add parameter for patient ID and populate creation date

darwinai · Aug 5, 2020 · f5dd628 · f5dd628
1 parent 6dbd9e8
commit f5dd628
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Showing 4 changed files with 21 additions and 5 deletions.
diff --git a/README.rst b/README.rst
@@ -57,6 +57,9 @@ Agruments
     [--imagefile]
     required field, the name of the patient chest X-Ray image
 
+    [--patientId]
+    patient's id
+
 
 Run
 ----
@@ -73,15 +76,17 @@ Now, prefix all calls with
 
 .. code:: bash
 
-    docker run --rm -v $(pwd)/out:/outgoing                             \
-            local/pl-pdfgeneration pdfgeneration.py                        \
+    docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing            \
+      local/pl-pdfgeneration pdfgeneration.py --imagefile ex-covid.jpeg             \
+      --patientId 1234567  /incoming /outgoing               \
+
 
 Examples
 --------
 
 
 docker build -t local/pl-pdfgeneration .
 
-docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing local/pl-pdfgeneration pdfgeneration.py --imagefile ex-covid.jpeg /incoming /outgoing
+docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing local/pl-pdfgeneration pdfgeneration.py --imagefile ex-covid.jpeg --patientId 1234567  /incoming /outgoing
 
 docker run --rm local/pl-pdfgeneration pdfgeneration.py --json
diff --git a/pdfgeneration/pdfgeneration.py b/pdfgeneration/pdfgeneration.py
@@ -15,6 +15,7 @@
 import json
 import shutil
 import pdfkit
+import datetime
 from pyvirtualdisplay import Display
 sys.path.append(os.path.dirname(__file__))
 
@@ -140,6 +141,11 @@ def define_parameters(self):
             type         = str, 
             optional     = False,
             help         = 'Name of image file submitted to the analysis')
+        self.add_argument('--patientId', 
+            dest         = 'patientId', 
+            type         = str, 
+            optional     = False,
+            help         = 'Patient ID')
 
     def run(self, options):
         """
@@ -166,11 +172,16 @@ def run(self, options):
         with open("pdftemplate/{}".format(template_file)) as f:
             txt = f.read()
             # replace the values
+            txt = txt.replace("${PATIENT_TOKEN}", options.patientId)
             txt = txt.replace("${PREDICTION_CLASSIFICATION}", classification_data['prediction'])
             txt = txt.replace("${COVID-19}", classification_data['COVID-19'])
             txt = txt.replace("${NORMAL}", classification_data['Normal'])
             txt = txt.replace("${PNEUMONIA}", classification_data['Pneumonia'])
             txt = txt.replace("${X-RAY-IMAGE}", options.imagefile)
+
+            time = datetime.datetime.now()
+            txt = txt.replace("${month-date}", time.strftime("%c"))
+            txt = txt.replace("${year}", time.strftime("%Y"))
             # add the severity value if prediction is covid
             if template_file == "pdf-covid-positive-template.html":
               txt = txt.replace("${GEO_SEVERITY}", severityScores["Geographic severity"])

diff --git a/pdfgeneration/pdftemplate/pdf-covid-negative-template.html b/pdfgeneration/pdftemplate/pdf-covid-negative-template.html
@@ -49,7 +49,7 @@ <h3>Pneumonia: <span>${PNEUMONIA}</span></h3>
         <hr>
         <div class="layout--half">
             <div class="footer-text">
-            <p>Output generated by COVID-Net on the ChRIS platform on $Day $Month $Year $HH:$MM $AM/PM.</p>
+            <p>Output generated by COVID-Net on the ChRIS platform on ${month-date}</p>
             </div>
             <div class="footer-text">
                 <p>For more information about COVID-NET:  <a href="https://github.com/lindawangg/COVID-Net/">https://github.com/lindawangg/COVID-Net/</a></p>

diff --git a/pdfgeneration/pdftemplate/pdf-covid-positive-template.html b/pdfgeneration/pdftemplate/pdf-covid-positive-template.html
@@ -61,7 +61,7 @@ <h3>Severity Scores</h3>
         <hr>
         <div class="layout--half">
             <div class="footer-text">
-            <p>Output generated by COVID-Net on the ChRIS platform on $Day $Month $Year $HH:$MM $AM/PM.</p>
+            <p>Output generated by COVID-Net on the ChRIS platform on ${month-date}</p>
             </div>
             <div class="footer-text">
                 <p>For more information about COVID-NET:  <a href="https://github.com/lindawangg/COVID-Net/">https://github.com/lindawangg/COVID-Net/</a></p>