fix(rwr): add max_iters

.github/workflows/build-containers.yml

@@ -58,6 +58,16 @@ jobs:
     with:
       path: docker-wrappers/ResponseNet
       container: reedcompbio/responsenet
+  build-and-remove-rwr:
+    uses: "./.github/workflows/build-and-remove-template.yml"
+    with:
+      path: docker-wrappers/RWR
+      container: reedcompbio/rwr
+  build-and-remove-strwr:
+    uses: "./.github/workflows/build-and-remove-template.yml"
+    with:
+      path: docker-wrappers/ST_RWR
+      container: reedcompbio/st-rwr
   build-and-remove-spras:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:

config/config.yaml

@@ -113,15 +113,17 @@ algorithms:
     params:
       include: true
       run1:
-        alpha: [0.85]
+        alpha: [0.85, 0.9]
         threshold: [100, 200]
+        max_iters: 10000
 
   - name: "rwr"
     params:
       include: true
       run1:
-        alpha: [0.85]
+        alpha: [0.85, 0.9]
         threshold: [100, 200]
+        max_iters: 10000
 
   - name: "bowtiebuilder"
     params:

docker-wrappers/RWR/Dockerfile

@@ -5,4 +5,4 @@ RUN pip install networkx==2.8.8 numpy==1.26.4 scipy==1.15.2
 
 WORKDIR /RWR
 
-RUN wget https://raw.githubusercontent.com/Reed-CompBio/rwr/9de14ac239df906f5ed0c19b9a42b83f5aa6f296/RWR.py
+RUN wget https://raw.githubusercontent.com/Reed-CompBio/rwr/bb8d61069376afa7ff1acb47f47b34589f025d6f/RWR.py

docker-wrappers/ST_RWR/Dockerfile

@@ -5,4 +5,4 @@ RUN pip install networkx==2.8.8 numpy==1.26.4 scipy==1.15.2
 
 WORKDIR /ST_RWR
 
-RUN wget https://raw.githubusercontent.com/Reed-CompBio/rwr/9de14ac239df906f5ed0c19b9a42b83f5aa6f296/ST_RWR.py
+RUN wget https://raw.githubusercontent.com/Reed-CompBio/rwr/bb8d61069376afa7ff1acb47f47b34589f025d6f/ST_RWR.py

docker-wrappers/ST_RWR/README.md

@@ -1,6 +1,6 @@
 # Source-Targets Random Walk with Restarts
 
-A Docker image for [ST-RWR](https://github.com/Reed-CompBio/rwr) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/st_rwr).
+A Docker image for [ST-RWR](https://github.com/Reed-CompBio/rwr) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/st-rwr).
 
 ## Notes
 The random walk with restarts algorithm requires a directed input network. However, the algorithm in its current form will accept an undirected input network and interpret it as a directed network. The resulting output from an undirected network does not accurately represent directionality.

spras/rwr.py

@@ -32,7 +32,7 @@ def generate_inputs(data, filename_map):
         edges.to_csv(filename_map['network'],sep='|',index=False,columns=['Interactor1','Interactor2'],header=False)
 
     @staticmethod
-    def run(network=None, nodes=None, alpha=None, output_file=None, container_framework="docker", threshold=None):
+    def run(network=None, nodes=None, alpha=None, max_iter=None, output_file=None, container_framework="docker", threshold=None):
         if not nodes:
             raise ValueError('Required RWR arguments are missing')
 
@@ -67,11 +67,13 @@ def run(network=None, nodes=None, alpha=None, output_file=None, container_framew
                    '--nodes', nodes_file,
                    '--output', mapped_out_prefix]
 
-        # Add alpha as an optional argument
+        # Add optional arguments
         if alpha is not None:
             command.extend(['--alpha', str(alpha)])
+        if max_iter is not None:
+            command.extend(['--max-iter', str(max_iter)])
 
-        container_suffix = 'rwr:v1'
+        container_suffix = 'rwr:v2'
         run_container_and_log(
             "RandomWalk with Restart",
             container_framework,

spras/strwr.py

@@ -32,7 +32,7 @@ def generate_inputs(data, filename_map):
         edges.to_csv(filename_map['network'],sep='|',index=False,columns=['Interactor1','Interactor2'],header=False)
 
     @staticmethod
-    def run(network=None, sources=None, targets=None, alpha=None, output_file=None, container_framework="docker", threshold=None):
+    def run(network=None, sources=None, targets=None, alpha=None, max_iter=None, output_file=None, container_framework="docker", threshold=None):
         if not sources or not targets or not network or not output_file:
             raise ValueError('Required local_neighborhood arguments are missing')
 
@@ -72,11 +72,13 @@ def run(network=None, sources=None, targets=None, alpha=None, output_file=None,
                    '--targets', target_file,
                    '--output', mapped_out_prefix]
 
-        # Add alpha as an optional argument
+        # Add optional arguments
         if alpha is not None:
             command.extend(['--alpha', str(alpha)])
+        if max_iter is not None:
+            command.extend(['--max-iter', str(max_iter)])
 
-        container_suffix = 'st-rwr:v1'
+        container_suffix = 'st-rwr:v2'
         run_container_and_log(
             "Source-Target RandomWalk with Restart",
             container_framework,

test/RWR/expected_output/rwr-output-high.txt

@@ -0,0 +1,6 @@
+Node	Score
+C	0.4164497171247451
+E	0.1978133496120127
+B	0.1978133496120127
+D	0.18792358365122955
+A	0.0

test/RWR/test_RWR.py

@@ -27,6 +27,21 @@ def test_rwr(self):
         expected_file = Path(TEST_DIR, 'expected_output', 'rwr-output.txt')
         assert cmp(OUT_FILE, expected_file, shallow=False), 'Output file does not match expected output file'
 
+    """
+    Run the RWR algorithm on the example input files and check the output matches the expected output,
+    specifying a higher max_iter and alpha than usual
+    """
+    def test_rwr_optional(self):
+        OUT_FILE.unlink(missing_ok=True)
+        RWR.run(network=Path(TEST_DIR, 'input', 'rwr-network.txt'),
+                nodes=Path(TEST_DIR, 'input','rwr-nodes.txt'),
+                alpha=0.95,
+                max_iter=10000,
+                output_file=OUT_FILE)
+        assert OUT_FILE.exists(), 'Output file was not written'
+        expected_file = Path(TEST_DIR, 'expected_output', 'rwr-output-high.txt')
+        assert cmp(OUT_FILE, expected_file, shallow=False), 'Output file does not match expected output file'
+
     """
     Run the RWR algorithm with a missing input file
     """

test/ST_RWR/expected_output/strwr-output-high.txt

@@ -0,0 +1,6 @@
+Node	Score
+A	0.321229089672757
+C	0.24396106359378425
+E	0.21206998743770886
+B	0.1142253832416095
+D	0.10851447605414039

test/ST_RWR/test_STRWR.py

@@ -29,6 +29,22 @@ def test_strwr(self):
         expected_file = Path(TEST_DIR, 'expected_output', 'strwr-output.txt')
         assert cmp(OUT_FILE, expected_file, shallow=False), 'Output file does not match expected output file'
 
+    """
+    Run the RWR algorithm on the example input files and check the output matches the expected output,
+    specifying a higher max_iter and alpha than usual
+    """
+    def test_strwr_optional(self):
+        OUT_FILE.unlink(missing_ok=True)
+        ST_RWR.run(network=Path(TEST_DIR, 'input', 'strwr-network.txt'),
+                   sources=Path(TEST_DIR, 'input', 'strwr-sources.txt'),
+                   targets=Path(TEST_DIR, 'input','strwr-targets.txt'),
+                   alpha=0.95,
+                   max_iter=10000,
+                   output_file=OUT_FILE)
+        assert OUT_FILE.exists(), 'Output file was not written'
+        expected_file = Path(TEST_DIR, 'expected_output', 'strwr-output-high.txt')
+        assert cmp(OUT_FILE, expected_file, shallow=False), 'Output file does not match expected output file'
+
     """
     Run the ST_RWR algorithm with a missing input file
     """