Merge pull request #66 from Reed-CompBio/cytoscape

Cytoscape

.github/workflows/test-spras.yml

@@ -52,7 +52,7 @@ jobs:
       uses: eWaterCycle/setup-apptainer@v2
       with:
         # Choose version from https://github.com/apptainer/apptainer/releases
-        apptainer-version: 1.1.3
+        apptainer-version: 1.2.2
     - name: Run tests
       shell: bash --login {0}
       # Verbose output and disable stdout and stderr capturing
@@ -146,6 +146,15 @@ jobs:
         tags: latest
         cache_froms: reedcompbio/domino:latest
         push: false
+    - name: Build Cytoscape Docker image
+      uses: docker/build-push-action@v1
+      with:
+        path: docker-wrappers/Cytoscape/.
+        dockerfile: docker-wrappers/Cytoscape/Dockerfile
+        repository: reedcompbio/py4cytoscape
+        tags: v1
+        cache_froms: reedcompbio/py4cytoscape:v1
+        push: false
 
   # Run pre-commit checks on source files
   pre-commit:

Snakefile

@@ -4,7 +4,7 @@ import shutil
 import yaml
 from src.dataset import Dataset
 from src.util import process_config
-from src.analysis import ml, summary, graphspace
+from src.analysis import ml, summary, graphspace, cytoscape
 
 # Snakemake updated the behavior in the 6.5.0 release https://github.com/snakemake/snakemake/pull/1037
 # and using the wrong separator prevents Snakemake from matching filenames to the rules that can produce them
@@ -68,7 +68,10 @@ def make_final_input(wildcards):
         # add graph and style JSON files.
         final_input.extend(expand('{out_dir}{sep}{dataset}-{algorithm_params}{sep}gs.json',out_dir=out_dir,sep=SEP,dataset=dataset_labels,algorithm_params=algorithms_with_params))
         final_input.extend(expand('{out_dir}{sep}{dataset}-{algorithm_params}{sep}gsstyle.json',out_dir=out_dir,sep=SEP,dataset=dataset_labels,algorithm_params=algorithms_with_params))
-
+
+    if config["analysis"]["cytoscape"]["include"]:
+        final_input.extend(expand('{out_dir}{sep}{dataset}-cytoscape.cys',out_dir=out_dir,sep=SEP,dataset=dataset_labels))
+
     if config["analysis"]["ml"]["include"]:  
         final_input.extend(expand('{out_dir}{sep}{dataset}-pca.png',out_dir=out_dir,sep=SEP,dataset=dataset_labels,algorithm_params=algorithms_with_params))
         final_input.extend(expand('{out_dir}{sep}{dataset}-pca-variance.txt',out_dir=out_dir,sep=SEP,dataset=dataset_labels,algorithm_params=algorithms_with_params))
@@ -225,7 +228,7 @@ rule summarize_pathway:
     run:
         summary.run(input.standardized_file,output.summary_file,directed=algorithm_directed[wildcards.algorithm])
 
-# Write GraphSpace JSON Graphs
+# Write GraphSpace JSON graphs
 rule viz_graphspace:
     input: standardized_file = SEP.join([out_dir, '{dataset}-{algorithm}-{params}', 'pathway.txt'])
     output:
@@ -234,6 +237,16 @@ rule viz_graphspace:
     run:
         graphspace.write_json(input.standardized_file,output.graph_json,output.style_json,directed=algorithm_directed[wildcards.algorithm])
 
+
+# Write a Cytoscape session file with all pathways for each dataset
+rule viz_cytoscape:
+    input: pathways = expand('{out_dir}{sep}{{dataset}}-{algorithm_params}{sep}pathway.txt', out_dir=out_dir, sep=SEP, algorithm_params=algorithms_with_params)
+    output: 
+        session = SEP.join([out_dir, '{dataset}-cytoscape.cys'])
+    run:
+        cytoscape.run_cytoscape(input.pathways, output.session, SINGULARITY)
+
+
 # Write a single summary table for all pathways for each dataset
 rule summary_table:
     input:

config/config.yaml

@@ -129,6 +129,9 @@
         # Create output files for each pathway that can be visualized with GraphSpace
         graphspace:
           include: true
+        # Create Cytoscape session file with all pathway graphs for each dataset
+        cytoscape:
+          include: true
         # Machine learning analysis (e.g. clustering) of the pathway output files for each dataset
         ml:
           include: true

config/egfr.yaml

@@ -88,6 +88,8 @@ reconstruction_settings:
 analysis:
   graphspace:
     include: false
+  cytoscape:
+    include: true
   summary:
     include: true
   ml:

docker-wrappers/Cytoscape/Cytoscape.vmoptions

@@ -0,0 +1,4 @@
+-Xms256m
+-Xmx2g
+-Xss5m
+-Duser.home=/spras

docker-wrappers/Cytoscape/Dockerfile

@@ -0,0 +1,31 @@
+# Dockerfile derived from
+# https://github.com/cytoscape/docker-cytoscape-desktop/blob/173ab46b4b5e5c148113ad0c9960a6af3fc50432/py4cytoscape/Dockerfile
+# by Kozo Nishida
+FROM python:3.9.13
+
+# Versions
+ENV CYTOSCAPE_VERSION=3.9.1
+ENV PY4CYTOSCAPE_VERSION=1.3.0
+ENV JAVA_HOME="/usr/lib/jvm/java-11-openjdk-amd64"
+# Workaround for java.util.zip.ZipException: Invalid CEN header https://cytoscape.org/common_issues.html#zipvalidation
+ENV EXTRA_JAVA_OPTS="-Djdk.util.zip.disableZip64ExtraFieldValidation=true"
+
+WORKDIR /py4cytoscape
+
+# Install py4cytoscape
+RUN pip install py4cytoscape==${PY4CYTOSCAPE_VERSION}
+
+# Install Java and Cytoscape
+RUN apt-get update && apt-get -y install default-jdk xvfb supervisor wget
+RUN wget https://github.com/cytoscape/cytoscape/releases/download/${CYTOSCAPE_VERSION}/cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz \
+    && tar xf cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz && rm cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz
+RUN cd cytoscape-unix-${CYTOSCAPE_VERSION}/framework/system/org/cytoscape/property-impl/${CYTOSCAPE_VERSION} \
+    && jar -xf property-impl-${CYTOSCAPE_VERSION}.jar cytoscape3.props \
+    && cat cytoscape3.props | sed "s/^cyrest.version.*/cyrest.version=3.12.3/g" > cytoscape3.props.tmp \
+    && mv cytoscape3.props.tmp cytoscape3.props \
+    && jar -uf property-impl-${CYTOSCAPE_VERSION}.jar cytoscape3.props \
+    && rm cytoscape3.props
+
+COPY Cytoscape.vmoptions ./cytoscape-unix-${CYTOSCAPE_VERSION}/Cytoscape.vmoptions
+COPY supervisord.conf /etc/supervisor/conf.d/supervisord.conf
+COPY cytoscape_util.py .

docker-wrappers/Cytoscape/README.md

@@ -0,0 +1,25 @@
+# Cytoscape image
+
+A Docker image for [Cytoscape](https://cytoscape.org/) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/py4cytoscape).
+It was originally derived from the [`docker-cytoscape-desktop/py4cytoscape`](https://github.com/cytoscape/docker-cytoscape-desktop/blob/173ab46b4b5e5c148113ad0c9960a6af3fc50432/py4cytoscape/Dockerfile) image.
+
+Thank you to Scooter Morris for help debugging problems running Cytoscape in Singularity.
+
+## Building the Docker image
+
+To create the Docker image run:
+```
+docker build -t reedcompbio/py4cytoscape -f Dockerfile .
+```
+from this directory.
+
+## Testing
+Test code is located in `test/analysis/test_cytoscape.py`.
+The Docker wrapper can be tested with `pytest`.
+
+## Versions:
+- v1: Use supervisord to launch Cytoscape from a Python subprocess, then connect to Cytoscape with py4cytoscape. Only loads undirected pathways. Compatible with Singularity in local testing (Apptainer version 1.2.2-1.el7) but fails in GitHub Actions.
+
+## TODO
+- Add an auth file for `xvfb-run`
+- Java initial heap size, maximum Java heap size, and thread stack size are hard-coded in `Cytoscape.vmoptions` file

docker-wrappers/Cytoscape/cytoscape_util.py

@@ -0,0 +1,135 @@
+import argparse
+import subprocess
+import time
+from typing import List
+
+import py4cytoscape as p4c
+from requests.exceptions import RequestException
+
+SLEEP_INTERVAL = 10
+MAX_CONNECTION_ATTEMPTS = 20
+
+
+def get_parser() -> argparse.ArgumentParser:
+    """
+    :return: an argparse ArgumentParser object for parsing command
+        line parameters
+    """
+    parser = argparse.ArgumentParser(
+        description='Visualize pathway files from SPRAS.')
+
+    parser.add_argument(
+        "--pathway",
+        dest='pathways',
+        type=str,
+        action='append',
+        required=True,
+        help='The path to a pathway file. Add the argument multiple times to visualize multiple pathways. '
+             'Optionally use a | to append a label for the pathway such as path/to/file.txt|pathway_label'
+    )
+
+    parser.add_argument(
+        "--output",
+        dest='output',
+        type=str,
+        default='cytoscape-session.cys',
+        help='The output filename of the Cytoscape session file, which will have the extension .cys added if it is not '
+             'already provided. Default: cytoscape-session.cys'
+    )
+    return parser
+
+
+def parse_arguments() -> argparse.Namespace:
+    """
+    Initialize a parser and use it to parse the command line arguments
+    :return: parsed dictionary of command line arguments
+    """
+    parser = get_parser()
+    opts = parser.parse_args()
+
+    return opts
+
+
+def start_remote_cytoscape() -> None:
+    """
+    Use supervisord to start the Cytoscape process. Ping Cytoscape until a connection is established and sleep in
+    between pings. Raises an error if Cytoscape cannot be reached within the maximum number of attempts.
+    """
+    try:
+        subprocess.run([
+            '/usr/bin/supervisord', '-c', '/etc/supervisor/conf.d/supervisord.conf'
+        ],
+            check=True)
+    except subprocess.CalledProcessError as e:
+        raise RuntimeError('An error has occurred while trying to run Cytoscape') from e
+
+    connected = False
+    attempts = 0
+    # Allow initial time to start up before trying to connect
+    time.sleep(SLEEP_INTERVAL)
+    while not connected and attempts < MAX_CONNECTION_ATTEMPTS:
+        attempts += 1
+        try:
+            p4c.cytoscape_ping()
+            print('Connected to Cytoscape', flush=True)
+            connected = True
+        except (RequestException, p4c.exceptions.CyError):
+            print('Pinging Cytoscape, waiting for connection... ', flush=True)
+            time.sleep(SLEEP_INTERVAL)
+            pass
+        except Exception as e:
+            print(e)
+            print('Pinging Cytoscape, waiting for connection... ', flush=True)
+            time.sleep(SLEEP_INTERVAL)
+
+    if not connected:
+        raise ConnectionError('Could not connect to Cytoscape')
+
+
+def parse_name(pathway: str) -> (str, str):
+    """
+    Extract the optional label from the pathway argument
+    @param pathway: the command line pathway argument, which may contain a | separated label
+    @return: a tuple with the file path and the label
+    """
+    parts = pathway.split('|')
+    # No label provided or empty label provided so the file path is the label
+    if len(parts) == 1 or len(parts[1]) == 0:
+        return parts[0], parts[0]
+    # A valid label was provided
+    else:
+        return parts[0], parts[1]
+
+
+def load_pathways(pathways: List[str], output: str) -> None:
+    """
+    Launch and connect to Cytoscape, import all pathways, and save a session file
+    @param pathways: the list of pathways to import
+    @param output: the name of the Cytoscape session file to save
+    """
+    if len(pathways) == 0:
+        raise ValueError('One or more pathway files are required')
+
+    start_remote_cytoscape()
+    for pathway in pathways:
+        path, name = parse_name(pathway)
+        suid = p4c.networks.import_network_from_tabular_file(
+            file=path,
+            column_type_list='s,t,x',
+            delimiters='\t'
+        )
+        p4c.networks.rename_network(name, network=suid)
+
+    p4c.session.save_session(output)
+
+
+def main():
+    """
+    Main function
+    """
+    opts = parse_arguments()
+    load_pathways(opts.pathways, opts.output)
+
+
+if __name__ == '__main__':
+    main()

docker-wrappers/Cytoscape/supervisord.conf

@@ -0,0 +1,13 @@
+[supervisord]
+nodaemon=false
+
+[program:cytoscape]
+# supervisord syntax for environment variable substitution http://supervisord.org/configuration.html#environment-variables
+# The variable is CYTOSCAPE_VERSION
+# Removed auth file from the original example because the file used was not present anyway
+# Should consider adding back an auth file
+# --auth-file /root/.Xauth
+command=/bin/bash -c 'xvfb-run -s "-screen 0 1920x1080x24" /py4cytoscape/cytoscape-unix-%(ENV_CYTOSCAPE_VERSION)s/cytoscape.sh'
+priority=10
+stdout_logfile=/dev/fd/1
+stdout_logfile_maxbytes=0

src/analysis/cytoscape.py

@@ -0,0 +1,60 @@
+from pathlib import Path, PurePath
+from shutil import rmtree
+from typing import List, Union
+
+from src.util import prepare_volume, run_container
+
+
+def run_cytoscape(pathways: List[Union[str, PurePath]], output_file: str, singularity: bool = False) -> None:
+    """
+    Create a Cytoscape session file with visualizations of each of the provided pathways
+    @param pathways: a list of pathways to visualize
+    @param output_file: the output Cytoscape session file
+    @param singularity: whether to run in a Singularity container
+    """
+    work_dir = '/spras'
+
+    # To work with Singularity, /spras must be mapped to a writeable location because that directory is fixed as
+    # the home directory inside the container and Cytoscape writes configuration files there
+    # $HOME cannot be set in the Dockerfile because Singularity overwrites home at launch
+    env = f'HOME={work_dir}'
+
+    # Each volume is a tuple (src, dest)
+    volumes = list()
+
+    # A temporary directory for Cytoscape output files
+    cytoscape_output_dir = Path(output_file.replace('.cys', '')).absolute()
+    cytoscape_output_dir.mkdir(parents=True, exist_ok=True)
+
+    # TODO update to the latest p4cytoscape and use env variable to control the log directory instead
+    # Requires generalizing the run_container function to support multiple environment variables
+    volumes.append((cytoscape_output_dir, PurePath(work_dir, 'logs')))
+    # Only needed when running in Singularity
+    volumes.append((cytoscape_output_dir, PurePath(work_dir, 'CytoscapeConfiguration')))
+
+    # Map the output file
+    bind_path, mapped_output = prepare_volume(output_file, work_dir)
+    volumes.append(bind_path)
+
+    # Create the initial Python command to run inside the container
+    command = ['python', '/py4cytoscape/cytoscape_util.py', '--output', mapped_output]
+
+    # Map the pathway filenames and add them to the Python command
+    for pathway in pathways:
+        bind_path, mapped_pathway = prepare_volume(pathway, work_dir)
+        volumes.append(bind_path)
+        # Provided the mapped pathway file path and the original file path as the label Cytoscape
+        command.extend(['--pathway', f'{mapped_pathway}|{pathway}'])
+
+    print('Running Cytoscape with arguments: {}'.format(' '.join(command)), flush=True)
+
+    # TODO consider making this a string in the config file instead of a Boolean
+    container_framework = 'singularity' if singularity else 'docker'
+    out = run_container(container_framework,
+                        'reedcompbio/py4cytoscape:v1',
+                        command,
+                        volumes,
+                        work_dir,
+                        env)
+    print(out)
+    rmtree(cytoscape_output_dir)