def collect_files_in_zip(ids, table):
                 # Desired behavior: The script should go on with the other
                 # ids, but the user should be informed about the missing files.
                 # How should we do this?
-                logger = logging.getLogger("linkaheadadvancedtools")
-                logger.error("Did not find Entity with ID={}.".format(
+                logger = logging.getLogger("caosadvancedtools")
+                logger.error("Did not find File with ID={}.".format(
                     file_id))
 
                 raise e
             savename = nc.get_unique_savename(os.path.basename(tmp.path))
             val_file = helper.get_file_via_download(
-                tmp, logger=logging.getLogger("linkaheadadvancedtools"))
+                tmp, logger=logging.getLogger("caosadvancedtools"))
 
             zf.write(val_file, savename)
 

src/server_side_scripting/ext_table_preview/pandas_table_preview.py

@@ -35,8 +35,8 @@ from datetime import datetime
 
 import linkahead as db
 import pandas as pd
-from linkaheadadvancedtools.serverside.helper import get_argument_parser
-from linkaheadadvancedtools.serverside.logging import configure_server_side_logging
+from caosadvancedtools.serverside.helper import get_argument_parser
+from caosadvancedtools.serverside.logging import configure_server_side_logging
 
 MAXIMUMFILESIZE = 1e8
 VALID_ENDINGS = [".csv", ".tsv", ".xls", ".xlsx"]
@@ -135,7 +135,7 @@ if __name__ == "__main__":
     args = parser.parse_args()
 
     debug_file = configure_server_side_logging()
-    logger = logging.getLogger("linkaheadadvancedtools")
+    logger = logging.getLogger("caosadvancedtools")
 
     db.configure_connection(auth_token=args.auth_token)
     entity_id = args.filename

test/docker/Dockerfile

-FROM debian:11
+FROM debian:12
 ADD node_gpg.asc /etc/apt/
 RUN  apt-get update \
     && apt-get install -y gnupg ca-certificates\
@@ -12,14 +12,15 @@ RUN  apt-get update \
       nodejs npm \
     && apt-get install -f
 
-RUN pip3 install pylint pytest
+RUN pip3 install --break-system-packages pylint pytest
+RUN pip3 install --break-system-packages sphinx-js sphinx-autoapi recommonmark sphinx-rtd-theme
+RUN pip3 install --break-system-packages pandas
+
 # TODO rename to linkahead
-# RUN pip3 install caosdb>=0.7.4
-RUN pip3 install git+https://gitlab.com/caosdb/caosdb-pylib.git@f-linkahead-rename
-RUN pip3 install pandas
+RUN pip3 install --break-system-packages git+https://gitlab.com/caosdb/caosdb-pylib.git@dev
 # TODO rename to linkahead
-RUN pip3 install git+https://gitlab.com/caosdb/caosdb-advanced-user-tools.git@f-linkahead-rename
+RUN pip3 install --break-system-packages git+https://gitlab.com/caosdb/caosdb-advanced-user-tools.git@dev
+
 # For automatic documentation
 # RUN npm install -g jsdoc
 # RUN npm install -g jsdoc-sphinx
-RUN pip3 install sphinx-js sphinx-autoapi recommonmark sphinx-rtd-theme

test/server_side_scripting/ext_file_download/test_zip_files.py

+#!/usr/bin/env python3
+# encoding: utf-8
+#
+# This file is a part of the LinkAhead Project.
+#
+# Copyright (C) 2024 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2024 Daniel Hornung <d.hornung@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+import os
+import unittest
+
+import linkahead as db
+from linkahead.common.models import _parse_single_xml_element
+from lxml import etree
+from zip_files import (collect_files_in_zip)
+
+
+class ZipTest(unittest.TestCase):
+    pass

test/server_side_scripting/ext_file_download/zip_files.py

+../../../src/server_side_scripting/ext_file_download/zip_files.py
\ No newline at end of file

test/server_side_scripting/ext_table_preview/requirements.txt

+linkahead
 # TODO rename to linkahead
-caosdb
 caosadvancedtools
 pandas