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21-01-2011: Writing Programs to Aid Analysis & Discovery
Part 2: 3rd Party Libraries ;
Automation via APIs
Mr. Andrew Jackson - andrewj@bcm.eduAutomation via APIs
Important Links:
Genboree API Help
Some Help pages with an overview of the Genboree REST API, as well as more detailed pages about specific aspects of the API (which include lists of exposed resources and such).
See also the example script from lecture, especially for uploading LFF data since that resource path is new.
Some Help pages with an overview of the Genboree REST API, as well as more detailed pages about specific aspects of the API (which include lists of exposed resources and such).
See also the example script from lecture, especially for uploading LFF data since that resource path is new.
Ruby Lecture 2 - Code Examples
The wireless problem I had in lecture was specific to the classroom. Connected immediately when I tried over in the Jewish wing. I've added notes or example output to certain ones below for when you try them yourselves.
The link above is to the handful of PowerPoint slides. Here are links where you can see the toy code examples we examined in class. Try running them yourself to see what they output.
- methodUse.rb
- classUse.rb
- correlation.rb
- getCutSite.rb
The wireless problem I had in lecture was specific to the classroom. Connected immediately when I tried over in the Jewish wing. I've added notes or example output to certain ones below for when you try them yourselves.
The link above is to the handful of PowerPoint slides. Here are links where you can see the toy code examples we examined in class. Try running them yourself to see what they output.
- methodUse.rb
- classUse.rb
- correlation.rb
- getCutSite.rb
$ ruby getCutSite.rb EcoRI EcoRI => G^AATTC- biorubyPubMed.rb
$ ruby biorubyPubMed.rb BRCA2 Daniels, M. S.Burzawa, J. K.Brandt, A. C.Schmeler, K. M.Lu, K. H. A clinical perspective on genetic counseling and testing during end of life care for women with recurrent progressive ovarian cancer: opportunities and challenges. 2011 Fam Cancer 10-15% of invasive epithelial ovarian... [and 9 more papers, separated by a blank line]- apiExample1.rb
Alter the code so it accesses a group you are in and it will list the databases in the group. First the raw response from the server (JSON-formated), then a little report build from that response.- apiExample2_putLFF.rb
RubyGems
Go here and download & install Rubygems on your system. If needed, there is lots of documentation about Rubygems there, but really what I covered should be more than enough for this class.
Once installed, use the gem command to install these gems:
- rest-open-uri
- bio
- json (Windows users: install the "json_pure" gem instead)
Go here and download & install Rubygems on your system. If needed, there is lots of documentation about Rubygems there, but really what I covered should be more than enough for this class.
Once installed, use the gem command to install these gems:
- rest-open-uri
- bio
- json (Windows users: install the "json_pure" gem instead)
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