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Bug Report: The figure of interactions of gene ... #454

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tharris opened this Issue Aug 31, 2012 · 4 comments

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tharris commented Aug 31, 2012

The figure of interactions of gene pal-1 is broken, please check it.

Reported by: Ken (heka****************) (obscured for privacy)

Contributor

vanaukenk commented Aug 31, 2012

Dear Ken,

Thank you for reporting this error to WormBase.

We've created a ticket for it in our tracker and will hopefully have it
fixed soon.

Regards,
--Kimberly Van Auken

Question:
The figure of interactions of gene pal-1 is broken, please check it.
Submitted From:
pal-1 (/species/c_elegans/gene/WBGene00003912)
This issue has been assigned ticket number: #454. Follow progress on our
issue tracker.

Reported by Ken (hekan803@hkbu.edu.hk)
31 Aug 12 02:50 This question was reported via the web interface at
wormbase.org. You can also email us directly.

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Member

chris-grove commented Sep 7, 2012

I've done some testing to check the Interactions widget on various gene
pages. Two types of errors are coming up, and only with some genes.

Error 1: The entire Interactions widget appears to be broken as neither
the table nor the Cytoscape view will appear and the following error
message appears: """
Sorry! An error has occured.

Let us know

Expected URL:
http://www.wormbase.org/rest/widget/gene/WBGeneXXXXXXXX/interactions
Server Error: 500 Error Message: Caught exception in
WormBase::Web::Controller::REST->widget "Null object tag "Gene" at
/usr/local/wormbase/website/production/lib/WormBase/API/Role/Interaction.pm
line 302."
"""

There are 6 genes I found to have this problem:

pal-1
unc-97
pmk-1
pie-1
gld-1
lag-1

Error 2: In the second type of error, the Interactions table loads OK, but
the Cytoscape view does not automatically appear, but rather remains
hidden until the user expands to see via the "View Interaction Network"
header. Once the header has been clicked, most genes that load this way
eventually (after 2 minutes) throw an error message: "Sorry! An error has
occured. Let us know"

I found 7 genes with this problem:

daf-16
let-60
let-23
sem-5
egl-15
lin-12
glp-1

Counter to what I said earlier on the conference call, these problems do
not necessarily appear to be correlated with the number of interactions.
For example, of the genes I looked at, daf-2 probably had the most
interactions (466), but the Interaction widget loads consistently without
any problem on that page (with a LOT of interactions displayed in the
Cytoscape view).

Here are a list of genes whose Interaction widgets appeared to load
without any problems:

daf-2
hlh-30
hlh-2
hlh-1
dsh-1
mex-3
clr-1
lin-15
lin-15A
lin-15B
lin-1
lin-3
lin-2
hlh-8
sup-46
sup-11
daf-18
daf-7 - (After expanding)
daf-5
daf-1
unc-3
unc-30
jnk-1
ego-1
dpy-2
dpy-7
emb-5
unc-52
smu-2
dpy-27
xol-1

One question I have is: Why do some gene pages load the Cytoscape view
automatically, and others do not? Again, this does not appear to be
correlated with the number of interactions, in my experience.

Owner

tharris commented Sep 10, 2012

Thanks for the summary, Chris.

Error 1: Interactions widget is broken.

This is fixed for WS233 (now on staging.wormbase.org)

Error 2: Regarding the View Interactions Network:

  1. If the number of interactions is < 450, the Cytoscape interactions field is opened automatically. Otherwise, it needs to be toggled open by the user. We do this because of the sheer time required to load this field. We can change this if you like.
  2. Since we are loading this field dynamically from a third party, if the request times out, we get an error. There isn't much we can do about this at the moment. This means that for any given gene, sometimes the network viewer will load and other times not.

On Sep 7, 2012, at 12:55 PM, Chris Grove notifications@github.com wrote:

I've done some testing to check the Interactions widget on various gene
pages. Two types of errors are coming up, and only with some genes.

Error 1: The entire Interactions widget appears to be broken as neither
the table nor the Cytoscape view will appear and the following error
message appears: """
Sorry! An error has occured.

Let us know

Expected URL:
http://www.wormbase.org/rest/widget/gene/WBGeneXXXXXXXX/interactions
Server Error: 500 Error Message: Caught exception in
WormBase::Web::Controller::REST->widget "Null object tag "Gene" at
/usr/local/wormbase/website/production/lib/WormBase/API/Role/Interaction.pm
line 302."
"""

There are 6 genes I found to have this problem:

pal-1
unc-97
pmk-1
pie-1
gld-1
lag-1

Error 2: In the second type of error, the Interactions table loads OK, but
the Cytoscape view does not automatically appear, but rather remains
hidden until the user expands to see via the "View Interaction Network"
header. Once the header has been clicked, most genes that load this way
eventually (after 2 minutes) throw an error message: "Sorry! An error has
occured. Let us know"

I found 7 genes with this problem:

daf-16
let-60
let-23
sem-5
egl-15
lin-12
glp-1

Counter to what I said earlier on the conference call, these problems do
not necessarily appear to be correlated with the number of interactions.
For example, of the genes I looked at, daf-2 probably had the most
interactions (466), but the Interaction widget loads consistently without
any problem on that page (with a LOT of interactions displayed in the
Cytoscape view).

Here are a list of genes whose Interaction widgets appeared to load
without any problems:

daf-2
hlh-30
hlh-2
hlh-1
dsh-1
mex-3
clr-1
lin-15
lin-15A
lin-15B
lin-1
lin-3
lin-2
hlh-8
sup-46
sup-11
daf-18
daf-7 - (After expanding)
daf-5
daf-1
unc-3
unc-30
jnk-1
ego-1
dpy-2
dpy-7
emb-5
unc-52
smu-2
dpy-27
xol-1

One question I have is: Why do some gene pages load the Cytoscape view
automatically, and others do not? Again, this does not appear to be
correlated with the number of interactions, in my experience.


Reply to this email directly or view it on GitHub.

Member

chris-grove commented Sep 11, 2012

OK, thanks Todd.

As for the number of interactions, there seems to be some inconsistency. For example, the daf-2 gene page Interactions widget (the Cytoscape view AND the table) consistently opens without any error despite having 466 interactions in total. Conversely, the Interaction widget for several genes with fewer than 450 interactions (daf-16 with 212 interactions, let-60 with 448 interactions, egl-15 with 252 interactions, sem-5 with 173 interactions, let-23 with 374 interactions) require the 'View Interaction Network' expansion to see the Cytoscape view. I looked at these on staging, and they're all as I say except for let-60, which now loads the Cytoscape view automatically despite having 454 interactions.

This seems a bit strange, no?

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