Merge remote-tracking branch 'origin/main'

rmassei · Aug 8, 2024 · a4d5d5d · a4d5d5d
2 parents 1814b7b + b9d952c
commit a4d5d5d
Show file tree

Hide file tree

Showing 32 changed files with 442 additions and 136 deletions.
diff --git a/.github/omero-docker-compose.yml b/.github/omero-docker-compose.yml
@@ -0,0 +1,54 @@
+# from https://github.com/TheJacksonLaboratory/ezomero/blob/main/tests/docker-compose.yml
+
+version: "3"
+
+services:
+
+  database:
+    image: "postgres:11"
+    environment:
+      POSTGRES_USER: omero
+      POSTGRES_DB: omero
+      POSTGRES_PASSWORD: omero
+    networks:
+      - omero
+    volumes:
+      - "database:/var/lib/postgresql/data"
+
+  omero:
+    # This container uses the tag for the latest server release of OMERO 5
+    # To upgrade to the next major release, increment the major version number
+    image: "openmicroscopy/omero-server:latest"
+    environment:
+      CONFIG_omero_db_host: database
+      CONFIG_omero_db_user: omero
+      CONFIG_omero_db_pass: omero
+      CONFIG_omero_db_name: omero
+      CONFIG_omero_policy_binary__access: +read,+write,+image,+plate
+      CONFIG_omero_glacier2_IceSSL_Ciphers: "HIGH:!DH"
+      ROOTPASS: omero
+    networks:
+      - omero
+    ports:
+      - "6063:4063"
+      - "6064:4064"
+    volumes:
+      - "omero:/OMERO"
+
+  omeroweb:
+    # This container uses the tag for the latest web release of OMERO 5
+    # To upgrade to the next major release, increment the major version number
+    image: "openmicroscopy/omero-web-standalone:latest"
+    environment:
+      OMEROHOST: omero
+    networks:
+      - omero
+    ports:
+      - "5080:4080"
+
+networks:
+  omero:
+
+volumes:
+  database:
+  omero:
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -156,6 +156,19 @@ jobs:
       uses: eWaterCycle/setup-apptainer@v2
     - name: Symlink singularity
       run: ln -s $(which apptainer) $(dirname apptainer)/singularity
+    - name: Install containers
+      run: |
+        echo "${{ needs.setup.outputs.repository-list }}" > repository_list.txt
+        if grep -q scripting repository_list.txt; then
+          singularity pull --dir /tmp docker://continuumio/anaconda3
+          singularity pull --dir /tmp docker://rocker/tidyverse
+        fi
+
+    - name: Start OMERO
+      uses: sudo-bot/action-docker-compose@latest
+      with:
+        cli-args: "-f .github/omero-docker-compose.yml up -d"
+
     # download or create large test data via script
     - name: Create test data
       run: |
@@ -182,6 +195,7 @@ jobs:
         repository-list: ${{ needs.setup.outputs.repository-list }}
         galaxy-fork: ${{ needs.setup.outputs.fork }}
         galaxy-branch: ${{ needs.setup.outputs.branch }}
+        additional-planemo-options: --docker_run_extra_arguments '--add-host=host.docker.internal:host-gateway'
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -297,6 +297,20 @@ jobs:
       uses: eWaterCycle/setup-apptainer@v2
     - name: Symlink singularity
       run: ln -s $(which apptainer) $(dirname apptainer)/singularity
+    - name: Install containers
+      run: |
+        echo "${{ needs.setup.outputs.repository-list }}" > repository_list.txt
+        if grep -q scripting repository_list.txt; then
+          singularity pull --dir /tmp docker://continuumio/anaconda3
+          singularity pull --dir /tmp docker://rocker/tidyverse
+        fi
+
+    # Start OMERO
+    - name: Start OMERO
+      uses: sudo-bot/action-docker-compose@latest
+      with:
+        cli-args: "-f .github/omero-docker-compose.yml up -d"
+
     # download or create large test data via script
     - name: Create test data
       run: |
@@ -323,6 +337,7 @@ jobs:
         repository-list: ${{ needs.setup.outputs.repository-list }}
         galaxy-fork: ${{ env.GALAXY_FORK }}
         galaxy-branch: ${{ env.GALAXY_BRANCH }}
+        additional-planemo-options: --docker_run_extra_arguments '--add-host=host.docker.internal:host-gateway'
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}

diff --git a/...nagers/data_manager_megan_tools/.shed.yml → ...nagers/data_manager_megan_tools/.shed.yml b/...nagers/data_manager_megan_tools/.shed.yml → ...nagers/data_manager_megan_tools/.shed.yml
diff --git a/..._megan_tools/data_manager/data_manager.py → ..._megan_tools/data_manager/data_manager.py b/..._megan_tools/data_manager/data_manager.py → ..._megan_tools/data_manager/data_manager.py
diff --git a/...ools/data_manager/megan_tools_fetcher.xml → ...ools/data_manager/megan_tools_fetcher.xml b/...ools/data_manager/megan_tools_fetcher.xml → ...ools/data_manager/megan_tools_fetcher.xml
diff --git a/...manager_megan_tools/data_manager_conf.xml → ...manager_megan_tools/data_manager_conf.xml b/...manager_megan_tools/data_manager_conf.xml → ...manager_megan_tools/data_manager_conf.xml
diff --git a/...an_tools/tool-data/megan_tools.loc.sample → ...an_tools/tool-data/megan_tools.loc.sample b/...an_tools/tool-data/megan_tools.loc.sample → ...an_tools/tool-data/megan_tools.loc.sample
diff --git a/...gan_tools/tool_data_table_conf.xml.sample → ...gan_tools/tool_data_table_conf.xml.sample b/...gan_tools/tool_data_table_conf.xml.sample → ...gan_tools/tool_data_table_conf.xml.sample
diff --git a/tools/megan_tools/daa-meganizer.xml → ...cated/tools/megan_tools/daa-meganizer.xml b/tools/megan_tools/daa-meganizer.xml → ...cated/tools/megan_tools/daa-meganizer.xml
diff --git a/tools/megan_tools/daa2rma.xml → deprecated/tools/megan_tools/daa2rma.xml b/tools/megan_tools/daa2rma.xml → deprecated/tools/megan_tools/daa2rma.xml
diff --git a/tools/megan_tools/macros.xml → deprecated/tools/megan_tools/macros.xml b/tools/megan_tools/macros.xml → deprecated/tools/megan_tools/macros.xml
diff --git a/...megan_tools/test-data/diamond_results.daa → ...megan_tools/test-data/diamond_results.daa b/...megan_tools/test-data/diamond_results.daa → ...megan_tools/test-data/diamond_results.daa
diff --git a/...megan_tools/test-data/diamond_results.rma → ...megan_tools/test-data/diamond_results.rma b/...megan_tools/test-data/diamond_results.rma → ...megan_tools/test-data/diamond_results.rma
diff --git a/...s/test-data/diamond_results_meganized.daa → ...s/test-data/diamond_results_meganized.daa b/...s/test-data/diamond_results_meganized.daa → ...s/test-data/diamond_results_meganized.daa
diff --git a/...an_tools/tool-data/megan_tools.loc.sample → ...an_tools/tool-data/megan_tools.loc.sample b/...an_tools/tool-data/megan_tools.loc.sample → ...an_tools/tool-data/megan_tools.loc.sample
diff --git a/...gan_tools/tool_data_table_conf.xml.sample → ...gan_tools/tool_data_table_conf.xml.sample b/...gan_tools/tool_data_table_conf.xml.sample → ...gan_tools/tool_data_table_conf.xml.sample
diff --git a/tools/omero/.shed.yml b/tools/omero/.shed.yml
@@ -0,0 +1,16 @@
+categories:
+- Imaging
+name: omero_upload
+description: Import images and metadata into an OMERO.server using omero-py
+long_description: Tool to import images into a target dataset in OMERO
+owner: ufz
+remote_repository_url: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero
+homepage_url: https://github.com/ome/omero-py/
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper command line tools of the omero-py and ezomero package: {{ tool_name }}."
+suite:
+  name: "suite_omero_py"
+  description: "A suite of tools that brings the omero-py and ezomero project into Galaxy."
+  long_description: |
+    OMERO.py provides an interface to the OMERO.blitz server.
diff --git a/tools/omero/README.md b/tools/omero/README.md
@@ -0,0 +1,19 @@
+# OMERO import images
+
+## Set up user credentials on Galaxy to connect to other omero instance
+
+To enable users to set their credentials for this tool,
+make sure the file `config/user_preferences_extra.yml` has the following section:
+
+```
+    omero_account:
+        description: Your OMERO instance connection credentials
+        inputs:
+            - name: username
+              label: Username
+              type: text
+              required: False
+            - name: password
+              label: Password
+              type:  password
+              required: False
diff --git a/tools/omero/omero_import.xml b/tools/omero/omero_import.xml
@@ -0,0 +1,77 @@
+<tool id="omero_import" name="OMERO Image Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
+    <description> with omero-py </description>
+    <macros>
+        <token name="@TOOL_VERSION@">5.18.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">omero</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">omero-py</requirement>
+        <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 -->
+        <requirement type="package" version="21.0.2">openjdk</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #import re
+
+        mkdir folder &&
+        #for $image in $folder:
+            #set image = $image
+            #set image_identifier = re.sub('[^\s\w\-]', '_', str($image.element_identifier))
+            ln -s '${image}' folder/'${image_identifier}.$image.ext' &&
+        #end for
+
+        omero import folder -T Dataset:name:$dataset_name
+            -s $omero_host
+            -p $omero_port
+            -u $__user__.extra_preferences.get('omero|username', $test_username)
+            -w $__user__.extra_preferences.get('omero|password', $test_password)
+        > $log &&
+
+        omero logout
+    ]]></command>
+    <inputs>
+        <param name="folder" type="data" format="avi,bmp,btf,cif,csv,eps,fits,fli,gif,hdr,html,jp2,jpg,mov,mrc,ndpi,nhdr,nrrd,ome.tiff,par,pbm,pcx,pgm,png,ppm,psd,scn,sif,svs,tf2,tf8,tif,tif,tiff,top,txt,vms,wav,xml,zip" multiple="true" optional="false" label="Images to import into OMERO"/>
+        <param name="dataset_name" type="text" optional="false" label="Target Dataset Name"/>
+        <param name="omero_host" type="text" label="OMERO host URL">
+            <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
+        </param>
+        <param name="omero_port" type="integer" value="4064" optional="false" label="OMERO port"/>
+        <param name="test_username" type="hidden" value=""/>
+        <param name="test_password" type="hidden" value=""/>
+    </inputs>
+    <outputs>
+        <data name="log" format="txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="folder" value="input1.tif,input2.tif"/>
+            <param name="dataset_name" value="galaxy_test_upload"/>
+            <param name="omero_host" value="host.docker.internal"/>
+            <param name="omero_port" value="6064"/>
+            <param name="test_username" value="root"/>
+            <param name="test_password" value="omero"/>
+            <output name="log" value="omero_output.txt" ftype="txt">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+            <assert_stderr>
+                <has_text_matching expression="IMPORT_DONE.*input1.tif"/>
+                <has_text_matching expression="IMPORT_DONE.*input2.tif"/>
+                <has_text text="files uploaded, 2 filesets created, 2 images imported, 0 errors"/>
+            </assert_stderr>
+        </test>
+    </tests>
+    <help>
+        - This tool allows the import of images into a user-defined OMERO server
+
+        - The user can define an existing dataset name where the images will be imported
+
+        - If the dataset does not exist, a new one will be created
+    </help>
+    <citations>
+        <citation type="doi">10.1038/nmeth.1896</citation>
+    </citations>
+</tool>
diff --git a/tools/omero/omero_metadata_import.xml b/tools/omero/omero_metadata_import.xml
@@ -0,0 +1,147 @@
+<tool id="omero_metadata_import" name="OMERO Metadata Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
+      profile="20.01" license="MIT">
+    <description> with ezomero </description>
+    <macros>
+        <token name="@TOOL_VERSION@">5.18.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">omero</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="3.0.1">ezomero</requirement>
+        <requirement type="package" version="2.2.2">pandas</requirement>
+        <requirement type="package" version="21.0.2">openjdk</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python $__tool_directory__/omero_metadata_upload.py
+        --user $__user__.extra_preferences.get('omero|username', $test_username)
+        --pws $__user__.extra_preferences.get('omero|password', $test_password)
+        --host $omero_host
+        --port $omero_port
+        --obj_type $obj_type
+        --ann_type $ann_type
+        --ann_file $ann_file
+        --an_name $an_name
+        --log_file $log
+        #if $object_id_selection == "existing_object"
+            --did "$did"
+        #end if
+    ]]></command>
+    <inputs>
+        <param argument="omero_host" type="text" optional="false" label="OMERO host URL"/>
+        <param argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/>
+        <param argument="obj_type" type="select" optional="true" label="Target Object Type">
+            <option value="project">Project</option>
+            <option value="screen">Screen</option>
+            <option value="dataset">Dataset</option>
+            <option value="image">Image</option>
+        </param>
+        <conditional name="object_id">
+        <param name="object_id_selection" type="select" label="Selection"  help="Create a new OMERO object or target an existing one">
+            <option value="new_object">Create new object</option>
+            <option value="existing_object">Target an existing object</option>
+        </param>
+        <when value="new_object"/>
+        <when value="existing_object">
+            <param name="did" type="integer" value="" optional="false" label="Object ID"/>
+        </when>
+        </conditional>
+        <param argument="ann_type" type="select" optional="false" label="Annotation type" help="Select annotation format">
+            <option value="table">Table</option>
+            <option value="KV">Key-Value Pairs</option>
+        </param>
+        <param argument="ann_file" type="data" format="tabular" optional="false" label="Annotation file" help="Select annotation file"/>
+        <param argument="an_name" type="text" optional="false" label="Annotation Name"/>
+        <param name="test_username" type="hidden" value=""/>
+        <param name="test_password" type="hidden" value=""/>
+    </inputs>
+    <outputs>
+        <data name="log" format="txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="omero_host" value="host.docker.internal"/>
+            <param name="omero_port" value="6064"/>
+            <param name="obj_type" value="project"/>
+            <param name="ann_type" value="table"/>
+            <param name="object_id_selection" value="new_object"/>
+            <param name="ann_file" value="metadata.tsv"/>
+            <param name="an_name" value="Table_Test"/>
+            <param name="test_username" value="root"/>
+            <param name="test_password" value="omero"/>
+            <output name="log" value="output_table_import.txt" ftype="txt">
+                <assert_contents>
+                    <has_text text="SUCCESS: Successfully uploaded metadata for project"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="omero_host" value="host.docker.internal"/>
+            <param name="omero_port" value="6064"/>
+            <param name="obj_type" value="dataset"/>
+            <param name="ann_type" value="KV"/>
+            <param name="object_id_selection" value="new_object"/>
+            <param name="ann_file" value="metadata.tsv"/>
+            <param name="an_name" value="KV_Test"/>
+            <param name="test_username" value="root"/>
+            <param name="test_password" value="omero"/>
+            <output name="log" value="output_KV_import.txt" ftype="txt">
+                <assert_contents>
+                    <has_text text="SUCCESS: Successfully uploaded metadata for dataset"/>
+                </assert_contents>
+            </output>
+        </test>
+            <test>
+            <param name="omero_host" value="host.docker.internal"/>
+            <param name="omero_port" value="6064"/>
+            <param name="obj_type" value="dataset"/>
+            <param name="ann_type" value="KV"/>
+            <param name="object_id_selection" value="existing_object"/>
+            <param name="did" value="1"/>
+            <param name="ann_file" value="metadata.tsv"/>
+            <param name="an_name" value="Additional_KV_Values"/>
+            <param name="test_username" value="root"/>
+            <param name="test_password" value="omero"/>
+            <output name="log" value="output_target_import.txt" ftype="txt">
+                <assert_contents>
+                    <has_text text="SUCCESS: Successfully uploaded metadata for dataset"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+Description
+-----------
+
+Tool to import metadata (Table and K/V pairs) into user defined OMERO.server.
+Metadata can be attached to an existing OMERO object (Project, Dataset, Screen, or Image).
+Optionally, a new OMERO object can be created before uploading the metadata.
+If the object does not exist, a new one will be created.
+
+**Tabular metadata file example**
+
+- Table
+
+  +------------+---------------+---------------+
+  | image_id   | attribute_1   | attribute_2   |
+  +============+===============+===============+
+  | 235        | 0             | 1             |
+  +------------+---------------+---------------+
+  | 564        | 1             | 1             |
+  +------------+---------------+---------------+
+  | 120        | 0             | 1             |
+  +------------+---------------+---------------+
+
+- Key-Value Pairs
+
+  +--------+---------+----------+
+  | Key1   | Key2    | Key3     |
+  +========+=========+==========+
+  | Value1 | Value2  | Value3   |
+  +--------+---------+----------+
+    </help>
+    <citations>
+        <citation type="doi">10.1038/nmeth.1896</citation>
+    </citations>
+</tool>