Compare revisions

Daniel Hornung · Daniel Hornung · Daniel Hornung · Daniel Hornung · Florian Spreckelsen · Florian Spreckelsen
--- a/.gitlab-ci.yml
+++ b/.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 $CI_REGISTRY
@@ -93,7 +93,8 @@ pages_prepare: &pages_prepare
    refs:
      - /^release-.*$/i
  script:
-    - npm install jsdoc jsdoc-sphinx
+    - npm install -g jsdoc
+    - npm install @indiscale/jsdoc-sphinx
    - echo "Deploying"
    - make doc
    - rm -r public || true ; cp -r build/doc/html public

--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

 ### Documentation ###

+## [0.15.1] - 2014-12-20 ##
+
+### Fixed ###
+
+- [#254](https://gitlab.com/linkahead/linkahead-webui/-/issues/254) "Download files referenced in the table" failed
+- [#230](https://gitlab.com/linkahead/linkahead-webui/-/issues/230)
+  `make doc` is now compatible with npm >= 9.0.0.
+
 ## [0.15.0] - 2024-10-01 ##

 ### Added ###

--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -80,13 +80,16 @@ See `build.properties.d/00_default.properties` for more information.

 ## Build the documentation #

-Build documentation in `build/` with `make doc`.
+Install the below requirements and build documentation in `build/`
+with `make doc`. You may need to set the environment variables used in
+`src/doc/Makefile`, especially `JSDOC_BIN` in case you didn't install
+jsdoc globally.

 ### Requirements ##

 - sphinx
 - sphinx-autoapi
 - jsdoc (`npm install jsdoc`)
- jsdoc-sphinx  (`npm install jsdoc-sphinx`)
+- @indiscale/jsdoc-sphinx  (`npm install @indiscale/jsdoc-sphinx`)
 - sphinx-js
 - recommonmark
--- a/src/doc/Makefile
+++ b/src/doc/Makefile
@@ -24,16 +24,15 @@
 # It is based upon the autocreated makefile for Sphinx documentation.

 # You can set these variables from the command line, and also
-# from the environment for the first two.
+# from the environment for the first four.
 SPHINXOPTS    ?= -a
 SPHINXBUILD   ?= sphinx-build
+NPM_PREFIX ?= ../..
+JSDOC_BIN ?= jsdoc
 # SPHINXAPIDOC  ?= javasphinx-apidoc
 SOURCEDIR      = .
 BUILDDIR       = ../../build/doc

-# npm is not always in the global PATH
-NPM_PATH = $(shell npm bin)
-NPM_PREFIX = $(shell npm prefix)

 .PHONY: doc-help Makefile api

@@ -44,8 +43,8 @@ doc-help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile api
-	PATH=$(NPM_PATH):$$PATH $(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 #	sphinx-build -M html . ../../build/doc

 api:
-	PATH=$(NPM_PATH):$$PATH jsdoc -t $(NPM_PREFIX)/node_modules/jsdoc-sphinx/template -d $@ -r "../../src/core"
+	$(JSDOC_BIN) -t $(NPM_PREFIX)/node_modules/@indiscale/jsdoc-sphinx/template -d $@ -r "../../src/core"
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -26,9 +26,9 @@ copyright = '2022 - 2024, IndiScale GmbH'
 author = 'Daniel Hornung'

 # The short X.Y version
-version = '0.15.1'
+version = '0.15.2'
 # The full version, including alpha/beta/rc tags
-release = '0.15.1-SNAPSHOT'
+release = '0.15.2-SNAPSHOT'


 # -- General configuration ---------------------------------------------------
@@ -196,7 +196,7 @@ primary_domain = 'js'  # Not strictly necessary?
 # -- Options for intersphinx extension ---------------------------------------

 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {}

 # TODO Which options do we want?
 autodoc_default_options = {

--- a/src/doc/index.rst
+++ b/src/doc/index.rst
@@ -28,5 +28,4 @@ the most important concepts and offers a range of
 Indices and tables
 ==================

-* :ref:`genindex`
 * :ref:`search`
--- a/src/server_side_scripting/ext_file_download/zip_files.py
+++ b/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)


--- a/src/server_side_scripting/ext_table_preview/pandas_table_preview.py
+++ b/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

--- a/test/docker/Dockerfile
+++ b/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
--- a/test/server_side_scripting/ext_file_download/test_zip_files.py
+++ b/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
--- a/test/server_side_scripting/ext_file_download/zip_files.py
+++ b/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
--- a/test/server_side_scripting/ext_table_preview/requirements.txt
+++ b/test/server_side_scripting/ext_table_preview/requirements.txt
+linkahead
 # TODO rename to linkahead
-caosdb
 caosadvancedtools
 pandas
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