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Update GFF3Record.java#2377

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danielabutano merged 2 commits intointermine:devfrom
sammyjava:patch-12
Dec 8, 2021
Merged

Update GFF3Record.java#2377
danielabutano merged 2 commits intointermine:devfrom
sammyjava:patch-12

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@sammyjava sammyjava commented Jun 3, 2021 •
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Added getSymbols() method to return "Symbol" attribute if it exists; otherwise null. Same deal as getNames() but we (and others) have explicit Symbol attributes in GFF.

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Sam Hokin added 2 commits June 3, 2021 09:32
Update GFF3Record.java
4d7ff93 
Added getSymbols() method to return "Symbol" attribute if it exists; otherwise null. Same deal as getNames() but we (and others) have explicit Symbol attributes in GFF.
Update GFF3Record.java
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sammyjava commented Jun 3, 2021

Bugger.

----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/intermine/intermine/client/tests/test_registry.py", line 18, in test_getData
    self.assertEqual(registry.getData('flymine'), None)
  File "/home/runner/work/intermine/intermine/client/intermine/registry.py", line 73, in getData
    service = Service(link)
  File "/home/runner/work/intermine/intermine/client/intermine/webservice.py", line 282, in __init__
    raise ServiceError("Could not validate service - is the root url (%s) correct? %s" % (root, e))
ServiceError: u'Could not validate service - is the root url (https://www.flymine.org/flymine/service) correct? [Errno 504] Gateway Time-out: \'<html>\\r\\n<head><title>504 Gateway Time-out</title></head>\\r\\n<body bgcolor="white">\\r\\n<center><h1>504 Gateway Time-out</h1></center>\\r\\n<hr><center>nginx/1.10.3</center>\\r\\n</body>\\r\\n</html>\\r\\n\''

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sammyjava commented Jun 4, 2021

@danielabutano how can I run this again? It looks to me that it failed because flymine wasn't online. My change shouldn't have any effect on unit tests. I think Travis had a "run again" option but I can't seem to find it here.

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sammyjava commented Jun 9, 2021

BUMP @danielabutano how can I run this again? It looks to me that it failed because flymine wasn't online. My change shouldn't have any effect on unit tests. I think Travis had a "run again" option but I can't seem to find it here.

@danielabutano danielabutano self-requested a review December 6, 2021 09:41
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danielabutano commented Dec 8, 2021

Hi @sammyjava I have a question. When the new method is called? I do no see any changes on the GFF3Converter class.
I would have expected something similar to:
List<?> names = record.getNames();

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sammyjava commented Dec 8, 2021 •
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I call it in my LIS extension of GFF3RecordHandler. :) But it ought to be in the core GFFRecord since it's an attribute of GFFs, quite general. Here's my example https://github.com/legumeinfo/lis-bio-sources/blob/d76f5e6db677c6d09ef4ee0f780d763a56236b17/lis-gff/src/main/java/org/intermine/bio/dataconversion/LISGFF3RecordHandler.java#L107

public class LISGFF3RecordHandler extends GFF3RecordHandler {
...
    public void process(GFF3Record record) {
        String type = record.getType();
        if (type.equals("protein_match") || type.equals("protein_hmm_match")) return;
        String id = record.getId();
        String name = null;
        if (record.getNames()!=null) name = record.getNames().get(0);
        String symbol = null;
        if (record.getSymbols()!=null) symbol = record.getSymbols().get(0);
        ....

@danielabutano danielabutano merged commit 42f065f into intermine:dev Dec 8, 2021
@danielabutano danielabutano added this to the InterMine 5.0.4 milestone Dec 8, 2021
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