Optional image writing to additional sheets

[jethror1]

Summary

Adds ability to pass in images to write to extra sheets in the workbook (i.e. graphs), can control sheet naming and image sizes with additional arguments -iimage_sheet_names and -iimage_sizes respectively.

If size not specified, will default to maximum of 90% of 1920*1080, retaining original image aspect ratio to fit nicely on standard 1080p monitors.

Python packages added:

• Pillow - used by openpyxl for handling image writing
• filteype - used in generate_workbook.verify_images to check if image files have been passed

New functions

• generate_workbook.verify_images: assertions to check validity of given image related arguments
• excel.write_images: controls writing of images to new sheets

Example jobs and outputs

• single image: https://platform.dnanexus.com/projects/GFFvFG042Zj7FxK74bpKVbjV/monitor/job/GFjPG2042Zj84x6ZG3gqBxBv

• single image w/ name and size specified (-iimage_sheet_names="thisIsFine" -iimage_sizes="960:540"): https://platform.dnanexus.com/projects/GFFvFG042Zj7FxK74bpKVbjV/monitor/job/GFjP8B042Zj78bZBGgJJ8XFp

• two images: https://platform.dnanexus.com/projects/GFFvFG042Zj7FxK74bpKVbjV/monitor/job/GFjPJ6042ZjJG8p1GBpvFGbV

• two images w/ names and sizes specified (-iimage_sheet_names="thisIsFine aNiceGraph" -iimage_sizes="960:540 1440:810"): https://platform.dnanexus.com/projects/GFFvFG042Zj7FxK74bpKVbjV/monitor/job/GFjPK3Q42Zj711yx90y9Zx8B

Unit tests

$ python3 -m pytest resources/home/dnanexus/generate_workbook/tests/
==================================== test session starts =====================================
platform linux -- Python 3.8.10, pytest-7.0.1, pluggy-1.0.0
rootdir: /home/jethro/Projects/eggd_vcf2xls_nirvana/resources/home/dnanexus/generate_workbook/tests, configfile: pytest.ini
collected 35 items                                                                                                                               

resources/home/dnanexus/generate_workbook/tests/test_columns.py ...........                                                                [ 31%]
resources/home/dnanexus/generate_workbook/tests/test_filters.py .......                                                                    [ 51%]
resources/home/dnanexus/generate_workbook/tests/test_utils.py ........                                                                     [ 74%]
resources/home/dnanexus/generate_workbook/tests/test_vcf.py .........                                                                      [100%]

============================================================== 35 passed in 28.34s ===============================================================

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This change is 

[pep8speaks]

Hello @jethror1! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file resources/home/dnanexus/generate_workbook/generate_workbook.py:

Line 382:28: W605 invalid escape sequence '\d' Line 382:32: W605 invalid escape sequence '\d'

• In the file resources/home/dnanexus/generate_workbook/tests/test_generate_workbook.py:

Line 33:5: E303 too many blank lines (2) Line 48:5: E303 too many blank lines (2) Line 63:5: E303 too many blank lines (2)

• In the file resources/home/dnanexus/generate_workbook/utils/excel.py:

Line 509:5: E303 too many blank lines (2)

Comment last updated at 2022-08-08 16:19:07 UTC