Fixed clobbering issue

.gitignore

@@ -9,3 +9,6 @@ htmlcov
 .idea/
 .vscode/
 covidnet/models
+
+
+out/

README.rst

@@ -77,9 +77,30 @@ Run
 .. code:: bash
 
     docker run --rm -v $PWD/in:/incoming -v $PWD/out:/outgoing    \
-        fnndsc/pl-covidnet:0.2.0 covidnet                         \
+        fnndsc/pl-covidnet covidnet                         \
                --imagefile ex-covid.jpeg /incoming /outgoing
 
+.. code:: bash
+
+    docker run --rm -u $(id -u)                                         \
+        -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing                  \
+        fnndsc/pl-covidnet covidnet  --parInst <insert ID>   \
+        /incoming /outgoing
+
+.. code:: bash
+
+    docker run --rm -u $(id -u)                                         \
+        -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing                  \
+        jonocameron/pl-covidnet covidnet --imagefile "ex-covid.jpeg" --savToDir "000"   \
+        /incoming /outgoing
+
+.. code:: bash
+
+    docker run --rm -u $(id -u)                                         \
+        -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing                  \
+        jonocameron/pl-covidnet covidnet --imagefile "ex-covid.jpeg"    \
+        /incoming /outgoing
+
 
 Links
 -----

covidnet/covidnet.py

@@ -62,6 +62,12 @@ def define_parameters(self):
         Define the CLI arguments accepted by this plugin app.
         Use self.add_argument to specify a new app argument.
         """
+        self.add_argument('--savToDir',
+        	        dest      = 'savToDir',
+        	        type      = str,
+        	        optional  = True,
+        	        help      = 'Parent instance ID',
+                    default   = '')
         self.add_argument('--metaname', 
                     dest         = 'metaname', 
                     type         = str, 

covidnet/inference.py

@@ -131,24 +131,49 @@ def generate_severity_data(self, imagePath):
     def generate_output_files(self, classification_data, severityScores):
         # remove this line to display model names mapped in dict
         self.args.modelused = 'default'
+        directory = self.args.savToDir
+
+        parent_dir = self.args.outputdir
+
+        if(directory == ''):
+            print("Creating prediction.json in {}...".format(self.args.outputdir))
+            with open('{}/prediction-{}.json'.format(self.args.outputdir, self.args.modelused), 'w') as f:
+                json.dump(classification_data, f, indent=4)
+            print("Copying over the input image to: {}...".format(self.args.outputdir))
+            shutil.copy(self.args.inputdir + '/' + self.args.imagefile,self.args.outputdir)
+            # Not covid positive
+            if severityScores is None:
+                return
+            print("Creating severity.json in {}...".format(self.args.outputdir))
+            with open('{}/severity.json'.format(self.args.outputdir), 'w') as f:
+                json.dump(severityScores, f, indent=4)
+            return
+
+
 
+        nPath = os.path.join(parent_dir , directory)
+        os.makedirs(nPath)
+
         # creates the output directory if not exists
         if not os.path.exists(self.args.outputdir):
-            os.makedirs(self.args.outputdir)
+            os.makedirs(nPath)
 
-        print("Creating prediction.json in {}...".format(self.args.outputdir))
-        with open('{}/prediction-{}.json'.format(self.args.outputdir, self.args.modelused), 'w') as f:
+        print("Creating prediction.json in {}...".format(nPath))
+        with open('{}/prediction-{}.json'.format(nPath, self.args.modelused), 'w') as f:
             json.dump(classification_data, f, indent=4)
+
+        print("Copying over the input image to: {}...".format(nPath))
+        shutil.copy(self.args.inputdir + '/' + self.args.imagefile,nPath)
+
 
-        print("Copying over the input image to: {}...".format(self.args.outputdir))
-        shutil.copy(self.args.inputdir + '/' + self.args.imagefile,self.args.outputdir)
 
         # Not covid positive
         if severityScores is None:
           return
 
-        print("Creating severity.json in {}...".format(self.args.outputdir))
-        with open('{}/severity.json'.format(self.args.outputdir), 'w') as f:
+
+        print("Creating severity.json in {}...".format(nPath))
+        with open('{}/severity.json'.format(nPath, self.args.modelused), 'w') as f:
             json.dump(severityScores, f, indent=4)
 
 

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name             =   'covidnet',
-    version          =   '0.2.2',
+    version          =   '0.3.2',
     description      =   'Plugin to ChRIS for covidnet functionalities',
     long_description =   readme,
     author           =   'Jeffer Peng',