dbfetch medlinedb errors when using pubmedxml or medlinexml

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dbfetch medlinedb errors when using pubmedxml or medlinexml

Carnë Draug-2
For those who receive notifications from the CPAN test matrix, there's
been some tests failing on Bio::DB::Biblio::biofetch [1].  There seems
to be some changes on EBI's dbfetch or medlinedb.  Is anyone aware of
anything?

Even changing the URL on biofetch.pm to point to the correct place will
not work since Bio::Biblio::IO seems to only support pubmedxml and
medlinexml and none seems to be being served from EBI.

Example, biofetch is currently making this type of URLs

    https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline&style=raw&format=medlinexml&id=10592273

But 'format=medlinexml' seems to be invalid.

For what is worth, I sent the email below to EBI support.

Carnë

[1] https://rt.cpan.org/Ticket/Display.html?id=119025

---

This following query

    https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline;id=2859121;format=pubmedxml

(which is one of the online examples [1] for the pubmedxml format) fails
with:

    ERROR 11 Unable to connect to database [medline].

On a related note, the format medlinexml is no longer listed on the
documentation although it worked until a few days ago [2].

Are this two formats no longer supported?

Thank you

Carnë

[1] https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#medline
[2] https://rt.cpan.org/Ticket/Display.html?id=119025&results=c5f91ab4407b80140fad7409ff66a478

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Re: dbfetch medlinedb errors when using pubmedxml or medlinexml

Fields, Christopher J
That error does make me think it has to do with the recent NCBI switch-over to HTTPS; the issue may be primarily on the EBI dbfetch though (maybe a redirect to grab the appropriate format directly from NCBI, which is now failing?).  



Chris

On 12/2/16, 1:29 PM, "Bioperl-l on behalf of Carnë Draug" <bioperl-l-bounces+cjfields=[hidden email] on behalf of [hidden email]> wrote:

>For those who receive notifications from the CPAN test matrix, there's
>been some tests failing on Bio::DB::Biblio::biofetch [1].  There seems
>to be some changes on EBI's dbfetch or medlinedb.  Is anyone aware of
>anything?
>
>Even changing the URL on biofetch.pm to point to the correct place will
>not work since Bio::Biblio::IO seems to only support pubmedxml and
>medlinexml and none seems to be being served from EBI.
>
>Example, biofetch is currently making this type of URLs
>
>    https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline&style=raw&format=medlinexml&id=         <https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline&style=raw&format=medlinexml&id=10592273>
>
>But 'format=medlinexml' seems to be invalid.
>
>For what is worth, I sent the email below to EBI support.
>
>Carnë
>
>[1] https://rt.cpan.org/Ticket/Display.html?id=119025
>
>---
>
>This following query
>
>    https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline;id=2859121;format=pubmedxml
>
>(which is one of the online examples [1] for the pubmedxml format) fails
>with:
>
>    ERROR 11 Unable to connect to database [medline].
>
>On a related note, the format medlinexml is no longer listed on the
>documentation although it worked until a few days ago [2].
>
>Are this two formats no longer supported?
>
>Thank you
>
>Carnë
>
>[1] https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#medline
>[2] https://rt.cpan.org/Ticket/Display.html?id=119025&results=c5f91ab4407b80140fad7409ff66a478
>
>_______________________________________________
>Bioperl-l mailing list
>[hidden email]
>http://mailman.open-bio.org/mailman/listinfo/bioperl-l

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Re: dbfetch medlinedb errors when using pubmedxml or medlinexml

Carnë Draug-2
On 2 December 2016 at 20:02, Fields, Christopher J
<[hidden email]> wrote:
> That error does make me think it has to do with the recent NCBI
> switch-over to HTTPS; the issue may be primarily on the EBI dbfetch
> though (maybe a redirect to grab the appropriate format directly from
> NCBI, which is now failing?).

When did the switch over happened?  I found a planed date for 30/09/2016 [1]
but this still worked on October 30 [2] and I got the first failure report
from cpantests on November 24 [3].


I originally though the cause to be same but unless that happens on the
EBI servers, I don't know how.  I did notice that the code was making
requests using an undocumented [4] format "medlinexml".  Actually, all
formats are failing other than default (seems to be medlinefull),
medlinefull, and medlineref.

  ## works
  https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline;id=2859121;format=medlinefull
  ## fails
  https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline;id=2859121;format=pubmedxml

Carnë

[1] https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/
[2] http://www.cpantesters.org/cpan/report/957a89f2-9ec4-11e6-a23c-a658b607aa42
[3] http://www.cpantesters.org/cpan/report/92af4674-b218-11e6-8dde-c5e727772ce6
[4] https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#medline

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Re: dbfetch medlinedb errors when using pubmedxml or medlinexml

Fields, Christopher J

On 12/2/16, 3:25 PM, "[hidden email] on behalf of Carnë Draug" <[hidden email] on behalf of [hidden email]> wrote:

>On 2 December 2016 at 20:02, Fields, Christopher J
><[hidden email]> wrote:
>> That error does make me think it has to do with the recent NCBI
>> switch-over to HTTPS; the issue may be primarily on the EBI dbfetch
>> though (maybe a redirect to grab the appropriate format directly from
>> NCBI, which is now failing?).
>
>When did the switch over happened?  I found a planed date for 30/09/2016 [1]
>but this still worked on October 30 [2] and I got the first failure report
>from cpantests on November 24 [3].

Sometime in November

>I originally though the cause to be same but unless that happens on the
>EBI servers, I don't know how.  I did notice that the code was making
>requests using an undocumented [4] format "medlinexml".  Actually, all
>formats are failing other than default (seems to be medlinefull),
>medlinefull, and medlineref.
>
>  ## works
>  https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline;id=2859121;format=medlinefull
>  ## fails
>  https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline;id=2859121;format=pubmedxml
>
>Carnë
>
>[1] https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/
>[2] http://www.cpantesters.org/cpan/report/957a89f2-9ec4-11e6-a23c-a658b607aa42
>[3] http://www.cpantesters.org/cpan/report/92af4674-b218-11e6-8dde-c5e727772ce6
>[4] https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#medline

Not sure, I’m hoping EBI can shed light on that.  But the timing is about right with the NCBI switch.

chris

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Re: dbfetch medlinedb errors when using pubmedxml or medlinexml

Carnë Draug-2
On 3 December 2016 at 15:32, Fields, Christopher J
<[hidden email]> wrote:

>
> On 12/2/16, 3:25 PM, "[hidden email] on behalf of Carnë Draug" <[hidden email] on behalf of [hidden email]> wrote:
>
>>On 2 December 2016 at 20:02, Fields, Christopher J
>><[hidden email]> wrote:
>>> That error does make me think it has to do with the recent NCBI
>>> switch-over to HTTPS; the issue may be primarily on the EBI dbfetch
>>> though (maybe a redirect to grab the appropriate format directly from
>>> NCBI, which is now failing?).
>>
>>When did the switch over happened?  I found a planed date for 30/09/2016 [1]
>>but this still worked on October 30 [2] and I got the first failure report
>>from cpantests on November 24 [3].
>
> Sometime in November
>
>>I originally though the cause to be same but unless that happens on the
>>EBI servers, I don't know how.  I did notice that the code was making
>>requests using an undocumented [4] format "medlinexml".  Actually, all
>>formats are failing other than default (seems to be medlinefull),
>>medlinefull, and medlineref.
>>
>>  ## works
>>  https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline;id=2859121;format=medlinefull
>>  ## fails
>>  https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline;id=2859121;format=pubmedxml
>>
>>Carnë
>>
>>[1] https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/
>>[2] http://www.cpantesters.org/cpan/report/957a89f2-9ec4-11e6-a23c-a658b607aa42
>>[3] http://www.cpantesters.org/cpan/report/92af4674-b218-11e6-8dde-c5e727772ce6
>>[4] https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#medline
>
> Not sure, I’m hoping EBI can shed light on that.  But the timing is about right with the NCBI switch.
>
> chris

Here's the reply I got from them. Seems like there's nothing to do on
the bioperl side


---------- Forwarded message ----------
From: Rodrigo Lopez via RT <[hidden email]>
Date: 5 December 2016 at 16:35
Subject: [Support #163271] dbfetch medlinedb errors when using
pubmedxml or medlinexml
To: [hidden email]


Dear User,

Thank you for your feedback. We are aware there is a problem with some formats
for MEDLINE in dbfetch. An engineer is looking into this as we speak.

Apologies for the inconvenience.

support@ebi

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