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Add search option for "contains any text separated by ORs" #224
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enhancement
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important
Things that are critical for getting Qurro in a working/useful state
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fedarko
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Feb 27, 2020
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Mar 8, 2020
Relevant to biocore#225. At least there's finally an official explanation for what "separated text fragments" does, but sheesh, this highlights the need for better searching methods (biocore#224).
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Add search option for "contains multiple possible text fragments"
Add search option for "contains any text separated by ORs"
Mar 18, 2020
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Mar 18, 2020
Still need to add tests for this code, but this seems to work fine. Uses | characters as the dividers. If the input text has no |s, then using this is identical to normal searching (*with the exception* that this will trim leading/trailing whitespace from the input text).
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Apr 26, 2020
The "global leak" problem (with currVal not being declared before its use inside orFilterFeatures()) was actually the first time I've seen Mocha find this sorta problem! (That I remember, at least.) Really cool that this infrastructure is paying off.
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Apr 26, 2020
This is close to being done. Want to test this works with taxonomy strings (would be good to add an example similar to Lisa's), then need to document this in the MP tutorial and address the whitespace junk as discussed in biocore#224.
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Apr 26, 2020
The error message improved has to do with what's thrown when a nonexistent field name is passed to filterFeatures(). Should never be seen by the user, but having a more detailed error message (that includes the name of said nonexistent field) will help with debugging. (I also modified the test for that error message to check that the error message is actually thrown.)
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you know, the last minute junk you think of while you're washing your hair in the shower. standard stuff. Think all that's left for biocore#224 now is documentation :)
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Remembered that I wanted to bake a guarantee for this in
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Labels
enhancement
New feature or request
important
Things that are critical for getting Qurro in a working/useful state
progress
|
s)|
s caseabc | def | ghi|jk
as your input text searches for matches againstabc
,def
,ghi
,jk
.|
s)description
Searching name is subject to change.
Essentially, this would let you search by multiple possible arbitrary substrings, without the limitations inherent to the current separated text fragment searching. The inputs would be separated by
OR
s, similar to SQL queries?An example input string would be
And any features with taxa containing
g__thing; s__speciesname
, ors__coli
, orp__Proteobacteria
would match. (We could just split up the input query byOR
s, then trim off any surrounding whitespace from each substring.)This would need to be properly documented (#123), but it's a much more natural way to search through multiple features at once than the current "contains the separated text fragment(s)" option. This is essentially another way of coming at #140, but I think this is much more doable in the short-term (and honestly it might be a bit more intuitive).
This would solve the case where you have polyphyletic taxa, e.g., the same species name in different genera—the current searching methods in Qurro are not fully equipped to handle that situation (you can search for a particular species using the "contains the text" searching option, but if you want to search for multiple features at once this isn't possible). An example of the "same species name in different genera" problem is e.g. P. gingivalis and H. gingivalis.
Thanks @lisa55asil for bringing this issue to my attention!
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