These are required initializes and paths functions to run greps for the Pubget environment.
To generate HTML docs, type “rdoc lib” from this directory. To view them, open docs/index.html in a web browser.
unix or OSX (will not run on windows)
The bug tracker is available here:
This includes a dummy rails project that can be used to run the project. To install dependancies, you need to run:
bundle install --gemfile=test/dummy/Gemfile
This gem will mock enough of rails in the dummy directory so you can run the gem without a separate rails environment.
To test all methods that are present should be present, run:
To test just one publisher like nature, run:
ruby test/greps/grep_test.rb --name=test_nature
To fast check single PMID, please run:
ruby run.rb -i PMID -p publisher_name
As we have the debugger gem in there, so you can break in with debugger as needed - that a good way to debug:
sudo gem install ruby-debug
(this will also work for rvm).
Objective of pdf_url
This gem is included in our main rails application and has the purpose of finding where PDFs and full text documents live on the publisher's websites.
This code is broken down per publishers (that each has its own class based on Publisher::Base). The main function to find the PDFs and HTML URLs is pdf_url which accepts parmas that include the :article. This Article is the object that has all the values that are needed to find the PDF or HTML full text. An Article is a published paper in an academic journal.
The normal way to look up a PDF url is to first find the journal's base URL and then navigate the publisher's site to find the PDF. Sometimes, it is possible to follow the DOI or other means and it will vary from publisher to publisher (this is why we separate the code per publisher like this).
It is useful to look at a few example publishers and follow the code to see how we get the 'title', 'volume', 'issue' and other information from the article and use this to find the PDF (or HTML url). The HTML url goes into article.url where the pdf is returned from pdf_url.
The issues tend to have a publisher, the paper/article pmid (id) and the expected URL or PDF URL that you should be able to find. These are added to the grep_test.rb and then the pdf_url method inside the publisher can be fixed to make the test pass.
Digital Object Identifier (DOI®) System
The Digital Object Identifier (DOI®) System is for identifying content objects in the digital environment www.doi.org/. Many publisher support DOIs for a number of their papers and it can be the only way to link to their papers. DOIs can be looked up via the crossref site (we have an agreement to do this) or by visiting the publisher and locating the DOI via the issue page or searching on their site.
Often if you can find the DOI, it makes the PDF URL easier to find (or in some cases just the DOI needs to be put into a URL to get the location).
The ISSN is a standardized international code which allows the identification of any journal (www.issn.org/2-22635-What-is-an-ISSN.php). There can be more than one ISSN per journal as well as print and electronic ISSNs. article.issn is an array of ISSNs (article.pissn, article.eissn) but we found most publishers tend to link via the electronic ISSN.
This is a term that is often abused. If you search, it will say it is a standard for linking to journals, issues and articles. However, each publisher has their own way of linking from an ISSN, volume, issue and page to an article. If you know the publisher you can google for their open url guide or page on how to link. Often knowing how to link and putting the volume, issue, etc into this Open URL will be a good start to get to the path. Having said that, it is often broken and you may be better off just linking at the URLs when navigating the publisher site. It might become clear after clicking around how they construct the URL and where the volume, issue, etc go and just using those patterns.
Acronyms in common use can be found here: dl.dropbox.com/u/4482603/Metadata-Acronyms.pdf
Common lookup pattern
We have included a string diff function that can help find titles on the table of content (issue) pages. If you know the volume and issue from the article, you can find the issue page for that journal and then match the title on the page. However, often the title is not an exact match but a few charaters different. If you look at the match loop in github.com/pubget/pubget_paths/blob/master/lib/pubget_paths/publisher/annual_reviews.rb line 13, you will see we loop through the articles in an issue and then find the closest match to know the URL.
This is a common method to find an article. Here is an example for a publisher. Say you have an article that is pmid 11920382, and is in a journal with (volume 266 issue 4 and page 198 to 206). You can see the article on pubget at pubget.com/paper/11920382.
article.issn = ["0003-276X", "1097-0185"] wiley explains how to link to them here: http://info.onlinelibrary.wiley.com/view/0/faqs.html#Linking which has an open url guide here: http://info.onlinelibrary.wiley.com/SpringboardWebApp/userfiles/wcp/file/WileyOnlineLibraryOpenURLv1_1.pdf (many publishers will have a guide how to link to volume, issues and articles via Open URL or DOI) which says how to link to the issue here: "http://onlinelibrary.wiley.com/resolve/openurl?genre=issue&sid=vendor:database&issn=0003-276X&volume=266&issue=4 and then you want to search for the title on the page to find the relavant PDF link: http://onlinelibrary.wiley.com/doi/10.1002/ar.10057/pdf
This is an example how to navigate from a known set of meta data (title, ISSN, volume, issue, page) to a paper. Once you have the paper, you can update the pdf url and even the DOI in the article.
Sometimes a publisher needs to be added. This can be done by coping the template from another publisher and added a new file that has a pdf_url and issue method. These can be added if needed and attached to an issue.
To know which journals are available on each of the publishers, there is an info method. This method will call update_source with the ISSN, title, base_url and other information available via the publisher site.
Please include the issue number in the commit preceded by the hash (#) character (see github.com/blog/831-issues-2-0-the-next-generation). This does not need to follow a 'fixes' or 'closed' but just include it so that we can see what commits are for which issues.
You must keep your diffs down the the minimum. Do not add extra spaces or remove extra spaces on lines that you do not need to change. Also, keep the tab set as two spaces and not reformat the code unless you are changing it. If your IDE reformats code, please disable this feature so that only the minimum diff is committed to keep the issue clean and self contained. We code review almost every commit so if the diffs are bigger than they need to be, we will be spending time looking into lines that just contain space changes which takes extra time and therefore money.
Don't break the build
If you are working on a long change, you can commit locally but do not push until you have the tests passing. If you push code with broken tests, this will break our continuous build and send alerts to our team.
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