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set regex pattern for CURIE and add URL, fixes #400 #406

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set regex pattern for CURIE and add URL, fixes #400 #406

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2c12281
tweak regexes to fit in the line length specified by tox.
sierra-moxon Mar 16, 2023
2a48936
change name of parameter to reflect ticket
sierra-moxon Mar 16, 2023
dff281b
fix description
sierra-moxon Mar 21, 2023
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10 changes: 8 additions & 2 deletions TranslatorReasonerAPI.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -1103,7 +1103,7 @@ components:
CURIE for a Biolink 'qualifier' association slot, generally taken
from Biolink association slots designated for this purpose
(that is, association slots with names ending in 'qualifier')
e.g. biolink:subject_aspect_qualifier,
e.g. biolink:subject_aspect_qualifier,
biolink:subject_direction_qualifier,
biolink:object_aspect_qualifier, etc. Such qualifiers are used
to elaborate a second layer of meaning of a knowledge graph edge.
Expand Down Expand Up @@ -1181,9 +1181,15 @@ components:
by a colon, such as UniProtKB:P00738. Via an external context
definition, the CURIE prefix and colon may be replaced by a URI
prefix, such as http://identifiers.org/uniprot/, to form a full
URI.
URI. Conforms to https://www.w3.org/TR/curie/
externalDocs:
url: https://www.w3.org/TR/2010/NOTE-curie-20101216/
pattern: ^\S+:\S+$
URL:
type: string
description: >-
A Uniform Resource Locator, such as https://www.example.com.
pattern: ^(http(s)?:\/\/.)?(www\.)?\S+$
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Isn't this regular expression anything without a space? Is that really helpful? Testing this regexp:

#!/bin/env python3
import re

inputs = [ 'http://arax.ncats.io', 'foo', '@*$&@#', 'PMID:123', 'http://peptideatlas.org/tmp/hello world.txt' ]

for input in inputs:
    match = re.search(r'^(http(s)?:\/\/.)?(www\.)?\S+$', input)
    if match:
        print(f"MATCHES {input}")
    else:
        print(f"    x   {input}")

yields

MATCHES http://arax.ncats.io
MATCHES foo
MATCHES @*$&@#
MATCHES PMID:123
    x   http://peptideatlas.org/tmp/hello world.txt

only the last one fails.

Yet if you paste that into your browser, it works!

Maybe this is useful with a more restrictive regular expression?

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My first thought too was to find a more comprehensive one. The one I found and tested that was more restrictive did fail the line length linting on this repo and before I tried to break it into many lines, I started asking around a bit for best practice on this. The feedback I got was that a very restrictive regex will mean constant tweaking with "in the wild" implementations of URLs and CURIEs. However, if we want to have a URI (not L) type, that is much more restrictive, we can do that.

MetaKnowledgeGraph:
type: object
description: >-
Expand Down