Merge pull request #85 from InPreD/82-hus-testing-of-pronto-latest-fails

82 hus testing of pronto latest fails

Author: xiaoliz0

Dockerfile

@@ -1,15 +1,15 @@
-FROM python:3.14.0a2-slim
+FROM python:3.14.0-slim
 LABEL maintainer="Xiaoli.Zhang@rr-research.no"
 # install dependencies
 COPY requirements.txt /
 RUN apt-get update \
     && apt-get install -y --no-install-recommends \
-        build-essential=12.9 \
-        libjpeg-dev=1:2.1.5-2 \
-        libxml2=2.9.14+dfsg-1.3~deb12u4 \
-        libxslt1-dev=1.1.35-1+deb12u3 \
-        poppler-utils=22.12.0-2+deb12u1 \
-        zlib1g-dev=1:1.2.13.dfsg-1 \
+        build-essential=12.12 \
+        libjpeg-dev=1:2.1.5-4 \
+        libxml2=2.12.7+dfsg+really2.9.14-2.1+deb13u1 \
+        libxslt1-dev=1.1.35-1.2+deb13u2 \
+        poppler-utils=25.03.0-5 \
+        zlib1g-dev=1:1.3.dfsg+really1.3.1-1+b1 \
     && rm -rf /var/lib/apt/lists/* \
     && apt-get clean \
     && pip install --no-cache-dir -r requirements.txt \

Script/PRONTO.py

@@ -1124,7 +1124,6 @@ def update_clinical_tsoppi_file(InPreD_clinical_tsoppi_data_file,sample_id,if_ge
 			fw.write(new_content)
 		fw.close()
 
-
 def pdf_page_image_to_ppt(pdf_file,output_ppt_file,pages,width_scale,height_scale):
 	ppt = Presentation(output_ppt_file)
 	slide = ppt.slides.add_slide(ppt.slide_layouts[6])
@@ -1144,8 +1143,6 @@ def pdf_page_image_to_ppt(pdf_file,output_ppt_file,pages,width_scale,height_scal
 		slide.shapes.add_picture(image_path, left=0, top=image_top, width=image_width, height=image_height)
 		os.remove(image_path)
 	ppt.save(output_ppt_file)
-	
-
 
 def usage(exit_status = 0):
 	print ("""Usage: python3  %s
@@ -1547,7 +1544,7 @@ def main(argv):
 					B3_C1_to_extract = [4, 5]
 				pdf_page_image_to_ppt(CNV_overview_plots_pdf,output_ppt_file,B3_C1_to_extract,width_scale=1,height_scale=0.5)
 
-        			# Change slides order.
+        		# Change slides order.
 				ppt = Presentation(output_ppt_file)
 				slides = ppt.slides._sldIdLst
 				slides_list = list(slides)