style refactoring

Author: Will Trimble

scripts/mg-download.py

@@ -43,8 +43,8 @@ def file_download(auth, info, dirpath="."):
         fhandle = open(os.path.join(dirpath, info['file_name']), 'w')
         file_from_url(info['url'], fhandle, auth=auth)
         fhandle.close()
-    else:   # don't open empty file is no download
-        sys.stderr.write("WARNING Download info does not contain url.  Possibly datasets suppressed")
+    else:   # Don't open empty file if download doesn't have url
+        sys.stderr.write("WARNING Download info does not contain url.  Possibly datasets pre- human screening?\n" + repr(info)+"\n")
     sys.stdout.write("Done\n")
 
 def main(args):
@@ -60,39 +60,44 @@ def main(args):
     parser.add_argument("--file", dest="file", default=None, help="file ID for given project or metagenome")
     parser.add_argument("--dir", dest="dir", default=".", help="directory to do downloads")
     parser.add_argument("--list", dest="list", action="store_true", default=False, help="list files and their info for given ID")
-    
+
     # get inputs
     opts = parser.parse_args()
-    if not (opts.project or opts.metagenome):
+    PROJECT = opts.project
+    DOWNDIR = opts.dir
+    METAGENOME = opts.metagenome
+    LIST = opts.list
+    FILE = opts.file
+    URL = opts.url
+
+    if not (PROJECT or METAGENOME):
         sys.stderr.write("ERROR: a project or metagenome id is required\n")
         return 1
-    if not os.path.isdir(opts.dir):
-        sys.stderr.write("ERROR: dir '%s' does not exist\n"%opts.dir)
+    if not os.path.isdir(DOWNDIR):
+        sys.stderr.write("ERROR: dir '%s' does not exist\n"%DOWNDIR)
         return 1
-    downdir = opts.dir
-    
+
     # get auth
     token = get_auth_token(opts)
-    
+
     # get metagenome list
     mgs = []
-    if opts.project:
-        url  = opts.url+'/project/'+opts.project+'?verbosity=full'
+    if PROJECT:
+        url = URL +'/project/'+PROJECT+'?verbosity=full'
         data = obj_from_url(url, auth=token)
         for mg in data['metagenomes']:
             mgs.append(mg["metagenome_id"])
-    elif opts.metagenome:
-        mgs.append(opts.metagenome)
-    
+    elif METAGENOME:
+        mgs.append(METAGENOME)
     # get file lists
     all_files = {}
     for mg in mgs:
-        url  = opts.url+'/download/'+mg
+        url = URL + '/download/' + mg
         data = obj_from_url(url, auth=token)
         all_files[mg] = data['data']
-    
+
     # just list
-    if opts.list:
+    if LIST:
         pt = PrettyTable(["Metagenome", "File Name", "File ID", "Checksum", "Byte Size"])
         for mg, files in all_files.items():
             for f in files:
@@ -102,32 +107,30 @@ def main(args):
         pt.align['Byte Size'] = "r"
         print(pt)
         return 0
-    
+
     # download all in dirs by ID
-    if opts.project:
-        downdir = os.path.join(downdir, opts.project)
-        if not os.path.isdir(downdir):
-            os.mkdir(downdir)
+    if PROJECT:
+        DOWNDIR = os.path.join(DOWNDIR, PROJECT)
+        if not os.path.isdir(DOWNDIR):
+            os.mkdir(DOWNDIR)
     for mg, files in all_files.items():
-        mgdir = os.path.join(downdir, mg)
+        mgdir = os.path.join(DOWNDIR, mg)
         if not os.path.isdir(mgdir):
             os.mkdir(mgdir)
         for f in files:
-            if opts.file:
+            if FILE:
                 filecount = 0
-                if f['file_id'] == opts.file:
-                    filecount +=1
+                if f['file_id'] == FILE:
+                    filecount += 1
                     file_download(token, f, dirpath=mgdir)
-                elif f['file_name'] == opts.file:
-                    filecount +=1
+                elif f['file_name'] == FILE:
+                    filecount += 1
                     file_download(token, f, dirpath=mgdir)
             else:
                 file_download(token, f, dirpath=mgdir)
             if filecount == 0:
-                sys.exit("Can't find file number "+opts.file)
-    
+                sys.exit("Didn't find file number " + FILE)
     return 0
 
-
 if __name__ == "__main__":
     sys.exit(main(sys.argv))