add safeguard

Author: bgruening

chemicaltoolbox/data_source/get_pubchem/get_pubchem_as_smiles.py

@@ -29,7 +29,7 @@ def main(output, processors = 4):
     result.get()
 
     for filename in os.listdir(td):
-        path = os.path.join(td, filename)
+        path = os.path.join(td, filename)  + '.smi'
         shutil.copyfileobj(open(path, 'rb'), output_handle)
 
     output_handle.close()
@@ -38,9 +38,9 @@ def main(output, processors = 4):
 def fetch_convert(args):
     (filename, td) = args
 
-    tmp_name = os.path.join( tempfile.gettempdir(), filename)
+    tmp_name = os.path.join( td, filename)
     subprocess.call( ['wget', '-O', tmp_name, os.path.join('ftp://ftp.ncbi.nih.gov/pubchem/Compound/CURRENT-Full/SDF/', filename)] )
-    output = os.path.join(td, filename)
+    output = os.path.join(td, filename) + '.smi'
     subprocess.call(["obabel", "-isdf", tmp_name, "-ocan", '-O', output])
     os.remove(tmp_name)
 

chemicaltoolbox/data_source/get_pubchem/get_pubchem_as_smiles.xml

@@ -1,5 +1,8 @@
 <tool id="ctb_pubchem_download_as_smiles" name="PubChem Download" Version="0.1" >
   <description>as canonical SMILES</description>
+  <requirements>
+    <requirement type="package" version="2.3.2">openbabel</requirement>
+  </requirements>
   <command interpreter="python">
         get_pubchem_as_smiles.py 
             -o $pubchem_smi 

chemicaltoolbox/data_source/tool_dependencies.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="openbabel" version="2.3.2">
+        <repository name="package_openbabel_2_3" owner="iuc" />
+    </package>
+</tool_dependency>