Dockerfile and tool xml for tad IT

.github/workflows/ci.yaml

@@ -10,8 +10,7 @@ env:
   GALAXY_FORK: galaxyproject
   GALAXY_BRANCH: release_25.1
   MAX_CHUNKS: 40
-  OPENAI_API_KEY: ${{secrets.OPENAI_API_KEY }}
-  OPENAI_ENDPOINT_URL: https://llm.ai.e-infra.cz/v1
+
 jobs:
   setup:
     name: Setup cache and determine changed repositories

.github/workflows/it_pr.yaml

@@ -0,0 +1,109 @@
+name: Galaxy Interactive Tool Linting and Tests for push and PR
+on:
+  workflow_dispatch:
+  pull_request:
+    paths-ignore:
+      - '.github/**'
+      - 'deprecated/**'
+      - 'docs/**'
+      - '*'
+  push:
+    branches:
+      - main
+      - master
+    paths-ignore:
+      - '.github/**'
+      - 'deprecated/**'
+      - 'docs/**'
+      - '*'
+env:
+  GALAXY_FORK: galaxyproject
+  GALAXY_BRANCH: release_25.1
+  MAX_CHUNKS: 4
+  MAX_FILE_SIZE: 1M
+
+concurrency:
+  # Group runs by PR, but keep runs on the default branch separate
+  # because we do not want to cancel ToolShed uploads
+  group: pr-${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && github.run_number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  changed_files:    
+    runs-on: ubuntu-latest  # windows-latest || macos-latest
+    name: Test changed-files
+    steps: # check out rep
+      - uses: actions/checkout@v6
+
+        # find files that are changed compared to master
+        # find dockerfiles that have changed and pick first or fail if more are changed
+      - name: Get all changed Dockerfiles
+        id: changed-dockerfiles
+        uses: tj-actions/changed-files@v47 # v47.0.6
+        with:
+          # Avoid using single or double quotes for multiline patterns
+          files: |
+            interactive_tools/**/Dockerfile
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.11'
+
+      - name: Install Planemo
+        shell: bash
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install planemo
+
+      - name: Validate Planemo installation
+        shell: bash
+        run: |
+          which planemo
+          planemo --version
+
+      # Expand macros and extract image name using planemo
+      - name: Expand macros and extract image name
+        id: expand-macros
+        shell: bash
+        run: |
+          # Get the directory containing the changed Dockerfile
+          changed_dockerfile="${{ steps.changed-dockerfiles.outputs.all_changed_files }}"
+          tool_dir=$(dirname "$changed_dockerfile")
+
+          # Find tool XML file
+          tool_xml=$(find "$tool_dir" -maxdepth 1 -name "*.xml" ! -name "macros.xml" | head -1 | xargs)
+
+          if [[ -z "$tool_xml" ]]; then
+            echo "No tool XML found in $tool_dir"
+            exit 1
+          fi
+
+           # Expand macros and capture output
+          expanded=$(planemo normalize --expand_macros "$tool_xml")
+
+          # Extract the container image name (only for type="docker")
+          image_name=$(echo "$expanded" | grep -oP '<container type="docker">\K[^<]+')
+
+          if [[ -z "$image_name" ]]; then
+            echo "No container tag with type=\"docker\" found after macro expansion"
+            exit 1
+          fi
+
+          echo "image_name=$image_name" >> "$GITHUB_OUTPUT"
+          echo "Extracted image: $image_name"
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v4
+
+        # built docker image locally using the action from eu repo
+      - name: Build docker image
+        env:
+          CHANGED_FILES: ${{ steps.changed-dockerfiles.outputs.all_changed_files }}
+        uses: docker/build-push-action@v7
+        with:
+          push: false
+          file: ${{ env.CHANGED_FILES }}
+          tags: ${{ steps.expand-macros.outputs.image_name }}
+
+    # use planemo to run the tests for interactivetool

interactive_tools/tad/.shed.yml

@@ -0,0 +1,13 @@
+name: tad
+owner: recetox
+type: unrestricted
+description: |
+  Interactive Tadviewer for viewing and manipulating tabular data in Galaxy.
+long_description: |
+  Tadviewer is a web-based adaptation of the Tad desktop application that enables
+  interactive exploration of tabular datasets from Galaxy, including SQL-like data
+  querying and filtering capabilities.
+homepage_url: https://github.com/RECETOX/tad
+remote_repository_url: https://github.com/RECETOX/galaxytools/tree/master/interactive_tools/tad
+categories:
+  - Visualization

interactive_tools/tad/Dockerfile

@@ -0,0 +1,35 @@
+FROM node:24-bookworm-slim
+
+ARG PORT=8765
+
+ENV PORT=$PORT
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    ca-certificates \
+    git \
+    xz-utils \
+    &&  apt-get clean \
+    &&  apt-get autoclean \
+    &&  apt-get autoremove --yes \
+    &&  rm -rf /var/lib/apt/lists/* \
+    &&  rm -rf /var/lib/dpkg/ \
+    &&  rm -rf /var/cache/ \
+    &&  rm -rf /var/log/ \
+    &&  rm -rf /tmp/* ;
+
+WORKDIR /app/tad
+# Clone git repo with modified code
+RUN git clone -b gxit https://github.com/RECETOX/tad.git . 
+
+RUN npm ci \
+    && npm install \
+    && npm run bootstrap \
+    && ./tools/build-all.sh
+
+WORKDIR /app/tad/packages/tadweb-server
+
+RUN npm run build && npm cache clean --force
+
+EXPOSE $PORT
+
+CMD ["npm", "start"]

interactive_tools/tad/interactivetool_tad.xml

@@ -0,0 +1,58 @@
+<tool id="interactive_tool_tad" tool_type="interactive" name="Tad" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>tadweb-server application to view and manipulate tabular data</description>
+    <icon src="tad.png"/>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator"/>
+
+    <requirements>
+        <container type="docker">recetox/tad:@TOOL_VERSION@</container>
+    </requirements>
+
+    <entry_points>
+        <entry_point name="tad-gxit" requires_domain="True">
+            <port>8765</port>
+            <url>/tadweb-app/index.html</url>
+        </entry_point>
+    </entry_points>
+
+    <environment_variables>
+        <!-- These will be accessible as environment variables inside the Docker container -->
+        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
+        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
+    </environment_variables>
+
+    <command><![CDATA[
+        ## Symlink or copy the galaxy input files into the TAD server directory
+        JOB_DIR=\$PWD &&
+        #for $file in $infiles:
+            ## We use the element_identifier (the name of the file in Galaxy history) 
+            ## to give it a sensible name, ensuring it ends with .csv
+            ln -s '$file' '${file.name}.${file.ext}' &&
+        #end for
+        cd /app/tad/packages/tadweb-server &&
+
+        ## Run the server
+        npm start -- -d \$JOB_DIR > $logfile 2>&1
+    ]]>
+    </command>
+
+    <inputs>
+        <param name="infiles" type="data" format="csv,tabular,tsv,parquet" multiple="true" label="Select one or more tabular datasets, or a dataset collection." help="Must be in CSV/tabular format."/>
+    </inputs>
+
+    <outputs>
+        <data name="logfile" format="txt"/>
+    </outputs>
+
+    <tests>
+    <!-- Currently does not have tests. -->
+    </tests>
+
+
+    <help>Tadviewer is a web-based adaptation of the Tad desktop application created by Antony Courtney: https://github.com/antonycourtney/tad
+          It enables viewing of tabular data from the Galaxy instance with built-in support of SQL features. 
+          This galaxy interactive tool is mainatained by RECETOX organization: https://github.com/RECETOX/tad </help>
+
+</tool>

interactive_tools/tad/macros.xml

@@ -0,0 +1,24 @@
+<macros>
+    <xml name="creator">
+        <creator>
+            <person
+                givenName="Helge"
+                familyName="Hecht"
+                url="https://github.com/hechth"
+                identifier="0000-0001-6744-996X" />
+            <person
+                givenName="Michaela"
+                familyName="Boďova"
+                url="https://github.com/mbodova"
+                identifier="" />
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+                name="RECETOX MUNI" />
+        </creator>
+    </xml>
+
+
+    <token name="@TOOL_VERSION@">0.14.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+</macros>

interactive_tools/tad/test-data/sample.csv

@@ -0,0 +1,4 @@
+firstName,lastName,email,phoneNumber
+John,Doe,john@doe.com,0123456789
+Jane,Doe,jane@doe.com,9876543210
+James,Bond,james.bond@mi6.co.uk,0612345678