HttpApplicationError #129

meghanakaranam1 · 2023-05-19T07:03:44Z

hi,
I'm getting this error. Is there a problem with my code, or is the api having any server side issues?
please help me out on this @eloyfelix @nclopezo @mnowotka @fredrikw @sshojiro

Acario · 2023-05-20T03:00:58Z

I am getting the same error. My code was working fine two weekends ago. Today I tried it on the same compound as two weeks ago and this error came up. I would like to know what is going on as well here.

fredrikw · 2023-05-22T07:10:07Z

Hello,
Did you check if the api hade any problems? Do you have a minimum reproducible example? It would be a lot better if you copied and pasted the code and error message as text instead of a screen shot. For one, it's possible to copy and paste to test instead of typing everything manually. Also, you have cut the error message, did it include anymore specifics on the server error?
I don't have the library installed on my main computer at the moment so I can't easily try but the API seems to work. (Checkable at https://www.ebi.ac.uk/chembl/api/data/docs)

Acario · 2023-05-22T18:59:52Z

Here is the code I am running:

from chembl_webresource_client.new_client import new_client

Here is the error:

`Exception Traceback (most recent call last)
Input In [1], in <cell line: 1>()
---> 1 from chembl_webresource_client.new_client import new_client

File ~\anaconda3\lib\site-packages\chembl_webresource_client\new_client.py:65, in
60 return client
63 #-----------------------------------------------------------------------------------------------------------------------
---> 65 new_client = client_from_url(Settings.Instance().NEW_CLIENT_URL + '/spore')

File ~\anaconda3\lib\site-packages\chembl_webresource_client\new_client.py:27, in client_from_url(url, base_url)
25 res = requests.get(url)
26 if not res.ok:
---> 27 raise Exception('Error getting schema from url {0} with status {1} and msg {2}'.format(url, res.status_code, res.text))
28 schema = res.json()
29 if 'base_url' not in schema:

Exception: Error getting schema from url https://www.ebi.ac.uk/chembl/api/data/spore with status 500 and msg <!doctype html>

<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- <link rel="stylesheet" media="all" href="/css/styles.css?" /> -->
<title>Error: 500 | EMBLâ��s European Bionformatics Institute</title>



<link rel="icon" type="image/x-icon"

href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.4/images/logos/EMBL-EBI/favicons/favicon.ico" />

<!-- Search indexing optimisations -->
<meta class="swiftype" name="what" data-type="string" content="none" />
<meta class="swiftype" name="where" data-type="string" content="EMBL-EBI" />


<!-- Descriptive meta -->
<meta name="title" content="Error: 500">
<meta name="author" content="European Bioinformatics Institute">
<meta name="robots" content="index, follow">
<meta name="keywords" content="">
<meta name="description" content="">

<!-- Open Graph / Facebook -->
<meta property="og:type" content="website">
<meta property="og:url" content="https://www.ebi.ac.uk/info/error-pages/500-standalone/">
<meta property="og:title" content="Error: 500">
<meta property="og:description" content="">


<!-- Twitter -->
<meta property="twitter:card" content="summary_large_image">
<meta property="og:url" content="https://www.ebi.ac.uk/info/error-pages/500-standalone/">
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<meta property="twitter:description" content="">


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<header id="masthead-black-bar" class="clearfix masthead-black-bar | ebi-header-footer vf-content vf-u-fullbleed"></header>

Error: 500

There was a technical error.

Something has gone wrong with our web server when attempting to make this page.

Unfortunately, the service you are trying to access is currently unavailable.
Please try again later.

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Acario · 2023-05-22T19:10:58Z

Sometimes it does successfully load the package but then I try to run the package over some compounds and get this below.

Code:
chembl_ids=[]
for h in range(0,len(comps)):
molecule=new_client.molecule
molS=molecule.filter(molecule_synonyms__molecule_synonym__iexact=comps[h])
if len(molS)>0:
chembl_ids.append(molS[0]['molecule_chembl_id']) # Synonym hit
else:
chembl_ids.append(0)

This is the error here:

`HttpApplicationError Traceback (most recent call last)
Input In [11], in <cell line: 2>()
3 molecule=new_client.molecule
4 molS=molecule.filter(molecule_synonyms__molecule_synonym__iexact=comps[h])
----> 5 if len(molS)>0:
6 chemblSyn.append(molS[0]['molecule_chembl_id']) # Synonym hit
7 else:

File ~\anaconda3\lib\site-packages\chembl_webresource_client\query_set.py:97, in QuerySet.len(self)
95 if not self.can_filter:
96 return 1
---> 97 return len(self.query)

File ~\anaconda3\lib\site-packages\chembl_webresource_client\url_query.py:144, in UrlQuery.len(self)
142 return
143 if not self.api_total_count:
--> 144 self.get_page()
145 return self.api_total_count

File ~\anaconda3\lib\site-packages\chembl_webresource_client\url_query.py:394, in UrlQuery.get_page(self)
392 self.logger.info('From cache: {0}'.format(res.from_cache if hasattr(res, 'from_cache') else False))
393 if not res.ok:
--> 394 handle_http_error(res)
395 if self.frmt == 'json':
396 json_data = res.json()

File ~\anaconda3\lib\site-packages\chembl_webresource_client\http_errors.py:113, in handle_http_error(request)
111 exception_class = status_to_exception.get(request.status_code, BaseHttpException)
112 if request.text:
--> 113 raise exception_class(request.url, request.text)
114 raise exception_class(request.url, request.content)

HttpApplicationError: Error for url https://www.ebi.ac.uk/chembl/api/data/molecule.json, server response: <!doctype html>

<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- <link rel="stylesheet" media="all" href="/css/styles.css?" /> -->
<title>Error: 500 | EMBLâ��s European Bionformatics Institute</title>



<link rel="icon" type="image/x-icon"

href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.4/images/logos/EMBL-EBI/favicons/favicon.ico" />

<!-- Search indexing optimisations -->
<meta class="swiftype" name="what" data-type="string" content="none" />
<meta class="swiftype" name="where" data-type="string" content="EMBL-EBI" />


<!-- Descriptive meta -->
<meta name="title" content="Error: 500">
<meta name="author" content="European Bioinformatics Institute">
<meta name="robots" content="index, follow">
<meta name="keywords" content="">
<meta name="description" content="">

<!-- Open Graph / Facebook -->
<meta property="og:type" content="website">
<meta property="og:url" content="https://www.ebi.ac.uk/info/error-pages/500-standalone/">
<meta property="og:title" content="Error: 500">
<meta property="og:description" content="">


<!-- Twitter -->
<meta property="twitter:card" content="summary_large_image">
<meta property="og:url" content="https://www.ebi.ac.uk/info/error-pages/500-standalone/">
<meta property="twitter:title" content="Error: 500">
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<!-- Content descriptors -->
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<meta name="embl:active" content="where">

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<meta name="embl:last-review" content="2021.04.01">
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<header id="masthead-black-bar" class="clearfix masthead-black-bar | ebi-header-footer vf-content vf-u-fullbleed"></header>

Error: 500

There was a technical error.

Something has gone wrong with our web server when attempting to make this page.

Unfortunately, the service you are trying to access is currently unavailable.
Please try again later.

Search

All Genomes & metagenomes Nucleotide sequences Protein sequences Small molecules Gene expression Gene-Disease Associations Diseases Molecular interactions Reactions & pathways Protein families Literature Samples & ontologies EMBL-EBI People EMBL-EBI web

      <button type="submit" class="vf-search__button | vf-button vf-button--primary">
        <span class="vf-button__text">Search</span>
      </button>
    </div>
  </form>
  <p class="vf-text-body--5 vf-u-margin__bottom--0">
    Example searches: <a class="vf-link" href="/ebisearch/search.ebi?db=allebi&amp;requestFrom=ebi_index&amp;query=blast">blast</a>
    <a class="vf-link" href="/ebisearch/search.ebi?db=allebi&amp;query=keratin&amp;requestFrom=ebi_index">keratin</a>
    <a class="vf-link" href="/ebisearch/search.ebi?db=allebi&amp;query=bfl1&amp;requestFrom=ebi_index">bfl1</a>
    | <a class="vf-link" href="https://www.ebi.ac.uk/ebisearch/overview.ebi/about">About EBI Search</a>
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eloyfelix · 2023-05-22T19:26:06Z

@juanfmx2 @nclopezo could you please take a look at it?

cc: @BZdrazil @FionaEBI

fredrikw · 2023-05-25T08:17:47Z

It's working perfectly fine for me both through the package and directly on the API docs page. Most likely they had some problems on the API side. The error messages certainly indicates that. You get a 500-error from the API. So I wouldn't say it's a bug with the client package.

juanfmx2 · 2023-05-30T14:20:56Z

@fredrikw @Acario @meghanakaranam1 sorry for the late response, we were having intermittent issues with our infrastructure, but the service should be stable now. Please let me know if you are experiencing any other issues.

Acario · 2023-05-30T15:46:31Z

Thanks for the help @fredrikw @juanfmx2!

juanfmx2 closed this as completed May 30, 2023

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HttpApplicationError #129

HttpApplicationError #129

meghanakaranam1 commented May 19, 2023 •

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Acario commented May 20, 2023

fredrikw commented May 22, 2023 •

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Acario commented May 22, 2023

Error: 500

Need assistance?

Acario commented May 22, 2023 •

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Error: 500

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eloyfelix commented May 22, 2023

fredrikw commented May 25, 2023

juanfmx2 commented May 30, 2023

Acario commented May 30, 2023

HttpApplicationError #129

HttpApplicationError #129

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meghanakaranam1 commented May 19, 2023 • edited Loading

Acario commented May 20, 2023

fredrikw commented May 22, 2023 • edited Loading

Acario commented May 22, 2023

Error: 500

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Acario commented May 22, 2023 • edited Loading

Error: 500

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eloyfelix commented May 22, 2023

fredrikw commented May 25, 2023

juanfmx2 commented May 30, 2023

Acario commented May 30, 2023

meghanakaranam1 commented May 19, 2023 •

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fredrikw commented May 22, 2023 •

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Acario commented May 22, 2023 •

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