moved plants executable inside the repo #1

.gitignore

@@ -1,4 +1,4 @@
-###Git ignore file for LIEStudio repository
+###Git ignore file for MDStudio repository
 
 ### LIEStudio specific
 app/typings/
@@ -127,4 +127,3 @@ cerise_config.json
 venv
 .env
 **/.settings.*.yml
-plants_linux

lie_plants_docking/schemas/endpoints/docking_request.v1.json

@@ -10,9 +10,6 @@
 	    "description": "Directory to run the docking simulation",
 	    "default": "/tmp/mdstudio/plants_docking"
 	},
-	"exec_path": {
-	    "$ref": "resource://mdgroup/common_resources/path_file/v1"	    
-	},
 	"scoring_function": {
 	    "type": "string",
 	    "description": "",
@@ -296,7 +293,6 @@
     "required": [
 	"bindingsite_center",
 	"ligand_file",
-	"protein_file",
-	"exec_path"
+	"protein_file"
     ]
 }

lie_plants_docking/utils.py

@@ -37,15 +37,6 @@ def _schema_to_data(schema, data=None, defdict=None):
     return default_data
 
 
-def copy_exec_to_workdir(content, workdir, name='plants_linux'):
-    """
-    Copy the executable to the workdir
-    """
-    path = os.path.join(workdir, name)
-    with open(path, 'wb') as f:
-        f.write(content)
-
-
 def prepare_work_dir(path, user=None, create=False):
     """
     Prepare a docking working directory at the target path.

lie_plants_docking/wamp_services.py

@@ -1,11 +1,9 @@
 # -*- coding: utf-8 -*-
 
 from lie_plants_docking.plants_docking import PlantsDocking
-from lie_plants_docking.utils import (
-    copy_exec_to_workdir, prepare_work_dir)
+from lie_plants_docking.utils import prepare_work_dir
 from mdstudio.component.session import ComponentSession
 from mdstudio.api.endpoint import endpoint
-import base64
 import os
 
 
@@ -27,23 +25,20 @@ def run_docking(self, request, claims):
         # Docking options are equal to the request
         plants_config = request.copy()
 
+        # Transfer the files content
+        plants_config['protein_file'] = request['protein_file']['content']
+        plants_config['ligand_file'] = request['ligand_file']['content']
+
         # Prepare docking directory
         workdir = os.path.abspath(request['workdir'])
         plants_config["workdir"] = prepare_work_dir(
             workdir, create=True)
 
-        exec_path = request['exec_path']
-        encoding = exec_path['encoding'].lower()
+        # location of the executable
+        file_path = os.path.realpath(__file__)
+        root = os.path.split(file_path)[0]
 
-        # The binaries are first encode to base64 then decode to ascii
-        # To get the original binary the inverse operation is applied
-        if 'bytes' == encoding:
-            content = exec_path['content']
-            binary = base64.b64decode(content.encode())
-            copy_exec_to_workdir(binary, workdir)
-        else:
-            msg = "expecting binary exec_path but the encoding is: {}".format(encoding)
-            raise RuntimeError(msg)
+        plants_config['exec_path'] = os.path.join(root, 'plants_linux')
 
         # Run d ocking
         docking = PlantsDocking(**plants_config)

tests/wamp_test/test_lie_plants_docking.py

@@ -1,36 +1,34 @@
 from mdstudio.deferred.chainable import chainable
 from mdstudio.component.session import ComponentSession
 from mdstudio.runner import main
-import base64
 import os
+import json
 
+file_path = os.path.realpath(__file__)
+root = os.path.split(file_path)[0]
 
-def create_path_file_obj(path, encoding='utf8'):
+
+def create_path_file_obj(path):
     """
     Encode the input files
     """
     extension = os.path.splitext(path)[1]
-    mode = 'rb' if encoding == 'bytes' else 'r'
-    with open(path, mode) as f:
+    with open(path, 'r') as f:
         content = f.read()
-    if encoding == 'bytes':
-        content = base64.b64encode(content).decode('ascii')
 
     return {
-        'path': path, 'encoding': encoding,
-        'content': content, 'extension': extension}
+        'path': path, 'content': content,
+        'extension': extension}
 
 
-workdir = "/tmp/lie_plants_docking"
+workdir = "/tmp"
 cwd = os.getcwd()
 os.makedirs(workdir, exist_ok=True)
 
 protein_file = create_path_file_obj(
-    os.path.join(cwd, "DT_conf_1.mol2"))
+    os.path.join(root, "DT_conf_1.mol2"))
 ligand_file = create_path_file_obj(
-    os.path.join(cwd, "ligand.mol2"))
-exec_path = create_path_file_obj(
-    os.path.join(cwd, "plants_linux"), encoding='bytes')
+    os.path.join(root, "ligand.mol2"))
 
 
 class Run_docking(ComponentSession):
@@ -49,8 +47,11 @@ def on_run(self):
              "bindingsite_radius": 12.0,
              "bindingsite_center": [
                  4.926394772324452, 19.079624537618873, 21.98915631296689],
-             "workdir": workdir,
-             "exec_path": exec_path})
+             "workdir": workdir})
+
+        with open("output.json", 'w') as f:
+            json.dump(result, f)
+
         assert result['status'] == 'completed'