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GeneNetwork (2nd generation)
http://gn2.genenetwork.org/
GNU Affero General Public License v3.0
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Error when "Searching All" by "Genes/Molecules" #375

Closed tantrev closed 4 years ago

tantrev commented 4 years ago

An example is currently live and may be viewed at https://genenetwork.org/gsearch?type=gene&terms=SULT1A1

Short version of error: `(GeneNetwork error: u'INIA_MacFas_AMG_RMA_0110')

GeneNetwork tux01:gene:2.11-rc2-HEAD-dce4f524a http://genenetwork.org/gsearch?type=gene&terms=SULT1A1 (10:28PM UTC Apr 07, 2020)
u'INIA_MacFas_AMG_RMA_0110' (error)
  File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 123, in __call__
    return self.datasets[name]`

Full stack-trace:

GeneNetwork tux01:gene:2.11-rc2-HEAD-dce4f524a  http://genenetwork.org/gsearch?type=gene&terms=SULT1A1 (10:28PM UTC Apr 07, 2020)
       Traceback (most recent call last):
         File "/usr/local/guix-profiles/gn-latest-20190905/lib/python2.7/site-packages/flask/app.py", line 1832, in full_dispatch_request
           rv = self.dispatch_request()
         File "/usr/local/guix-profiles/gn-latest-20190905/lib/python2.7/site-packages/flask/app.py", line 1818, in dispatch_request
           return self.view_functions[rule.endpoint](**req.view_args)
         File "/export/local/home/gn2/production/gene/wqflask/wqflask/views.py", line 200, in gsearchact
           result = gsearch.GSearch(request.args).__dict__
         File "/export/local/home/gn2/production/gene/wqflask/wqflask/gsearch.py", line 96, in __init__
           trait_ob = GeneralTrait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False)
         File "/export/local/home/gn2/production/gene/wqflask/base/trait.py", line 45, in __init__
           self.dataset = create_dataset(kw.get('dataset_name'))
         File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 69, in create_dataset
           dataset_type = Dataset_Getter(dataset_name)
         File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 123, in __call__
           return self.datasets[name]
       KeyError: u'INIA_MacFas_AMG_RMA_0110'
robwwilliams commented 4 years ago

Dear Zach, Arthur Global search is broken,

Trevor: Thanks. Will have this fixed.

(GeneNetwork error: u'INIA_MacFas_AMG_RMA_0110')

GeneNetwork tux01:gene:2.11-rc2-HEAD-dce4f524a

http://genenetwork.org/gsearch?type=gene&terms=grin2b (10:45PM UTC Apr 07, 2020) u'INIA_MacFas_AMG_RMA_0110' (error) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 123, in call return self.datasets[name]

On Tue, Apr 7, 2020 at 5:31 PM Trevor Tanner notifications@github.com wrote:

An example is currently live and may be viewed at https://genenetwork.org/gsearch?type=gene&terms=SULT1A1

Short version of error: `(GeneNetwork error: u'INIA_MacFas_AMG_RMA_0110')

GeneNetwork tux01:gene:2.11-rc2-HEAD-dce4f524a http://genenetwork.org/gsearch?type=gene&terms=SULT1A1 (10:28PM UTC Apr 07, 2020) u'INIA_MacFas_AMG_RMA_0110' (error) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 123, in call return self.datasets[name]`

Full stack-trace:

GeneNetwork tux01:gene:2.11-rc2-HEAD-dce4f524a http://genenetwork.org/gsearch?type=gene&terms=SULT1A1 (10:28PM UTC Apr 07, 2020) Traceback (most recent call last): File "/usr/local/guix-profiles/gn-latest-20190905/lib/python2.7/site-packages/flask/app.py", line 1832, in full_dispatch_request rv = self.dispatch_request() File "/usr/local/guix-profiles/gn-latest-20190905/lib/python2.7/site-packages/flask/app.py", line 1818, in dispatch_request return self.view_functionsrule.endpoint File "/export/local/home/gn2/production/gene/wqflask/wqflask/views.py", line 200, in gsearchact result = gsearch.GSearch(request.args).dict File "/export/local/home/gn2/production/gene/wqflask/wqflask/gsearch.py", line 96, in init trait_ob = GeneralTrait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False) File "/export/local/home/gn2/production/gene/wqflask/base/trait.py", line 45, in init self.dataset = create_dataset(kw.get('dataset_name')) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 69, in create_dataset dataset_type = Dataset_Getter(dataset_name) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 123, in call return self.datasets[name] KeyError: u'INIA_MacFas_AMG_RMA_0110'

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-- Rob

Robert W. Williams, Ph.D. Chair: Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center 71 S Manassas St, Memphis TN 38103-3310, TSRB Room 405 Tele/Cell: 901 604 4752 EMAIL: rwilliams@uthsc.edu or labwilliams@gmail.com

zsloan commented 4 years ago

It's fixed now.

Does anyone know if the dataset "INIA_MacFas_AMG_RMA_0110" is new? This error usually only happens when new datasets are added.

On Tue, Apr 7, 2020 at 5:49 PM robwwilliams notifications@github.com wrote:

Dear Zach, Arthur Global search is broken,

Trevor: Thanks. Will have this fixed.

(GeneNetwork error: u'INIA_MacFas_AMG_RMA_0110')

GeneNetwork tux01:gene:2.11-rc2-HEAD-dce4f524a http://genenetwork.org/gsearch?type=gene&terms=grin2b (10:45PM UTC Apr 07, 2020) u'INIA_MacFas_AMG_RMA_0110' (error) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 123, in call return self.datasets[name]

On Tue, Apr 7, 2020 at 5:31 PM Trevor Tanner notifications@github.com wrote:

An example is currently live and may be viewed at https://genenetwork.org/gsearch?type=gene&terms=SULT1A1

Short version of error: `(GeneNetwork error: u'INIA_MacFas_AMG_RMA_0110')

GeneNetwork tux01:gene:2.11-rc2-HEAD-dce4f524a http://genenetwork.org/gsearch?type=gene&terms=SULT1A1 (10:28PM UTC Apr 07, 2020) u'INIA_MacFas_AMG_RMA_0110' (error) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 123, in call return self.datasets[name]`

Full stack-trace:

GeneNetwork tux01:gene:2.11-rc2-HEAD-dce4f524a http://genenetwork.org/gsearch?type=gene&terms=SULT1A1 (10:28PM UTC Apr 07, 2020) Traceback (most recent call last): File "/usr/local/guix-profiles/gn-latest-20190905/lib/python2.7/site-packages/flask/app.py", line 1832, in full_dispatch_request rv = self.dispatch_request() File "/usr/local/guix-profiles/gn-latest-20190905/lib/python2.7/site-packages/flask/app.py", line 1818, in dispatch_request return self.view_functionsrule.endpoint File "/export/local/home/gn2/production/gene/wqflask/wqflask/views.py", line 200, in gsearchact result = gsearch.GSearch(request.args).dict File "/export/local/home/gn2/production/gene/wqflask/wqflask/gsearch.py", line 96, in init trait_ob = GeneralTrait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False) File "/export/local/home/gn2/production/gene/wqflask/base/trait.py", line 45, in init self.dataset = create_dataset(kw.get('dataset_name')) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 69, in create_dataset dataset_type = Dataset_Getter(dataset_name) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 123, in call return self.datasets[name] KeyError: u'INIA_MacFas_AMG_RMA_0110'

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/genenetwork/genenetwork2/issues/375, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AC55V7FBJAKGOQQJDKTOUWDRLOSUPANCNFSM4MDPGIFQ

.

-- Rob

Robert W. Williams, Ph.D. Chair: Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center 71 S Manassas St, Memphis TN 38103-3310, TSRB Room 405 Tele/Cell: 901 604 4752 EMAIL: rwilliams@uthsc.edu or labwilliams@gmail.com

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tantrev commented 4 years ago

Woohoo! Not sure about the dataset, but thanks for getting the search back!