Better table header handling

[creisle]

I've been using the lineraized tables but one thing I've noticed is that when we have something complex like a multi-level header just linearizing makes the number of cells not always match up. so something like this

example article used: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873663/

Currently gets turned into

p53 MUTATION	FUNCTIONALa STATUS	IARC DATABASEb	FEATURESc	SOMATIC	GERMLINE FAMILIES	TOTAL	BREAST

And we lose a lot of meaning, not to mention it becomes impossible to match these up properly to the cells text from the body of the table. (see below)

p53 MUTATION	FUNCTIONALa STATUS	IARC DATABASEb	FEATURESc	SOMATIC	GERMLINE FAMILIES	TOTAL	BREAST
T125R	ALTERED	2	1	0

So i'd like to try something more complex where we simplfiy the header into a single row before we linearize but it would require making the text differ slightly from the original by repeating some words which I am not sure on. The end results would look like this

p53 MUTATION	FUNCTIONALa STATUS	IARC DATABASEb SOMATIC TOTAL	IARC DATABASEb SOMATIC BREAST	IARC DATABASEb GERMLINE FAMILIES	FEATURESc
T125R	ALTERED	2	1	0

@jakelever what do you think? I've already been implementing this for my own purposes but would be happy to put up a PR if you like the idea

[jakelever]

Sure. Go for it. I don't really use the table information that much, but this does remind me that I need to make sure that CIViCmine is properly aware of the tables. Remind me, there's some metadata on these passages that indicate that they are tables, right?

[creisle]

Sure. Go for it. I don't really use the table information that much, but this does remind me that I need to make sure that CIViCmine is properly aware of the tables. Remind me, there's some metadata on these passages that indicate that they are tables, right?

yup, the xml_path infon can be used for that

[jakelever]

Thanks