Phenotype Search GeneNetwork tux01:gene:

[gabrielacorona]

Hello, I was browsing gene network to see how it works and I encountered an error. I went to search, then selected phenotypes and typed 'human'. I have no biology knowledge so I don't even know if the search was relevant. thank you! Nevertheless, here's the stack trace:

GeneNetwork tux01:gene:2.11-rc2-production-91675f055 http://gn2.genenetwork.org/gsearch?type=phenotype&terms=human ( 8:55PM UTC Apr 03, 2019) Traceback (most recent call last): File "/usr/local/guix-profiles/gn-latest-20181119/lib/python2.7/site-packages/flask/app.py", line 1639, in full_dispatch_request rv = self.dispatch_request() File "/usr/local/guix-profiles/gn-latest-20181119/lib/python2.7/site-packages/flask/app.py", line 1625, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/export/local/home/gn2/production/gene/wqflask/wqflask/views.py", line 197, in gsearchact result = gsearch.GSearch(request.args).__dict__ File "/export/local/home/gn2/production/gene/wqflask/wqflask/gsearch.py", line 171, 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 47, in __init__ self.dataset = create_dataset(kw.get('dataset_name')) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 65, in create_dataset dataset_type = Dataset_Getter(dataset_name) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 117, in __call__ return self.datasets[name] KeyError: 'HSBPublish'

[zsloan]

Thanks for mentioning this! It seems that a recent change may have caused an issue with human phenotypes being added to this file that compiles the list of data sets. I should be able to fix it pretty fast.

On Wed, Apr 3, 2019 at 4:03 PM Gabriela Corona notifications@github.com wrote:

Hello, I was browsing gene network to see how it works and I encountered an error. I went to search, then selected phenotypes and typed 'human'. I have no biology knowledge so I don't even know if the search was relevant. thank you! Nevertheless, here's the stack trace:

GeneNetwork tux01:gene:2.11-rc2-production-91675f055 http://gn2.genenetwork.org/gsearch?type=phenotype&terms=human ( 8:55PM UTC Apr 03, 2019) Traceback (most recent call last): File "/usr/local/guix-profiles/gn-latest-20181119/lib/python2.7/site-packages/flask/app.py", line 1639, in full_dispatch_request rv = self.dispatch_request() File "/usr/local/guix-profiles/gn-latest-20181119/lib/python2.7/site-packages/flask/app.py", line 1625, in dispatch_request return self.view_functionsrule.endpoint File "/export/local/home/gn2/production/gene/wqflask/wqflask/views.py", line 197, in gsearchact result = gsearch.GSearch(request.args).dict File "/export/local/home/gn2/production/gene/wqflask/wqflask/gsearch.py", line 171, 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 47, in init self.dataset = create_dataset(kw.get('dataset_name')) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 65, in create_dataset dataset_type = Dataset_Getter(dataset_name) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 117, in call return self.datasets[name] KeyError: 'HSBPublish'

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[zsloan]

This issue should be fixed now. This actually helped me find another related issue, so thanks a lot for bringing it to my attention; a lot of the time things slip through the cracks where one fix/change causes some other unexpected issue.

One thing I should probably mention is that the global search is currently not very sophisticated. If you search "human" it will also pull up some non-human results, because it will be searching for the word "human" in a variety of fields, such as the trait description. That being said, it's possible to sort by species among the global search results, or to search within those results for specific terms (using the "Search this table for..." option).

On Wed, Apr 3, 2019 at 4:20 PM Zachary Sloan zachary.a.sloan@gmail.com wrote:

Thanks for mentioning this! It seems that a recent change may have caused an issue with human phenotypes being added to this file that compiles the list of data sets. I should be able to fix it pretty fast.

On Wed, Apr 3, 2019 at 4:03 PM Gabriela Corona notifications@github.com wrote:

Hello, I was browsing gene network to see how it works and I encountered an error. I went to search, then selected phenotypes and typed 'human'. I have no biology knowledge so I don't even know if the search was relevant. thank you! Nevertheless, here's the stack trace:

GeneNetwork tux01:gene:2.11-rc2-production-91675f055 http://gn2.genenetwork.org/gsearch?type=phenotype&terms=human ( 8:55PM UTC Apr 03, 2019) Traceback (most recent call last): File "/usr/local/guix-profiles/gn-latest-20181119/lib/python2.7/site-packages/flask/app.py", line 1639, in full_dispatch_request rv = self.dispatch_request() File "/usr/local/guix-profiles/gn-latest-20181119/lib/python2.7/site-packages/flask/app.py", line 1625, in dispatch_request return self.view_functionsrule.endpoint File "/export/local/home/gn2/production/gene/wqflask/wqflask/views.py", line 197, in gsearchact result = gsearch.GSearch(request.args).dict File "/export/local/home/gn2/production/gene/wqflask/wqflask/gsearch.py", line 171, 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 47, in init self.dataset = create_dataset(kw.get('dataset_name')) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 65, in create_dataset dataset_type = Dataset_Getter(dataset_name) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 117, in call return self.datasets[name] KeyError: 'HSBPublish'

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[robwwilliams]

Dear Gabriela,

Thanks very much for forwarding this error. We will look into this HSBPublish error.

On Wed, Apr 3, 2019 at 4:03 PM Gabriela Corona notifications@github.com wrote:

Hello, I was browsing gene network to see how it works and I encountered an error. I went to search, then selected phenotypes and typed 'human'. I have no biology knowledge so I don't even know if the search was relevant. thank you! Nevertheless, here's the stack trace:

GeneNetwork tux01:gene:2.11-rc2-production-91675f055 http://gn2.genenetwork.org/gsearch?type=phenotype&terms=human ( 8:55PM UTC Apr 03, 2019) Traceback (most recent call last): File "/usr/local/guix-profiles/gn-latest-20181119/lib/python2.7/site-packages/flask/app.py", line 1639, in full_dispatch_request rv = self.dispatch_request() File "/usr/local/guix-profiles/gn-latest-20181119/lib/python2.7/site-packages/flask/app.py", line 1625, in dispatch_request return self.view_functionsrule.endpoint File "/export/local/home/gn2/production/gene/wqflask/wqflask/views.py", line 197, in gsearchact result = gsearch.GSearch(request.args).dict File "/export/local/home/gn2/production/gene/wqflask/wqflask/gsearch.py", line 171, 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 47, in init self.dataset = create_dataset(kw.get('dataset_name')) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 65, in create_dataset dataset_type = Dataset_Getter(dataset_name) File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 117, in call return self.datasets[name] KeyError: 'HSBPublish'

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-- Rob

Robert W. Williams, Ph.D. Chair: Department of Genetics, Genomics and Informatics 71 S Manassas St, Memphis TN 38163 University of Tennessee Health Science Center Office 901 448-7050 CELL 901 604 4752 Office: Translational Science Research Building, Room 407 EMAIL: rwilliams@uthsc.edu Alternative email: labwilliams@gmail.com SKYPE: robwwilliams

[pjotrp]

Can we close this?

[zsloan]

Yes, it is fixed.