diff --git a/Dockerfile b/Dockerfile index 4e4943d..ec22c84 100644 --- a/Dockerfile +++ b/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 \ diff --git a/Script/PRONTO.py b/Script/PRONTO.py index 30718df..4f0f436 100755 --- a/Script/PRONTO.py +++ b/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) diff --git a/test_data/hus/191206_NB501498_0174_AHWCNMBGXC/191206_NB501498_0174_AHWCNMBGXC_ppr/CL-AcroMetrix-D01/CL-AcroMetrix-D01_CNV_overview_plots.pdf b/test_data/hus/191206_NB501498_0174_AHWCNMBGXC/191206_NB501498_0174_AHWCNMBGXC_ppr/CL-AcroMetrix-D01/CL-AcroMetrix-D01_CNV_overview_plots.pdf index e69de29..203cbda 100644 Binary files a/test_data/hus/191206_NB501498_0174_AHWCNMBGXC/191206_NB501498_0174_AHWCNMBGXC_ppr/CL-AcroMetrix-D01/CL-AcroMetrix-D01_CNV_overview_plots.pdf and b/test_data/hus/191206_NB501498_0174_AHWCNMBGXC/191206_NB501498_0174_AHWCNMBGXC_ppr/CL-AcroMetrix-D01/CL-AcroMetrix-D01_CNV_overview_plots.pdf differ diff --git a/test_data/hus/191206_NB501498_0174_AHWCNMBGXC/191206_NB501498_0174_AHWCNMBGXC_ppr/CL-NA12878N25-D01/CL-NA12878N25-D01_CNV_overview_plots.pdf b/test_data/hus/191206_NB501498_0174_AHWCNMBGXC/191206_NB501498_0174_AHWCNMBGXC_ppr/CL-NA12878N25-D01/CL-NA12878N25-D01_CNV_overview_plots.pdf index e69de29..203cbda 100644 Binary files a/test_data/hus/191206_NB501498_0174_AHWCNMBGXC/191206_NB501498_0174_AHWCNMBGXC_ppr/CL-NA12878N25-D01/CL-NA12878N25-D01_CNV_overview_plots.pdf and b/test_data/hus/191206_NB501498_0174_AHWCNMBGXC/191206_NB501498_0174_AHWCNMBGXC_ppr/CL-NA12878N25-D01/CL-NA12878N25-D01_CNV_overview_plots.pdf differ