pdf generation bugfix & bump up version

FNNDSC · Jul 14, 2021 · 9b49446 · 9b49446
1 parent dbdc805
commit 9b49446
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Showing 6 changed files with 14 additions and 177 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -24,7 +24,7 @@
 FROM python:3.9.1-slim-buster
 LABEL maintainer="Sandip Samal <[email protected]>"
 RUN apt-get update \
-    && apt-get install -y libsm6 libxext6 libxrender-dev wkhtmltopdf xvfb \
+    && apt-get install -y wkhtmltopdf xvfb \
     && rm -rf /var/lib/apt/lists/*
 
 ENV XDG_RUNTIME_DIR=/bin/wkhtmltopdf

diff --git a/mgz2lut_report/assets/[email protected] b/mgz2lut_report/assets/[email protected]
diff --git a/mgz2lut_report/assets/[email protected] b/mgz2lut_report/assets/[email protected]
diff --git a/mgz2lut_report/assets/pdfstyle.css b/mgz2lut_report/assets/pdfstyle.css
diff --git a/mgz2lut_report/mgz2lut_report.py b/mgz2lut_report/mgz2lut_report.py
@@ -259,15 +259,25 @@ def run(self, options):
                 if report_type == 'pdf':
                     f = open("/tmp/report.html",'a')
                     f.write(result)
+
+                    # Certain .html files fail to be saved by pdfkit,
+                    # a hack is to open the file in read mode and then 
+                    # save it.
+                    f = open("/tmp/report.html",'r')
                     opt = {
                         'quiet':''
                         }
+
+                    # Ensure pdfkit config is available
                     try:
                         config = pdfkit.configuration()
                         print (config)
                     except OSError:
                         print ("missing wkhtmltopdf")
-                    pdfkit.from_file("/tmp/report.html",report_path,options=opt,configuration=config)
+                    try:
+                        pdfkit.from_file("/tmp/report.html",report_path,options=opt,configuration=config)
+                    except OSError:
+                        print ("failed to save pdf")
                 continue;
             for k in sorted(counter.keys()):
                 res_df=df_FSColorLUT.loc[df_FSColorLUT['#No'] == str(k),['LabelName']]
@@ -282,9 +292,7 @@ def run(self, options):
             else:
                 f.write(rep.to_string(index=False))
             f.close()
-
-        f = open(report_path,'r')
-        #print(f.read())
+
         print("Report saved as %s/%s in %s format(s)" %(options.outputdir,options.report_name, options.report_types))
 
     def show_man_page(self):

diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
 
 setup(
     name             = 'mgz2lut_report',
-    version          = '1.2.5',
+    version          = '1.3.0',
     description      = 'An app to generate a report on volumes of various brain segments listed in a Look-up Table (Default =     FreeSurferColorLUT.txt',
     long_description = readme,
     author           = 'Sandip Samal',
@@ -19,9 +19,6 @@
     license          = 'MIT',
     zip_safe         = False,
     python_requires  = '>=3.8',
-    package_data     = {
-        'mgz2lut_report': ['assets/*']
-    },
     entry_points     = {
         'console_scripts': [
             'mgz2lut_report = mgz2lut_report.__main__:main'