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monica 
Group: Members
Posts: 3
Joined: Nov. 2007
Member Rating: None
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Posted on: May 06 2008,20:47 |
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I have been using the DAVID API casually for several months. I find it more convenient to link directly to a DAVID result than it is to save it somewhere.
Since the update to DAVID 2008, none of my links seem to work anymore, but I can't figure out what is wrong. I noticed that the categories for the analyses have changed a little, so I'll have to update those, but even the basic Gene Report just doesn't work.
Example (with the link header of course)
david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=
171716,171901,171939,171975,172610,172755,172885,172901,173206,173278,173279,173335,173372
,173449,173510,174050,174106,174229,174469,174596,174671,174725,174771,174899,174908,17506
9,175070,175195,175300,175307,175315,175316,175413,175441,175443,175467,175469,175519,1755
24,175530,175596,175650,175660,175757,175765,175766,175786,175789,175826,175827,175890,175
922,175966,176126,176315,176321,176363,176437,176439,176503,176504,176512,176516,176544,17
6573,176688,176707,176961,176966,176982,176983,176988,177161,177181,177212,177217,177356,1
77458,177787,178207,178279,178362,178398,178489,178507,178629,178908,178989,179043,179150,
179184,179441,179488,179493,179500,179981,180328,180360,180368,180460,180461,180468,180554
,180583,180597,180727,180737,180771,180792,180793,180808,180827,180842,180855,180881,18098
7,180990,181062,181065,181184,181190,181207,181348,181353,181374,181577,181587,181600,1816
24,181676,181729,181772,181796,184935,185535,185574,186132,186176,186182,186483,187156,187
433,187916,188364,189900,190251,190278,190511,191146,259340,266897,353418,3564821,3564910,
3565044,3565132,3565441,3565618,4363126&tool=gene2gene
Result (after many minutes):
H**P Status 500 -
Session already invalidated <snip>
note The full stack trace of the root cause is available in the Ap*che Tomc*t/5.5.23 logs.
The DAVID forum software won't let me post the link properly nor will it let me post the error message.
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| Post Number: 2
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david
Group: Super Administrators
Posts: 698
Joined: Mar. 2006
Member Rating: None
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Posted on: May 07 2008,09:37 |
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Sorry for the inconvenience. As part of the update, we also changed several category names. We have removed "_NAME" from those category names that had previously ended with it. There are also some other slight changes. The current naming conventions can be found on the DAVID API page.
DAVID Team
Edited by david on May 07 2008,09:38
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| Post Number: 3
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monica
Group: Members
Posts: 3
Joined: Nov. 2007
Member Rating: None
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Posted on: May 07 2008,20:39 |
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Thanks for your reply.
I realize that some of the category names have changed.
However, I don't see any changes to the simpler API functions such as Gene Report and Gene Functional Classification.
I don't see any difference between the link that I posted and the API examples on the DAVID API page, except in the Entrez ID list itself.
Nevertheless I can not get my links to work.
Does DAVID still support C. elegans?
Can you tell me what is wrong with my link?
Monica
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| Post Number: 4
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david
Group: Super Administrators
Posts: 698
Joined: Mar. 2006
Member Rating: None
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Posted on: May 08 2008,09:25 |
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The reply was based off of one of your previous posts(we received several emails for the same post), which referenced an api call with some of the changed annotation categories. Sorry for the discrepency. As for the current example, I believe that you are running into a url length limit. This is a limit of the process by which your data is sent to our server. Unfortunately, we cannot control this limit. Once a url reaches the limit, it is truncated. Therefore, the tool parameters(gene2gene, etc) are never reaching the server which causes the error. I would suggest that you place the id parameter at the very end of your url. This will ensure that all critical parameters reach the server. This also means that some of your ids may not reach the server. While this is not optimal, it will give you results. We are currently exploring new methods for the api that will overcome this limit. Below is your example, rearranged as previously described:
http://david.abcc.ncifcrf.gov/api.jsp....4363126
DAVID Team
Edited by david on May 08 2008,09:32
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| Post Number: 5
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monica
Group: Members
Posts: 3
Joined: Nov. 2007
Member Rating: None
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Posted on: May 08 2008,19:17 |
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Alright! It's working properly now. Putting the "tool" parameter at the beginning of the link is a good idea.
It's much slower than before though. Analyses that used to take seconds now take minutes, almost as if some tables weren't indexed properly.
Thanks for your help! It works well enough for the time being.
Monica
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| Post Number: 6
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david
Group: Super Administrators
Posts: 698
Joined: Mar. 2006
Member Rating: None
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Posted on: May 09 2008,10:56 |
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Good to hear. The Entrez Gene mapping was in memory before the update, but has temporarily moved back to the database as of the new update. Hopefully you will see previous speeds return in the near future.
DAVID Team
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| Post Number: 7
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david_user
Group: Guests
Posts: 471
Joined: Mar. 2006
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Posted on: May 25 2008,19:26 |
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How long has this API been available for and where can I find the documentation for how to access?
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| Post Number: 8
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david
Group: Super Administrators
Posts: 698
Joined: Mar. 2006
Member Rating: None
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Posted on: May 27 2008,09:31 |
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Please see the DAVID API page for more details.
DAVID Team
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