python plex_init in auto_run mode (#624)

labdao · Aug 31, 2023 · c7328d7 · c7328d7
1 parent e3faea2
commit c7328d7
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Showing 3 changed files with 23 additions and 7 deletions.
diff --git a/docs/docs/reference/python.md b/docs/docs/reference/python.md
@@ -17,7 +17,8 @@ The following functions are considered core when using the plex [pip package](ht
 def plex_init(
     tool_path: str, 
     scattering_method=ScatteringMethod.DOT_PRODUCT.value, 
-    plex_path="plex", 
+    plex_path="plex",
+    auto_run=False,
     **kwargs
 )
 ```
@@ -42,6 +43,7 @@ initial_io_cid = plex_init(
     * **dotProduct:** Pairs corresponding elements from each input vector into subarrays. Requires all input vectors to have the same length. 
     * **crossProduct:** Generates all combinations of elements across input vectors, forming the Cartesian product. Input vector lengths can vary.
 * `plex_path` *str*, *optional* - path pointing to plex binary
+* `auto_run` *bool*, *optional* - automatically submits the job for computation based on the IO JSON
 * `**kwargs` *keyword arguments*, *optional* - additional parameters in the form of a list, where keys are input names and values are input values; see each tool config for specific arguments accepted
 
 ---

diff --git a/python/dev/example.py b/python/dev/example.py
@@ -12,15 +12,29 @@
 small_molecules = [f"{test_data_dir}/binding/abl/ZINC000003986735.sdf", f"{test_data_dir}/binding/abl/ZINC000019632618.sdf"]
 proteins = [f"{test_data_dir}/binding/abl/7n9g.pdb"]
 
-initial_io_cid = plex_init(
+# Custom annotations for testing
+custom_annotations = ["python_example", "test"]
+
+print(f"Testing plex_init with auto_run flag set to True")
+
+test_io_cid = plex_init(
     CoreTools.EQUIBIND.value,
     ScatteringMethod.CROSS_PRODUCT.value,
+    auto_run=True,
     plex_path=plex_path,
     small_molecule=small_molecules,
-    protein=proteins)
+    protein=proteins,
+)
 
-# Custom annotations for testing
-custom_annotations = ["python_example", "test"]
+print(f"Testing plex_init with auto_run flag set to False")
+
+initial_io_cid = plex_init(
+    CoreTools.EQUIBIND.value,
+    ScatteringMethod.CROSS_PRODUCT.value,
+    plex_path=plex_path,
+    small_molecule=small_molecules,
+    protein=proteins
+)
 
 # check that environmental variable for recipient wallet is set
 if not os.environ.get('RECIPIENT_WALLET'):

diff --git a/python/src/plex/__init__.py b/python/src/plex/__init__.py
@@ -36,7 +36,7 @@ def __init__(self, message):
         super().__init__(f"{self.message}\n{self.github_issue_message}")
 
 
-def plex_init(tool_path: str, scattering_method=ScatteringMethod.DOT_PRODUCT.value, plex_path="plex", **kwargs):
+def plex_init(tool_path: str, scattering_method=ScatteringMethod.DOT_PRODUCT.value, plex_path="plex", auto_run=False, **kwargs):
     cwd = os.getcwd()
     plex_work_dir = os.environ.get("PLEX_WORK_DIR", os.path.dirname(os.path.dirname(cwd)))
 
@@ -55,7 +55,7 @@ def plex_init(tool_path: str, scattering_method=ScatteringMethod.DOT_PRODUCT.val
     # Convert kwargs dictionary to a JSON string
     inputs = json.dumps(kwargs)
 
-    cmd = [plex_path, "init", "-t", tool_path, "-i", inputs, f"--scatteringMethod={scattering_method}"]
+    cmd = [plex_path, "init", "-t", tool_path, "-i", inputs, f"--scatteringMethod={scattering_method}", f"--autoRun={str(auto_run).lower()}"]
 
     print(' '.join(cmd))