updated genereate inputs test case

test/generate-inputs/expected/allpairs-network-expected.txt

@@ -1,3 +1,3 @@
 #Interactor1	Interactor2	Weight
-A	B	0.98
+test_A	B	0.98
 B	C	0.77

test/generate-inputs/expected/domino-network-expected.txt

@@ -1,3 +1,3 @@
 ID_interactor_A	ppi	ID_interactor_B
-ENSG0A	ppi	ENSG0B
+ENSG0test_A	ppi	ENSG0B
 ENSG0B	ppi	ENSG0C

test/generate-inputs/expected/meo-edges-expected.txt

@@ -1,2 +1,2 @@
-A	(pp)	B	0.98
+test꧁SEP꧂A	(pp)	B	0.98
 B	(pp)	C	0.77

test/generate-inputs/expected/mincostflow-edges-expected.txt

@@ -1,4 +1,4 @@
-A	B	0.98
+test_A	B	0.98
 B	C	0.77
-B	A	0.98
+B	test_A	0.98
 C	B	0.77

test/generate-inputs/expected/omicsintegrator1-edges-expected.txt

@@ -1,3 +1,3 @@
 protein1	protein2	weight	directionality
-A	B	0.98	U
+test_A	B	0.98	U
 B	C	0.77	U

test/generate-inputs/expected/omicsintegrator2-edges-expected.txt

@@ -1,3 +1,3 @@
 protein1	protein2	cost
-A	B	0.52
+test_A	B	0.52
 B	C	0.73

test/generate-inputs/expected/pathlinker-network-expected.txt

@@ -1,5 +1,5 @@
 #Interactor1	Interactor2	Weight
-A	B	0.98
+test_A	B	0.98
 B	C	0.77
-B	A	0.98
+B	test_A	0.98
 C	B	0.77

test/generate-inputs/inputs/network.txt

@@ -0,0 +1,2 @@
+test_A	B	0.98	U
+B	C	0.77	U

test/generate-inputs/inputs/node-prizes.txt

@@ -0,0 +1,3 @@
+NODEID	prize	active
+test_A	2	true
+C	5.7	true

test/generate-inputs/inputs/sources.txt

@@ -0,0 +1 @@
+test_A

test/generate-inputs/inputs/targets.txt

@@ -0,0 +1 @@
+C

test/generate-inputs/inputs/test_config.yaml

@@ -0,0 +1,69 @@
+hash_length: 7
+container_framework: docker
+unpack_singularity: false
+container_registry:
+   base_url: docker.io
+   owner: reedcompbio
+
+algorithms:
+      - name: "pathlinker"
+        params:
+              include: true
+              run1:
+                  k: range(100,201,100)
+
+      - name: "omicsintegrator1"
+        params:
+              include: true
+              run1:
+                  b: [5, 6]
+                  w: np.linspace(0,5,2)
+                  d: [10]
+
+      - name: "omicsintegrator2"
+        params:
+              include: true
+              run1:
+                  b: [4]
+                  g: [0]
+              run2:
+                  b: [2]
+                  g: [3]
+
+      - name: "meo"
+        params:
+              include: true
+              run1:
+                  max_path_length: [3]
+                  local_search: ["Yes"]
+                  rand_restarts: [10]
+
+      - name: "mincostflow"
+        params:
+              include: true
+              run1:
+                  flow: [1] # The flow must be an int
+                  capacity: [1]
+
+      - name: "allpairs"
+        params:
+              include: true
+
+      - name: "domino"
+        params:
+              include: true
+              run1:
+                  slice_threshold: [0.3]
+                  module_threshold: [0.05]
+
+datasets:
+    -
+      # Labels can only contain letters, numbers, or underscores
+      label: test_data
+      node_files: ["node-prizes.txt", "sources.txt", "targets.txt"]
+      # DataLoader.py can currently only load a single edge file, which is the primary network
+      edge_files: ["network.txt"]
+      # Placeholder
+      other_files: []
+      # Relative path from the spras directory
+      data_dir: "test/generate-inputs/inputs"

test/generate-inputs/test_generate_inputs.py

@@ -29,14 +29,14 @@ def setup_class(cls):
         Path(OUTDIR).mkdir(parents=True, exist_ok=True)
 
     def test_prepare_inputs_networks(self):
-        config_loc = os.path.join("config", "config.yaml")
+        config_loc = os.path.join("test","generate-inputs", "inputs", "test_config.yaml")
 
         with open(config_loc) as config_file:
             config = yaml.load(config_file, Loader=yaml.FullLoader)
         test_file = "test/generate-inputs/output/test_pickled_dataset.pkl"
 
-        data0_dataset = next((ds for ds in config["datasets"] if ds["label"] == "data0"), None)
-        runner.merge_input(data0_dataset, test_file)
+        test_dataset = next((ds for ds in config["datasets"] if ds["label"] == "test_data"), None)
+        runner.merge_input(test_dataset, test_file)
 
         for algo in algo_exp_file.keys():
             inputs = runner.get_required_inputs(algo)