fix: make omicsintegrator2 work offline

docker-wrappers/OmicsIntegrator2/0001-disable-graph-exports.patch

@@ -0,0 +1,26 @@
+From 5dc0e69fa3d1049ae8e1d8f51859335910245ad7 Mon Sep 17 00:00:00 2001
+From: "Tristan F.-R." <pub.tristanf@gmail.com>
+Date: Mon, 26 May 2025 09:52:34 -0700
+Subject: [PATCH] fix: disable graph exports
+
+this allows OI2 to work offline; plus, SPRAS already has graph visualizers.
+---
+ src/__main__.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/__main__.py b/src/__main__.py
+index 49ef402..b7afbca 100644
+--- a/src/__main__.py
++++ b/src/__main__.py
+@@ -80,7 +80,7 @@ def main():
+         forest, augmented_forest = graph.output_forest_as_networkx(vertex_indices, edge_indices)
+
+     #oi.output_networkx_graph_as_graphml_for_cytoscape(augmented_forest, args.output_dir)
+-    oi.output_networkx_graph_as_interactive_html(augmented_forest, args.output_dir, args.filename+'.html')
++    # oi.output_networkx_graph_as_interactive_html(augmented_forest, args.output_dir, args.filename+'.html')
+     augmented_forest_df = oi.get_networkx_graph_as_dataframe_of_edges(augmented_forest)
+     output_dataframe_to_tsv(augmented_forest_df, args.output_dir, args.filename+'.tsv')
+
+-- 
+2.47.0
+

docker-wrappers/OmicsIntegrator2/Dockerfile

@@ -2,5 +2,14 @@
 # https://github.com/fraenkel-lab/OmicsIntegrator2
 FROM continuumio/miniconda3:4.9.2
 
+COPY 0001-disable-graph-exports.patch .
+
+RUN git clone https://github.com/agitter/OmicsIntegrator2 && \
+    cd OmicsIntegrator2 && \
+    git reset --hard 568f170eae388e42e923c478ac9f3308b487760b && \
+    git config user.email "email@example.com" && \
+    git config user.name "Non-existent User" && \
+    git am /0001-disable-graph-exports.patch
+
 COPY environment.yml .
 RUN conda env update --name base --file environment.yml --prune

docker-wrappers/OmicsIntegrator2/environment.yml

@@ -18,4 +18,4 @@ dependencies:
   - pcst_fast==1.0.7
   - goenrich==1.7.0
   - axial==0.1.10
-  - git+https://github.com/agitter/OmicsIntegrator2@568f170eae388e42e923c478ac9f3308b487760b
+  - git+file:///OmicsIntegrator2

spras/containers.py

@@ -125,7 +125,7 @@ def prepare_dsub_cmd(flags: dict):
 # run_container_singularity assumes a single string
 # Follow docker-py's naming conventions (https://docker-py.readthedocs.io/en/stable/containers.html)
 # Technically the argument is an image, not a container, but we use container here.
-def run_container(framework: str, container_suffix: str, command: List[str], volumes: List[Tuple[PurePath, PurePath]], working_dir: str, environment: str = 'SPRAS=True'):
+def run_container(framework: str, container_suffix: str, command: List[str], volumes: List[Tuple[PurePath, PurePath]], working_dir: str, environment: str = 'SPRAS=True', network_disabled=False):
     """
     Runs a command in the container using Singularity or Docker
     @param framework: singularity or docker
@@ -134,6 +134,7 @@ def run_container(framework: str, container_suffix: str, command: List[str], vol
     @param volumes: a list of volumes to mount where each item is a (source, destination) tuple
     @param working_dir: the working directory in the container
     @param environment: environment variables to set in the container
+    @param network_disabled: Disables the network on the container. Only works for docker for now. This acts as a 'runtime assertion' that a container works w/o networking.
     @return: output from Singularity execute or Docker run
     """
     normalized_framework = framework.casefold()
@@ -150,7 +151,7 @@ def run_container(framework: str, container_suffix: str, command: List[str], vol
 
 
 # TODO any issue with creating a new client each time inside this function?
-def run_container_docker(container: str, command: List[str], volumes: List[Tuple[PurePath, PurePath]], working_dir: str, environment: str = 'SPRAS=True'):
+def run_container_docker(container: str, command: List[str], volumes: List[Tuple[PurePath, PurePath]], working_dir: str, environment: str = 'SPRAS=True', network_disabled=False):
     """
     Runs a command in the container using Docker.
     Attempts to automatically correct file owner and group for new files created by the container, setting them to the
@@ -189,6 +190,7 @@ def run_container_docker(container: str, command: List[str], volumes: List[Tuple
                                     stderr=True,
                                     volumes=bind_paths,
                                     working_dir=working_dir,
+                                    network_disabled=network_disabled,
                                     environment=[environment]).decode('utf-8')
 
         # TODO does this cleanup need to still run even if there was an error in the above run command?

spras/omicsintegrator2.py

@@ -125,7 +125,8 @@ def run(edges=None, prizes=None, output_file=None, w=None, b=None, g=None, noise
                             container_suffix,
                             command,
                             volumes,
-                            work_dir)
+                            work_dir,
+                            network_disabled=True)
         print(out)
 
         # TODO do we want to retain other output files?