powerpak / mendeley-pmid-updater Goto Github PK

Hey @powerpak , not sure if you're still maintaining or using this, but there are some changes to the local database in the latest version of Mendeley which will break your script. We're currently collecting use cases to officially support local database access, so if you'd like to give the Mendeley developers some feedback on what data you need to access so we can make sure to support your use case, please get in touch via email.

You mentioned that you can't sync across machines, I've found that too

The trick I used was to copy the data directory from the old to new computer. you might be able to get by with just copying the database. Of course back it up ahead of time, and you may want to clean out your downloaded folder to avoid duplicates from creeping in

http://support.mendeley.com/customer/en/portal/articles/227951-how-do-i-locate-mendeley-desktop-database-files-on-my-computer-

Hi Thanks a lot for putting the effort to help! I was able to follow up the instruction and update the PMCID. I saw the .sqlite files created. However, when I enter into Mendeley, I see no where the PMCID, not in the notes either. As a result the bibliography only has the PMID but not PMCID...

Did I miss any steps between rake update_ids and open the Mendeley?

--Waiting online for the answers! Thanks!

The updater runs successfully, but the notes field is not updated even though most records have a PMCID returned.
I managed to parse the output and update the sqlite database externally. So, somehow the updating of records is not succeeding.

I tried to figure out how to pass a flag to the process to overwrite or perfotm quitely (the rake and ruby files suggest the options are available), but it was not obvious how to pass options.

While running through my author list, I consistently receive an abort message, which also comes up during the full replace function. No PMCIDs are being pulled or into my Mendeley library. Any insight would be appreciated. Here's the error message (starting with the last author in the list):

Fix author "Todd A Florin" --> "Todd A Florin"
rake aborted!
SocketError: getaddrinfo: nodename nor servname provided, or not known
/Users/michaeljohnson/Documents/Programs/Mendeley PMCID updater/mendeley-pmid-updater/lib/pmc-id-converter.rb:38:in pmc_api_convert' /Users/michaeljohnson/Documents/Programs/Mendeley PMCID updater/mendeley-pmid-updater/lib/pmc-id-converter.rb:23:in convert'
/Users/michaeljohnson/Documents/Programs/Mendeley PMCID updater/mendeley-pmid-updater/lib/mendeley-database.rb:83:in block (2 levels) in fix_article_ids' /Users/michaeljohnson/Documents/Programs/Mendeley PMCID updater/mendeley-pmid-updater/lib/mendeley-database.rb:80:in each'
/Users/michaeljohnson/Documents/Programs/Mendeley PMCID updater/mendeley-pmid-updater/lib/mendeley-database.rb:80:in block in fix_article_ids' /Library/Ruby/Gems/2.0.0/gems/sqlite3-1.3.9/lib/sqlite3/database.rb:144:in block (2 levels) in execute'
/Library/Ruby/Gems/2.0.0/gems/sqlite3-1.3.9/lib/sqlite3/statement.rb:110:in block in each' /Library/Ruby/Gems/2.0.0/gems/sqlite3-1.3.9/lib/sqlite3/statement.rb:107:in loop'
/Library/Ruby/Gems/2.0.0/gems/sqlite3-1.3.9/lib/sqlite3/statement.rb:107:in each' /Library/Ruby/Gems/2.0.0/gems/sqlite3-1.3.9/lib/sqlite3/database.rb:140:in block in execute'
/Library/Ruby/Gems/2.0.0/gems/sqlite3-1.3.9/lib/sqlite3/database.rb:95:in prepare' /Library/Ruby/Gems/2.0.0/gems/sqlite3-1.3.9/lib/sqlite3/database.rb:134:in execute'
/Users/michaeljohnson/Documents/Programs/Mendeley PMCID updater/mendeley-pmid-updater/lib/mendeley-database.rb:60:in fix_article_ids' /Users/michaeljohnson/Documents/Programs/Mendeley PMCID updater/mendeley-pmid-updater/lib/mendeley-database.rb:47:in dry_run'
/Users/michaeljohnson/Documents/Programs/Mendeley PMCID updater/mendeley-pmid-updater/Rakefile:21:in `block in <top (required)>'
Tasks: TOP => default => dry_run
(See full trace by running task with --trace)
ped-03300m:mendeley-pmid-updater michaeljohnson$