Bringing in changes from thehanriver/pl-tpdf but making them so that …

.gitignore

@@ -9,5 +9,4 @@ htmlcov
 .idea/
 .vscode/
 
-in/
 out/

README.rst

@@ -53,3 +53,12 @@ Examples
         -v $PWD/covidnet-out:/incoming:ro -v $PWD/pdfgeneration-out:/outgoing:rw \
         fnndsc/pl-covidnet-pdfgeneration:0.2.0 pdfgeneration \
         --imagefile chest-scan.jpg --patientId 12345678 /incoming /outgoing
+
+    docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing \
+        jonocameron/pl-pdfgeneration pdfgeneration --imagefile "ex-covid.jpeg" --patientId "77812345" \
+        /incoming /outgoing
+
+    docker run --rm -u $(id -u)                             \
+        -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
+        jonocameron/pl-tpdf tpdf --dir "41"                      \
+        --imagefile "ex-covid.jpeg" --patientId 12345678 /incoming /outgoing

in/41/prediction-default.json

@@ -0,0 +1,7 @@
+{
+    "**DISCLAIMER**": "Do not use this prediction for self-diagnosis. You should check with your local authorities for the latest advice on seeking medical assistance.",
+    "prediction": "COVID-19",
+    "Normal": "0.00052875147",
+    "Pneumonia": "0.010959083",
+    "COVID-19": "0.98851216"
+}

in/41/severity.json

@@ -0,0 +1,8 @@
+{
+    "Geographic severity": "52",
+    "Geographic extent score": "4.2",
+    "GeoInfo": "For each lung: 0 = no involvement; 1 = <25%; 2 = 25-50%; 3 = 50-75%; 4 = >75% involvement.",
+    "Opacity severity": "52",
+    "Opacity extent score": "3.1",
+    "OpcInfo": "For each lung: 0 = no opacity; 1 = ground glass opacity; 2 =consolidation; 3 = white-out."
+}

in/prediction-default.json

@@ -0,0 +1,7 @@
+{
+    "**DISCLAIMER**": "Do not use this prediction for self-diagnosis. You should check with your local authorities for the latest advice on seeking medical assistance.",
+    "prediction": "COVID-19",
+    "Normal": "0.00052875147",
+    "Pneumonia": "0.010959083",
+    "COVID-19": "0.98851216"
+}

in/severity.json

@@ -0,0 +1,8 @@
+{
+    "Geographic severity": "52",
+    "Geographic extent score": "4.2",
+    "GeoInfo": "For each lung: 0 = no involvement; 1 = <25%; 2 = 25-50%; 3 = 50-75%; 4 = >75% involvement.",
+    "Opacity severity": "52",
+    "Opacity extent score": "3.1",
+    "OpcInfo": "For each lung: 0 = no opacity; 1 = ground glass opacity; 2 =consolidation; 3 = white-out."
+}

pdfgeneration/pdfgeneration.py

@@ -66,6 +66,12 @@ 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('--dir',
+        	dest = 'dir',
+        	type = str,
+        	optional = True,
+        	default = '',
+        	help = 'directory')
         self.add_argument('--imagefile', 
             dest         = 'imagefile', 
             type         = str, 
@@ -84,11 +90,17 @@ def run(self, options):
         """
         print(Gstr_title)
         print('Version: %s' % self.get_version())
+
+
+        directory = options.dir
+        parent_dir = options.inputdir
+        nPath = os.path.join(parent_dir , directory)
+
         # fetch input data
-        with open('{}/prediction-default.json'.format(options.inputdir)) as f:
+        with open('{}/prediction-default.json'.format(nPath)) as f:
           classification_data = json.load(f)
         try: 
-            with open('{}/severity.json'.format(options.inputdir)) as f:
+            with open('{}/severity.json'.format(nPath)) as f:
                 severityScores = json.load(f)
         except:
             severityScores = None
@@ -120,9 +132,11 @@ def run(self, options):
         # when input is a string
         for asset_file in files('pdfgeneration').joinpath('template/assets').iterdir():
             os.symlink(asset_file, path.join('/tmp', asset_file.name))
-        os.symlink(path.join(options.inputdir, options.imagefile), path.join('/tmp', options.imagefile))
+        os.symlink(path.join(nPath, options.imagefile), path.join('/tmp', options.imagefile))
 
         pdfkit.from_string(txt, path.join(options.outputdir, 'patient_analysis.pdf'))
-
     def show_man_page(self):
-        self.print_help()
+        """
+        Print the app's man page.
+        """
+        print(Gstr_synopsis)

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name             =   'pdfgeneration',
-    version          =   '0.2.0',
+    version          =   '0.3.0',
     description      =   'An app that takes in COVID-Net prediction results and generates PDF',
     long_description =   readme,
     author           =   'DarwinAI',