eertgif

This is an experimental-stage project.

Yet another attempt to scrape phylogenetic trees in an interoperable format from a pdf with an image of a tree in it.

Install

python3 -mvenv env
source env/bin/activate
pip install 'svg-path>=6.2'
python setup.py develop

Running (in dangerous DEBUG mode for local install only!)

pserve dev.ini --reload

Developer notes

home page

• Uploading a pdf will create a tmp directory in the server's scratch directory. You can clear the contents of the scratch directory and restart the server to throw away old downloads.
• an info.json file in the temp directory holds the "state" of the project. (see below)

info.json

A JSON serialization object with properties:

• page_status_list list for each region of either {"no trees" | "unknown" }
• tag holds the "nickname" that will be shown to the user and in URLs
• to_clean list of filepaths (relative to the top of the repo) to be removed if the use removes the project.
• unprocessed a list of pickled object for each region found in the pdf. Accessed called via the object_for_region method for the StudyContainer

Upload view

ENDPOINT/view/tag page with no query parameters shows a table of parsable regions detected. Clicking on one of them adds the page=#-# query parameter.

Region view

ENDPOINT/view/tag?page=x-y shows a view of region y of page x of upload tag.

Use "Previous region" and "Next region" to navigate.

Use "Flag as lacking tree" or "Begin extracting tree Next region" to either note that the region doesn't hold a tree or start trying to extract the tree.

If you flag a region as lacking a tree, you have to "revert region status to 'unknown'" to undo that. These actions affect the "page_status_list" attribute of the upload's info.json

ENDPOINT/extract/tag?page=x-y shows controls for helping you guide a tree extraction from retgion y of page x of upload tag

Credits

• Relies heavily on pdfminer.six
• See attribution in Pt and PointMap classes to Ned Batchelder's blog post about a dict implementation that maps close floats to the same key
• jQuery see https://jquery.org/license/
• svg-drag-select https://github.com/luncheon/svg-drag-select