Dom refactor tab loader #554
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…ing mzml argument with origin
Merge from master
merge from master
Issue 497 fix
…serialized in isatab2json conversion
Fix to determining JSON directory location.
The previous regex didn't match any DOI I tried. I found this one in a blog post from Crossref where they say it matched 74.4M out of 74.9M DOIs that they have seen. The post is here: https://www.crossref.org/blog/dois-and-matching-regular-expressions/
Since the DOI regex works now there are 2 fewer warnings. Previously it was warning about valid DOIs.
Testing changes to run on Windows.
Update defaults.py
The last changes were initially tested and created on Windows, but had errors on GitHub. I fixed those errors, but didn't retest on Windows. This has been tested on both and is problem free.
i_df and investigation_df are not a DataFrame as indicated in parameter typing or as the name would suggest. It's actually a dictionary of DataFrames and lists of DataFrames. I have renamed them to reflect this.
There were 2 tests that needed to be changed to match the new naming.
More changes
Rename i_df and investigation_df.
Fix rule and check.
I started editing this function because of the "Only one protocol reference should be used in a Protocol REF column." message(s), but I found some other issues to address as well.
The messaging on the 2 checks dealing with study assays did not make it clear exactly which assay and which study had the issue. I changed the messaging so it clearly indicates the affected study and assay.
Fairly significant changes to check_protocol_fields
Changed messaging on study assays errors
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First pass at refactoring isa tab loader