Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] parsing error

Erick Antezana erick.antezana at gmail.com
Tue Feb 5 01:41:55 PST 2013


Hi Paul,

I just launched the command you told me. I didn't work:


# bpdeploy deployui
Stopping httpd:                                            [FAILED]
deploying release 1058 to
/srv/ncbo/rails/BioPortal/releases/1058_2013-02-05-1360057074
svn: OPTIONS of
'https://bmir-gforge.stanford.edu/svn/bioportalui/tags/1058': Could
not resolve hostname `bmir-gforge.stanford.edu': Host not found
(https://bmir-gforge.stanford.edu)
/bin/cp: target
`/srv/ncbo/rails/BioPortal/releases/1058_2013-02-05-1360057074/' is
not a directory
svn: OPTIONS of
'https://bmir-gforge.stanford.edu/svn/flexviz/tags/prod/flex': Could
not resolve hostname `bmir-gforge.stanford.edu': Host not found
(https://bmir-gforge.stanford.edu)
ln: creating symbolic link
`/srv/ncbo/rails/BioPortal/releases/1058_2013-02-05-1360057074/log':
No such file or directory
chown: cannot access
`/srv/ncbo/rails/BioPortal/releases/1058_2013-02-05-1360057074': No
such file or directory
/usr/local/bin/bpdeploy: line 167: cd:
/srv/ncbo/rails/BioPortal/current: No such file or directory
Could not locate Gemfile
rake aborted!
No Rakefile found (looking for: rakefile, Rakefile, rakefile.rb, Rakefile.rb)

(See full trace by running task with --trace)
Stopping memcached:                                        [FAILED]
Starting memcached:                                        [  OK  ]
Starting httpd: Warning: DocumentRoot
[/srv/ncbo/rails/BioPortal/current/public] does not exist
                                                           [  OK  ]


Now, I cannot access anymore the web interface:

Forbidden
You don't have permission to access / on this server.
--------------------------------------------------------------------------------

Apache/2.2.15 (CentOS) Server at
vm-rdi-ncboportal-prod.be.bayercropscience Port 80

The ncbo services (ncbostart) were launched without any problem...

any suggestions?

cheers,
Erick

On 4 February 2013 20:45, Paul R Alexander <palexander at stanford.edu> wrote:
> The visualization functionality on the Appliance was indeed using a newer mechanism that we don't support for the Appliance yet. You can fix this by running a `bpdeploy deployui` command and it should pull some new code that I added to address the problem.
>
> Paul
>
>
> On Feb 4, 2013, at 2:55 AM, Erick Antezana <erick.antezana at gmail.com> wrote:
>
>> Hi Trish,
>>
>> I will wait for Paul's comments then.
>>
>> cheers,
>> Erick
>>
>> On 1 February 2013 18:48, Trish Whetzel <whetzel at stanford.edu> wrote:
>>> For some BioPortal releases the visualization was using the Google app engine site, I wonder if this might be the issue with the 1.0 version of the appliance you are using and not able to see the visualization. Paul, who generates the VM, can provide more details.
>>>
>>> Trish
>>>
>>>
>>> On Feb 1, 2013, at 8:47 AM, Erick Antezana wrote:
>>>
>>>> Hi Trish,
>>>>
>>>> I managed to load my ontology by playing a bit with the ontology
>>>> version IDs: I was using number such as 1, 2, 3, ...which didn't
>>>> work... but later it worked with numbers such as 10002, 10003, ...
>>>>
>>>> The problem I am facing now is to actually visualise it...After
>>>> clicking on the "Visualization" tab, the only thing I can see is a
>>>> progress bar that is still running since 2 hours ago...
>>>>
>>>> I have no other issues (the tree view works fine, etc)...
>>>>
>>>> I am working with the sequence ontology.
>>>>
>>>> cheers,
>>>> Erick
>>>>
>>>>
>>>> On 1 February 2013 17:08, Trish Whetzel <whetzel at stanford.edu> wrote:
>>>>> Erick,
>>>>>
>>>>> What ontology were you trying to load?
>>>>>
>>>>> Trish
>>>>>
>>>>>
>>>>> On Feb 1, 2013, at 2:59 AM, Erick Antezana wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I got similar error messages:
>>>>>
>>>>>  BioPortal returned an error: Error Parsing Ontologies: [(Id: 1004) -
>>>>> Ontology version with the given id does not exist]
>>>>>
>>>>> any suggestions where to check?  log files or so?
>>>>>
>>>>> cheers,
>>>>> erick
>>>>>
>>>>> On 25 January 2013 22:29, Holt, Jonathan <jonathan.holt at vanderbilt.edu>
>>>>> wrote:
>>>>>>
>>>>>> When I tried to upload the ontology manually, I got the error,
>>>>>>
>>>>>>
>>>>>> "we are sorry, but something has gone wrong. We have been notified of this
>>>>>> error."
>>>>>>
>>>>>>
>>>>>>
>>>>>> <image003.jpg>
>>>>>>
>>>>>>
>>>>>> jonathan
>>>>>>
>>>>>>
>>>>>> .................................
>>>>>> Jonathan Holt, DO, MS
>>>>>>
>>>>>> Assistant Professor of Biomedical Informatics and Medicine
>>>>>> Departments of Biomedical Informatics & Medicine, Division of Genetic
>>>>>> Medicine
>>>>>> Vanderbilt University Medical Center
>>>>>> 2209 Garland Ave
>>>>>> 412 Eskind Biomedical Library
>>>>>> Nashville, TN  37232-8340
>>>>>> Phone:  615-322-8683
>>>>>> Fax: 615-875-1424
>>>>>>
>>>>>> jonathan.holt at vanderbilt.edu
>>>>>> http://dbmi.mc.vanderbilt.edu/people/holt.html
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Jan 25, 2013, at 3:02 PM, "Lian, Zonghui" <Lian.Zonghui at mayo.edu>
>>>>>> wrote:
>>>>>>
>>>>>> One you uploaded the files, you can run the parser through this page:
>>>>>> http://rest.bioontology.org/bioportal_admin/parseontologies.jsf
>>>>>>
>>>>>> From: Holt, Jonathan [mailto:jonathan.holt at Vanderbilt.Edu]
>>>>>> Sent: Friday, January 25, 2013 2:38 PM
>>>>>> To: Lian, Zonghui
>>>>>> Cc: Paul R Alexander (palexander at stanford.edu); support at bioontology.org
>>>>>> Support
>>>>>> Subject: Re: [bioontology-support] parsing error
>>>>>>
>>>>>> any update?
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Jonathan
>>>>>>
>>>>>>
>>>>>> .................................
>>>>>> Jonathan Holt, DO, MS
>>>>>>
>>>>>> Assistant Professor of Biomedical Informatics and Medicine
>>>>>> Departments of Biomedical Informatics & Medicine, Division of Genetic
>>>>>> Medicine
>>>>>> Vanderbilt University Medical Center
>>>>>> 2209 Garland Ave
>>>>>>
>>>>>> 412 Eskind Biomedical Library
>>>>>> Nashville, TN  37232-8340
>>>>>> Phone:  615-322-8683
>>>>>> Fax: 615-875-1424
>>>>>>
>>>>>> jonathan.holt at vanderbilt.edu
>>>>>> http://dbmi.mc.vanderbilt.edu/people/holt.html
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Jan 21, 2013, at 11:01 AM, "Jonathan Holt, DO, MS"
>>>>>> <jonathan.holt at vanderbilt.edu> wrote:
>>>>>>
>>>>>>
>>>>>> sure,
>>>>>>
>>>>>> mine is in a slightly different place.
>>>>>>
>>>>>> for ICD-9 is is located in: /srv/ncbo/bioportal_resources/uploads/1101/1
>>>>>>
>>>>>> see below:
>>>>>>
>>>>>> root at ncbo 1]# pwd
>>>>>> /srv/ncbo/bioportal_resources/uploads/1101/1
>>>>>> [root at ncbo 1]# ls -hal
>>>>>> total 25M
>>>>>> drwxr-xr-x 2 tomcat tomcat 4.0K Jan 18 13:30 .
>>>>>> drwxr-xr-x 3 tomcat tomcat 4.0K Jan 18 13:30 ..
>>>>>> -rw-r--r-- 1 tomcat tomcat  25M Jan 18 13:30 icd9cm.rrf
>>>>>>
>>>>>>
>>>>>>
>>>>>> <Screen Shot 2013-01-21 at 11.01.05 AM.png>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Jonathan
>>>>>>
>>>>>>
>>>>>> .................................
>>>>>> Jonathan Holt, DO, MS
>>>>>>
>>>>>> Assistant Professor of Biomedical Informatics and Medicine
>>>>>> Departments of Biomedical Informatics & Medicine, Division of Genetic
>>>>>> Medicine
>>>>>> Vanderbilt University Medical Center
>>>>>> 2209 Garland Ave
>>>>>>
>>>>>> 412 Eskind Biomedical Library
>>>>>> Nashville, TN  37232-8340
>>>>>> Phone:  615-322-8683
>>>>>> Fax: 615-875-1424
>>>>>>
>>>>>> jonathan.holt at vanderbilt.edu
>>>>>> http://dbmi.mc.vanderbilt.edu/people/holt.html
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Jan 21, 2013, at 10:35 AM, "Lian, Zonghui" <Lian.Zonghui at mayo.edu>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>> Dr Holt,
>>>>>>
>>>>>> The error may be caused by the file uploader. Can you check if the file
>>>>>> was uploaded correctly? For example, for the below ontology, its ontology id
>>>>>> is (1290).
>>>>>>
>>>>>> <image001.png>
>>>>>>
>>>>>> In the linux box, you can find its uploaded files are under
>>>>>> <image006.png>
>>>>>>
>>>>>> Please use this method to check the file for your case. As what I know,
>>>>>> the file uploader is not stable when the file size is big. Once you find
>>>>>> this file you can manually replace them with the right one.  (For rrf
>>>>>> format, you need to unzip the zipped file) .
>>>>>>
>>>>>> Thanks,
>>>>>> -Lian
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> From: Holt, Jonathan [mailto:jonathan.holt at Vanderbilt.Edu]
>>>>>> Sent: Friday, January 18, 2013 4:09 PM
>>>>>> To: Lian, Zonghui
>>>>>> Cc: support at bioontology.org Support
>>>>>> Subject: Re: [bioontology-support] parsing error
>>>>>>
>>>>>> Lian,
>>>>>>
>>>>>> After trying to up load the zipped file i get,
>>>>>>
>>>>>> "we are sorry, but something has gone wrong. We have been notified of this
>>>>>> error."  (see below)
>>>>>>
>>>>>> <image003.jpg>
>>>>>>
>>>>>>
>>>>>> if i try from the import_ontologies.rb script and point to Stanford's
>>>>>> server with my apikey,  I get a parsing error as shown below.
>>>>>>
>>>>>>
>>>>>> <image005.jpg>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Of note, this does NOT happen when I import an ontology in a different
>>>>>> format, such as OWL or OBO, as shown in my other ontologies that I have
>>>>>> successfully imported using the script.
>>>>>>
>>>>>>
>>>>>> I've tried getting a new build using:
>>>>>>
>>>>>> bpdeploy deployui
>>>>>>
>>>>>> but that does help things either.
>>>>>>
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Jonathan
>>>>>>
>>>>>>
>>>>>> .................................
>>>>>> Jonathan Holt, DO, MS
>>>>>>
>>>>>> Assistant Professor of Biomedical Informatics and Medicine
>>>>>> Departments of Biomedical Informatics & Medicine, Division of Genetic
>>>>>> Medicine
>>>>>> Vanderbilt University Medical Center
>>>>>> 2209 Garland Ave
>>>>>>
>>>>>>
>>>>>> 412 Eskind Biomedical Library
>>>>>> Nashville, TN  37232-8340
>>>>>> Phone:  615-322-8683
>>>>>> Fax: 615-875-1424
>>>>>>
>>>>>> jonathan.holt at vanderbilt.edu
>>>>>> http://dbmi.mc.vanderbilt.edu/people/holt.html
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Jan 18, 2013, at 10:26 AM, "Lian, Zonghui" <Lian.Zonghui at mayo.edu>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> Hi Dr Holt,
>>>>>>
>>>>>> It looks like the rrf files you used may be not correct(in the figure 2,
>>>>>> the icd9cm.rrf was incorrect). Can you download the rrf zip from
>>>>>> http://bioportal.bioontology.org/ontologies? After that, you can unzip them
>>>>>> into the upload folder and overwrite the old one. Please let me know if it
>>>>>> works. Thanks.
>>>>>>
>>>>>> -Lian
>>>>>>
>>>>>>
>>>>>>
>>>>>> From: Paul R Alexander [mailto:palexander at stanford.edu]
>>>>>> Sent: Thursday, January 17, 2013 4:11 PM
>>>>>> To: Lian, Zonghui
>>>>>> Subject: Fwd: [bioontology-support] parsing error
>>>>>>
>>>>>>
>>>>>>
>>>>>> Begin forwarded message:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> From: "Holt, Jonathan" <jonathan.holt at Vanderbilt.Edu>
>>>>>> Subject: [bioontology-support] parsing error
>>>>>> Date: January 9, 2013 3:04:05 PM PST
>>>>>> To: "support at bioontology.org" <support at bioontology.org>
>>>>>>
>>>>>> I have recently tried to get my ncbo virtual appliance back up and
>>>>>> running.
>>>>>>
>>>>>> So, I tried to import some ontologies from the bioportal to my own hosted
>>>>>> vm, but got a parsing error.
>>>>>>
>>>>>> I also tried to manually and still got a java error.
>>>>>>
>>>>>>
>>>>>> see attached.
>>>>>>
>>>>>>
>>>>>> Any thoughts?
>>>>>>
>>>>>>
>>>>>> Jonathan
>>>>>>
>>>>>>
>>>>>>
>>>>>> <image002.jpg>
>>>>>>
>>>>>> <image003.png><image005.jpg>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> .................................
>>>>>> Jonathan Holt, DO, MS
>>>>>>
>>>>>> Assistant Professor of Biomedical Informatics and Medicine
>>>>>> Departments of Biomedical Informatics & Medicine, Division of Genetic
>>>>>> Medicine
>>>>>> Vanderbilt University Medical Center
>>>>>> 2209 Garland Ave
>>>>>>
>>>>>>
>>>>>>
>>>>>> 412 Eskind Biomedical Library
>>>>>> Nashville, TN  37232-8340
>>>>>> Phone:  615-322-8683
>>>>>> Fax: 615-936-1427
>>>>>>
>>>>>> jonathan.holt at vanderbilt.edu
>>>>>> http://dbmi.mc.vanderbilt.edu/people/holt.html
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> bioontology-support mailing list
>>>>>> bioontology-support at lists.stanford.edu
>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> bioontology-support mailing list
>>>>>> bioontology-support at lists.stanford.edu
>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> bioontology-support mailing list
>>>>> bioontology-support at lists.stanford.edu
>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>>
>>>>>
>>>
>


More information about the bioontology-support mailing list