pass string as arguments instead of file paths #7

lie_structures/cheminfo_wamp/cheminfo_molhandle_wamp.py

@@ -42,10 +42,9 @@ def convert_structures(self, request, claims):
            lie_structures/schemas/endpoints/convert_response_v1.json
         """
         molobject = self.read_mol(request)
-        file_path = self.create_output_file(request)
 
         outfmt = request.get('output_format', request['input_format'])
-        output = mol_write(molobject, mol_format=outfmt, file_path=file_path)
+        output = mol_write(molobject, mol_format=outfmt, file_path=None)
 
         # Update session
         status = 'completed'
@@ -66,9 +65,8 @@ def addh_structures(self, request, claims):
             correctForPH=request['correctForPH'],
             pH=request['pH'])
 
-        file_path = self.create_output_file(request)
         outfmt = request.get('output_format', request['input_format'])
-        output = mol_write(molobject, mol_format=outfmt, file_path=file_path)
+        output = mol_write(molobject, mol_format=outfmt, file_path=None)
 
         # Update session
         status = 'completed'
@@ -84,10 +82,9 @@ def removeh_structures(self, request, claims):
            lie_structures/schemas/endpoints/removeh_response_v1.json
         """
         molobject = mol_removeh(self.read_mol(request))
-        file_path = self.create_output_file(request)
 
         outfmt = request.get('output_format', request['input_format'])
-        output = mol_write(molobject, mol_format=outfmt, file_path=file_path)
+        output = mol_write(molobject, mol_format=outfmt, file_path=None)
 
         # Update session
         status = 'completed'
@@ -109,9 +106,8 @@ def make3d_structures(self, request, claims):
             localopt=request['localopt'],
             steps=request['steps'])
 
-        file_path = self.create_output_file(request)
         outfmt = request.get('output_format', request['input_format'])
-        output = mol_write(molobject, mol_format=outfmt, file_path=file_path)
+        output = mol_write(molobject, mol_format=outfmt, file_path=None)
 
         # Update session
         status = 'completed'
@@ -151,13 +147,7 @@ def rotate_structures(self, request, claims):
 
         rotations = request['rotations']
         if rotations:
-            result = mol_combine_rotations(molobject, rotations=rotations)
-
-            if 'workdir' in request:
-                file_path = os.path.join(request['workdir'], 'rotations.mol2')
-                with open(file_path, 'w') as otp:
-                    otp.write(result)
-                output = file_path
+            output = mol_combine_rotations(molobject, rotations=rotations)
             status = 'completed'
         else:
             status = 'failed'

lie_structures/schemas/endpoints/addh_request.v1.json

@@ -17,7 +17,7 @@
     },
     "mol": {
       "type": "string",
-      "description": "Moleculare file"
+      "description": "Molecular representation"
     },
     "input_format": {
       "type": "string",

lie_structures/schemas/endpoints/remove_residues_request.v1.json

@@ -6,11 +6,8 @@
   "type": "object",
   "properties": {
     "mol": {
-      "type": [
-        "string",
-        "object"
-      ],
-      "description": "Moleculare file"
+      "type": "string",
+      "description": "Molecular representation"
     },
     "from_file": {
       "type": "boolean",

lie_structures/schemas/resources/read_write_mol.v1.json

@@ -22,7 +22,7 @@
     },
     "mol": {
       "type": "string",
-      "description": "Moleculare file"
+      "description": "Molecular representation"
     },
     "input_format": {
       "type": "string",

tests/wamp_test/test_lie_structures.py

@@ -7,95 +7,83 @@
 import numpy as np
 import os
 import pybel
-import shutil
 
 file_path = os.path.realpath(__file__)
 root = os.path.split(file_path)[0]
 
-def create_workdir(name, path="/tmp/mdstudio/lie_structures"):
-    """Create temporal workdir dir"""
-    workdir = join(path, name)
-    if not os.path.isdir(workdir):
-        os.makedirs(workdir)
-    return workdir
-
 
 def read_mol(mol, fmt="mol2"):
     """Read a molecular object either from a file or string"""
-    if not os.path.isfile(mol):
-        name = '/tmp/structure.{}'.format(fmt)
-        with open(name, 'w') as f:
-            f.write(mol)
-        mol = name
+    if os.path.isfile(mol):
+        mol = pybel.readfile(fmt, mol).next()
+    else:
+        mol = pybel.readstring(fmt, mol)
+
+    return mol
 
-    return pybel.readfile(fmt, mol).next()
 
+def read_file(file_path):
+    """ Returns file content"""
+    with open(file_path, 'r') as f:
+        content = f.read()
 
-def copy_to_workdir(file_path, workdir):
-    shutil.copy(file_path, workdir)
-    base = os.path.basename(file_path)
-    return join(workdir, base)
+    return content
 
 
-def compare_molecules(mol1, mol2, rtol=1e-5, atol=1e-8):
-    """Compare the coordinates of two molecules"""
+def compare_molecules(mol1, mol2):
+    """Compare if the coordinates array are the same shape"""
     m1 = read_mol(mol1)
     m2 = read_mol(mol2)
 
     arr = np.array([x.coords for x in m1])
     brr = np.array([x.coords for x in m2])
 
-    return np.allclose(arr, brr, rtol, atol)
+    return arr.shape == brr.shape
 
 
 dict_convert = {
     "output_format": "mol2",
-    "workdir": create_workdir("convert"),
+    "workdir": "/tmp",
     "input_format": "smi",
-    "mol": "O1[C@@H](CCC1=O)CCC",
-    "from_file": False,
-    "to_file": True
+    "mol": "O1[C@@H](CCC1=O)CCC"
 }
 
 dict_make3d = {
-    "from_file": True,
-    "workdir": create_workdir("make3d"),
+    "workdir": "/tmp",
     "input_format": "mol2",
     "output_format": "mol2",
-    "mol": join(root, 'files/structure.mol2')
+    "mol": read_file(join(root, 'files/structure.mol2'))
 }
 
 dict_addh = {
-    "from_file": True,
-    "workdir": create_workdir("addh"),
+    "workdir": "/tmp",
     "input_format": "mol2",
     "output_format": "mol2",
-    "mol": join(root, "files/structure3D.mol2"),
+    "mol": read_file(join(root, "files/structure3D.mol2")),
     "pH": 7.4,
     "correctForPH": False
 }
 
 dict_info = {
-    "mol": join(root, "files/structure3D.mol2"),
-    "workdir": create_workdir("info"),
+    "mol": read_file(join(root, "files/structure3D.mol2")),
+    "workdir": "/tmp",
     "input_format": "mol2",
 }
 
 dict_rotate = {
-    "from_file": True,
-    "workdir": create_workdir("rotate"),
+    "workdir": "/tmp",
     "input_format": "mol2",
     "output_format": "mol2",
     "rotations": [
         [1, 0, 0, 90], [1, 0, 0, -90], [0, 1, 0, 90],
         [0, 1, 0, -90], [0, 0, 1, 90], [0, 0, 1, -90]],
-    "mol": join(root, "files/structureHs.mol2"),
+    "mol": read_file(join(root, "files/structureHs.mol2")),
 }
 
 dict_similarity = {
     "mol_format": "smi",
     "ci_cutoff": 0.3617021276595745,
-    "workdir": create_workdir('similarity'),
+    "workdir": "/tmp",
     "test_set": ["O1[C@@H](CCC1=O)CCC"],
     "reference_set": [
       "c1(c(cccc1Nc1c(cccc1)C(=O)O)C)C",
@@ -152,27 +140,21 @@ def on_run(self):
 
         convert = yield self.call(
             "mdgroup.lie_structures.endpoint.convert", dict_convert)
-        print(convert)
         assert compare_molecules(convert['mol'], join(root, 'files/structure.mol2'))
         print("converting {} from smile to mol2 succeeded!".format(
             dict_convert['mol']))
 
-        dict_make3d['mol'] = copy_to_workdir(dict_make3d['mol'], dict_make3d['workdir'])
         make3d = yield self.call(
             "mdgroup.lie_structures.endpoint.make3d", dict_make3d)
-        # assert compare_molecules(make3d['mol'], join(root, 'files/structure3D.mol2'), atol=1e-2)
-        print(make3d)
+        assert compare_molecules(make3d['mol'], join(root, 'files/structure3D.mol2'))
         print("successful creation of a 3D structure for {}".format(
             dict_convert['mol']))
 
-        dict_addh['mol'] = copy_to_workdir(dict_addh['mol'], dict_addh['workdir'])
         addh = yield self.call(
             "mdgroup.lie_structures.endpoint.addh", dict_addh)
-        print(addh)
         assert compare_molecules(addh['mol'], join(root, 'files/structureHs.mol2'))
         print("added hydrogens sucessfully!")
 
-        dict_info['mol'] = copy_to_workdir(dict_info['mol'], dict_info['workdir'])
         info = yield self.call(
             "mdgroup.lie_structures.endpoint.info", dict_info)
         print("info", info)
@@ -181,17 +163,16 @@ def on_run(self):
             atts['formula'] == 'C7H12O2', atts['exactmass'] - 128.083729624 < 1e-5))
         print('attributes information successfully retrieved!')
 
-        dict_rotate['mol'] = copy_to_workdir(dict_rotate['mol'], dict_info['workdir'])
         rotate = yield self.call(
             "mdgroup.lie_structures.endpoint.rotate", dict_rotate)
-        print("rotate: ", rotate)
         assert compare_molecules(rotate['mol'], join(root, 'files/rotations.mol2'))
         print("rotatation method succeeded!")
 
         similarity = yield self.call(
             "mdgroup.lie_structures.endpoint.chemical_similarity",
             dict_similarity)
-        print("similarity: ", similarity)
+        assert similarity['results']['idx_max_sim']['0'] == 20
+        print("Similarity method succeeded!")
 
 
 if __name__ == "__main__":