Bioinformatics.org
[NEU MS in Bioinformatics]
Not logged in
  • Log in
  • Bioinformatics.org
    Membership (37460+) Group hosting [?]
  • Wiki
  • Franklin Award
  • Sponsorships
  • Careers
    About bioinformatics
    Bioinformatics training
    Bioinformatics jobs

    Research
    All information groups
    Online databases Online analysis tools Online education tools More tools

    Development
    All software groups
    FTP repository
    SVN & CVS repositories [?]
    Mailing lists

    Forums
    News & Commentary
  • Submit
  • Archives
  • Subscribe

  • Jobs Forum
    (Career Center)
  • Submit
  • Archives
  • Subscribe
  • I, Librarian: bibliography manager - Message forums

    Discussion forums: Help

    Expanded view | Monitor forum | Save place

    Welcome to Help
    Submitted by Unset; posted on Wednesday, March 27, 2002
    Welcome to Help
    Editing categories
    Submitted by Oscar Moya; posted on Friday, October 10, 2003
    Hi, I have installed librarian after some difficulties (the instructions are quite good, but sometimes not easy for people like me, without experience in that kind of installations). Now it is working with some minor problems, I hope to be able to solve them with time. The program seems to be really useful, we find it a very good way to store, classify, share and find the documents we have. I have a question regarding the management of the database. When uploading files, I have to create categories to classify the PDFs. Is it possible to delete or edit a category? how? Thanks a lot Óscar
    Editing categories
    Submitted by Martin Kucej; posted on Monday, October 13, 2003
    Submitter Hi, thanks for trying Librarian. I don't deny; it's not as easy to install as other software. You can always write me (or to this forum) with your 'minor problems. You can also subscribe into the Librarian mailing list. As to your question. It is possible to alter categories. Unfortunetly, I did not write any administration pages yet. So you'll have to do that either by clicking 'Edit' on every article you want to change, or by much quicker way. Via SQL commands. You have to start Command Prompt and go to mysql/bin directory. Login to your database, e.g. mysql -uusername -p databasename Than type for instance: UPDATE library SET category='newcategory' WHERE category='oldcategory'; martin
    Editing categories
    Submitted by Nobody; posted on Sunday, December 28, 2003
    This should be a great help, so far it appears to be working except I haven't retrieved anything yet. Is there a reason for not retrieving extracts based on PMID? Thank you
    Editing categories
    Submitted by Martin Kucej; posted on Sunday, December 28, 2003
    Submitter There was a bug in version 1.1. You may want to fix it with patch, which you can find on: http://bioinformatics.org/librarian martin
    directory to store pdfs
    Submitted by Nobody; posted on Friday, October 24, 2003
    Hi- I am running into two problems. First, I have designated /volumes/work/pdfdb/library as the directory for storing PDFs. It seems that PDFs get uploaded there, but when I hit the "Full Text" link to retrieve the PDF, the program looks for the PDF in the librarian folder. There is some code in the index.php file: if (isset($_SESSION["auth"])) { echo " | <A HREF=\"library/$paper[file]\">Full text</A> | <A HREF=\"index.php?action=edit&file=$paper[file]\">Edit</A>"; Is this the problem? My second problem is that although the program initially worked, I can no longer upload PDFs. When I completely fill out the form and hit the upload button at the bottom of the page, I am sent back to the starting page with the info downloaded from pubmed, but no pdf or authors. Thanks, Grant Hartzog
    directory to store pdfs
    Submitted by Martin Kucej; posted on Monday, October 27, 2003
    Submitter Hi Grant, the first problem is due to poor installation instructions, I apologize. The directory to store PDFs MUST be /library subdirectory of the directory, where Librarian is installed. Please just create such directory and copy PDF files there. It will work well. The second problem is strange. Can you describe it in more detail? What could have changed since you installed Librarian? Best wishes, martin
    directory to store pdfs
    Submitted by Nobody; posted on Tuesday, October 28, 2003
    Hi Martin- I have reloaded Librarian 1_1 and PHP on my machine with the library folder in the correct location. I still have the problem that I cannot upload a file. When I hit the upload button, I am sent back to the previous version of that page without the PDF or pull down menus filled in. I am not sure what changed. I had tried entering different locations for the library on the installation page prior to this problem cropping up...... I am trying to get this running on a Mac with OS 10.2.8 using PHP 4.3.3 and MYSQL 4.0.15. Should I load an earlier version of PHP? I have reloaded Librarian 1_1 and PHP on my machine with the library folder in the correct location, but this has not solved my problem. I have noticed that when I select a PDF for uploading, it is listed on the browser page as "343.pdf" as opposed to "/Users/downloads/343.pdf". Thanks, Grant
    directory to store pdfs
    Submitted by Nobody; posted on Wednesday, October 29, 2003
    Just to follow up on the last message, I get the same behaviour when I hit the "upload" button that I get when I hit the "reset" button. Grant
    directory to store pdfs
    Submitted by Nobody; posted on Wednesday, November 05, 2003
    > When I hit the upload button, I am sent back to > the previous version of that page without the > PDF or pull down menus filled in. But if there is no error message, it is how upload works. There is no message confirming succesful upload. > Should I load an earlier version of PHP? Your software is Okay. > I have noticed that when I select a PDF for > uploading, it is listed on the browser page > as "343.pdf" as opposed to > "/Users/downloads/343.pdf". This I don't understand. Where it is listed as 343.pdf? In first row of web form on upload page? martin
    directory to store pdfs
    Submitted by Nobody; posted on Tuesday, May 04, 2004
    Hi, I just downloaded and installed librarian 1.3. I was able to successfully upload 2 pdf files, but I have tried 3 other ones, and I keep receiving the error "Error! All fields in the form are mandatory." I have filled out all the fields, yet I keep receiving this message, and no new pdfs are added to the library!
    same error message!
    Submitted by Nobody; posted on Friday, June 25, 2004
    I have recently installed librarian 1.3 and have same problem now!. My environment is Mac OS X 10.3.4, PHP 4.3.6, mysql-standard-4.0.20.
    same error message!
    Submitted by Mr. Sniggles; posted on Monday, June 28, 2004
    Submitter Also after two successful uploads? That is strange. Wish I could help you, but I really don't know why the incosistency. :-( martin
    same error message!
    Submitted by Nobody; posted on Monday, June 28, 2004
    Thank you for the reply, In my case, I could upload eight files successfully. Then, when I tried to upload other pdf files a few day after, it failed. I am sorry, but I can not remember if I changed or updated something in the system during the time...
    Endnote
    Submitted by Nobody; posted on Thursday, December 18, 2003
    Can I use the database with endnote?
    Installed
    Submitted by Nobody; posted on Wednesday, December 31, 2003
    I installed Librarian 1.1a sucessfully, but I get as far as a list of PMID's to select from and then it keeps telling me to complete the form and the fields Publication and Category are emptied out each time, so I assume these are not doing anything. A couple of things were not mentioned. Normally after installation of modules I remove the install.php, so I did. Then chmod files, but it didn't say which ones. So I had to guess. Although I installed this separate from similar databases in mysql, there are other databases running on php and I'm wondering if its possible its affected them, because some have disappeared. The data is not important because we are still setting them up, but if its affected php then I need to know, in a separate database I have library, topics and category. The thing is that I only want to use librarian to do a data check on our records in a new database that needs to be set up, once I understand how it works I'd like to just check records with PMID's. Any and all suggestions are welcome. Thank you maz
    PDF sometimes does not upload - SOLVED!
    Submitted by Martin Kucej; posted on Wednesday, August 11, 2004
    Submitter Some people here wrote me that they uploaded 2, 3 or 7 PDFs and than nothing. First, check if you have only one copy of Apache, PHP and MySQL installed in your machine, and that you have only one php.ini file. On some platforms, the directive magic_quotes_gpc is Off. This will cause the above problems. It is because all quotation marks must be escaped by backslash, before they are recorded to the database. This is secured by magic_quotes_gpc being On. Check your php.ini! Hope this will help. Martin
    PDF sometimes does not upload - SOLVED!
    Submitted by Nobody; posted on Thursday, December 16, 2004
    There is also an 8Mb limit imposed in the php.ini file (on windows) and within the upload.php (search for 8000000). A LARGE pdf will return erroneous error messages
    Re: PDF sometimes does not upload - SOLVED!
    Submitted by Joe Toth; posted on Monday, June 18, 2007
    Hi, I discovered that a file which didn't upload did successfully upload once I changed the name from file to file.pdf I don't know enough php to find out if the code really needs the .pdf in the filename- I just know that my uploads now work. The other fixes posted here didn't make a difference.
    Re: PDF sometimes does not upload - SOLVED!
    Submitted by Martin Kucej; posted on Tuesday, April 07, 2009
    Submitter Yes, the old Librarian is checking for the .pdf file name.
    INstalling LIbrarian On Linux
    Submitted by Einar; posted on Wednesday, August 03, 2005
    Hello there: Been trying to contact DR. Kucej Thru email but failed to. I've been trying to install librarian for a month now I have all the requeriments for it met, the only problem is in the httpd.conf file of the Apache server, the Action command isnt recognized by it, already sent that file to Dr. Kucej I've been inspecting the file install.php, the script works onto the part it writes the info down to the data.php file, then when the $link variable is told to do an mysql connection the browser just stop execution. All the daemons necessary are running, the part i dont get is how php is supposed to make a connection to mysql if the database havent been created yet. I also tried to put the part of the script before the connection and nuthin. I even created the database manually using the mysql command and nothin. PLease help me out.
    INstalling LIbrarian On Linux
    Submitted by Einar; posted on Thursday, August 04, 2005
    Hello: What if the server doesnt recognize the functions used in php to manage mysql and returns an error like this: Fatal error: Call to undefined function: mysql_connect() in /var/www/librarian/install.php on line 189
    Automating PDF Uploading?
    Submitted by Wes Denton; posted on Tuesday, April 03, 2007
    Hi, I guess there hasn't been any activity to this forum since 2005, but I am curious to find out if there is a way to automate the uploading of pdf files to the library? As an individual I do a lot of reading online and save a lot of files to pdf everyday. It becomes cumbersome to enter each one manually. Thanks
    Re: Automating PDF Uploading?
    Submitted by Martin Kucej; posted on Tuesday, April 07, 2009
    Submitter Sorry for the late answer :-), but I am working on a new version, which will be able to upload PDF if it contains a unique DOI.
    Start a new thread:
    You have to be logged in to post a reply.

     

    Copyright © 2016 · Scilico, LLC