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2012-07-20
2013-05-28
  • Hi Jeff,

    the link url is incorrect for ex. i have  http://hcntpentweb01v:81/pubmed/22795509

    I'm not exactly sure what kind of links you are referring to. Do you mean the links that are displayed in Details view with a black arrow and "www" printed on top?

    And does this happen for just one (or a few) record(s), or does it happen for all records that have these links?

    Also, how did you import the record data, could it be that the original import data did contain this link? Or maybe, did it contain just a relative/partial link, instead of a full/absolute URL?

    What happens if you go to the refbase Import page, and enter 22795509 into the lower form ("Import IDs")? After the record data have been fetched from PubMed, what value is displayed in the URL field (at the bottom of the page)? It should contain this URL:

    http://www.ncbi.nlm.nih.gov/pubmed/22795509

    Can you confirm this?

    Thanks, Matthias

     
  • Jeff Mather
    Jeff Mather
    2012-07-20

    Thanks for the response Matthias (cool name),  See inline below

    I'm not exactly sure what kind of links you are referring to. Do you mean the links that are displayed in Details view with a black arrow and "www" printed on top?
    Yes, I'm referring to the black arrows, either on detail view of on the basic view.

    And does this happen for just one (or a few) record(s), or does it happen for all records that have these links?
    all records

    Also, how did you import the record data, could it be that the original import data did contain this link? Or maybe, did it contain just a relative/partial link, instead of a full/absolute URL?
    I import PubMed csv extracts into the sql database using Pentaho

    What happens if you go to the refbase Import page, and enter 22795509 into the lower form ("Import IDs")? After the record data have been fetched from PubMed, what value is displayed in the URL field (at the bottom of the page)? It should contain this URL:

    http://www.ncbi.nlm.nih.gov/pubmed/22795509

    **I get an error message right on top of the Import IDs box:
    Error occurred: Failed to open http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=text&rettype=medline&tool=refbase&email=info%40refbase.net&id=22795509… and in red above:

    There were validation errors regarding the data you entered:
    **

     
  • Hi Jeff,

    thanks for the answers.

    Could it be that your record's contain only partial URLs in the refbase URL field? In that case, refbase assumes this links to be relative to the server. Normally, it keeps them as relative links then. However, in some cases (e.g. when returning results for CLI clients, for include mechanisms, or when returning only a partial document structure), it uses an absolute base URL, which is generated in variable '$databaseBaseURL' in file 'ini.inc.php'.

    If your records contain only partial URLs to PubMed resources in the refbase URL field, you'd need to issue a batch & replace action on the URL field of the SQL database to create full URLs from the partial data. Some examples for batch SQL modifications are given here:

    http://www.refbase.net/index.php/Batch_SQL_modifications

    Let me know if you need further help with this.

    I import PubMed csv extracts into the sql database using Pentaho

    Ok. I haven't heard about Pentaho before. refbase does set or autofill quite a few fields automatically when importing bibliographic data via its import functions. By importing data directly into the SQL database, none of this "smartness" can be applied.

    Generally speaking, if you've just started to setup your refbase database, it may be a good idea to start from scratch and import all PubMed records via the "Import IDs" feature instead (see below).

    I get an error message right on top of the Import IDs box:
    Error occurred: Failed to open http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=text&rettype=medline&tool=refbase&email=info%40refbase.net&id=22795509…

    Maybe your server's 'php.ini' setting for 'allow_url_fopen' is disabled? For more info, please see:

    https://sourceforge.net/projects/refbase/forums/forum/218758/topic/4990751

    HTH, Matthias

     
  • Jeff Mather
    Jeff Mather
    2012-07-25

    Hi Matthias,
    Thanks for the response.  I had been trying to bulk load ~2400 references to pub med using Pentaho.  My problem was that I was not storing the url correctly.  I ran a few references through your import application, which worked great, and was able to retrieve the correct format from that import.  I then updated the format in all records to reflect the required revision and, presto - all is working great.

    Thanks again for the suggestions and for developing such an awesome application!

    Jeff

     
  • Hi Jeff,

    thanks for the follow-up and for the kind words, I appreciate it!

    I'm happy to hear that things are working for you now.

    Cheers, Matthias