Merge pull request Helmholtz-UFZ#34 from rmassei/omero-upload

OMERO basic upload using omero-py
rmassei · Jul 29, 2024 · 5497619 · 5497619
2 parents 4ad36d1 + bf77ca1
commit 5497619
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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 +156,18 @@ 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
+      run: docker-compose -f .github/omero-docker-compose.yml up -d
+
     # download or create large test data via script
     - name: Create test data
       run: |
@@ -182,6 +194,7 @@ 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 +297,18 @@ 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
+      run: docker-compose -f .github/omero-docker-compose.yml up -d
+
     # download or create large test data via script
     - name: Create test data
       run: |
@@ -323,6 +335,7 @@ 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/tools/omero/.shed.yml b/tools/omero/.shed.yml
@@ -0,0 +1,16 @@
+categories:
+- Imaging
+name: omero_upload
+description: Import images to an OMERO instance
+long_description: Import images to an OMERO.server from Galaxy
+owner: ufz
+remote_repository_url: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero/omero_basic_upload
+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 package: {{ tool_name }}."
+suite:
+  name: "suite_omero_py"
+  description: "A suite of tools that brings the omery-py 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)
+        > $log &&
+
+        omero logout
+    ]]></command>
+    <inputs>
+        <param name="folder" type="data" format="avi,bmp,btf,cif,csv,eps,fits,fli,gif,hdr,html,jp2,jpg,mov,mrc,ndpi,nhdr,nrrd,ome.tiff,par,pbm,pcx,pgm,png,ppm,psd,scn,sif,svs,tf2,tf8,tif,tif,tiff,top,txt,vms,wav,xml,zip" multiple="true" optional="false" label="Images to import into OMERO"/>
+        <param name="dataset_name" type="text" optional="false" label="Dataset where to import the images"/>
+        <param name="omero_host" type="text" label="OMERO host URL">
+            <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</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/test-data/input1.tif b/tools/omero/test-data/input1.tif
diff --git a/tools/omero/test-data/input2.tif b/tools/omero/test-data/input2.tif
diff --git a/tools/omero/test-data/omero_output.txt b/tools/omero/test-data/omero_output.txt
@@ -0,0 +1,2 @@
+Image:1
+Image:2