Updated documentation to reflect new file structure

docs/ads.md

@@ -105,4 +105,4 @@ Search the Astrophysics Data System (ADS) for ArXiV preprints associated with a
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/ads.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/ads.rb).

docs/ads_fulltext.md

@@ -133,4 +133,4 @@ Search the fulltext content of the Astrophysics Data System (ADS) for scholarly
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/ads_fulltext.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/ads_fulltext.rb).

docs/bitbucket.md

@@ -91,4 +91,4 @@ Number of forks and followers for Bitbucket repos.
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/bitbucket.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/bitbucket.rb).

docs/bmc_fulltext.md

@@ -83,4 +83,4 @@ Search the fulltext content of BioMed Central articles for scholarly works.
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/bmc_fulltext.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/bmc_fulltext.rb).

docs/citeulike.md

@@ -76,4 +76,4 @@ title: "CiteULike"
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/citeulike.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/citeulike.rb).

docs/copernicus.md

@@ -72,7 +72,7 @@ This source is providing usage stats from the Open Access publisher [Copernicus
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/copernicus.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/copernicus.rb).
 
 ## Further information
 * [Copernicus Publications website](http://publications.copernicus.org)

docs/crossref.md

@@ -180,7 +180,7 @@ For articles without a publisher the `openurl_username` in the `Configuration` t
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/cross_ref.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/cross_ref.rb).
 
 ## Further Documentation
 * [CrossRef Cited-by Linking](http://www.crossref.org/citedby.html)

docs/datacite.md

@@ -91,7 +91,7 @@ title: "DataCite"
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/datacite.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/datacite.rb).
 
 ## Further Documentation
 * [DataCite Metadata Search](http://search.datacite.org/help.html)

docs/datacite_data.md

@@ -91,7 +91,7 @@ title: "DataCite Data"
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/datacite_data.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/datacite_data.rb).
 
 ## Further Documentation
 * [DataCite Metadata Search](http://search.datacite.org/help.html)

docs/dataone_counter.md

@@ -116,7 +116,7 @@ title: "DataCONE Counter"
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/dataone_counter.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/dataone_counter.rb).
 
 ## Further Documentation
 * [DataONE usage stats](http://mdc.lagotto.io/dataone-usage-stats/)

docs/dataone_usage.md

@@ -116,7 +116,7 @@ title: "DataCONE Usage"
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/dataone_usage.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/dataone_usage.rb).
 
 ## Further Documentation
 * [DataONE usage stats](http://mdc.lagotto.io/dataone-usage-stats/)

docs/europe_pmc.md

@@ -340,7 +340,7 @@ Europe PubMed Central ([Europe PMC](http://europepmc.org/)) is an archive of lif
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/europe_pmc.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/europe_pmc.rb).
 
 ## API Documentation
 * [PMC Europe RESTful Web Service](http://europepmc.org/RestfulWebService)

docs/europe_pmc_data.md

@@ -243,7 +243,7 @@ Europe PubMed Central ([Europe PMC](http://europepmc.org/)) is an archive of lif
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/europe_pmc_data.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/europe_pmc_data.rb).
 
 ## API Documentation
 * [PMC Europe RESTful Web Service](http://europepmc.org/RestfulWebService)

docs/europe_pmc_fulltext.md

@@ -100,7 +100,7 @@ Search the Europe PMC fulltext corpus for scholarly works.
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/europe_pmc_fulltext.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/europe_pmc_fulltext.rb).
 
 ## Further Documentation
 * [Europe PMC RESTful Web Service](http://europepmc.org/RestfulWebService)

docs/facebook.md

@@ -95,7 +95,7 @@ https://graph.facebook.com/fql?access_token=%{access_token}&q=select url, share_
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/facebook.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/facebook.rb).
 
 ## Further Documentation
 * [Facebook Graph API](https://developers.facebook.com/docs/graph-api/using-graph-api/v2.1)

docs/github.md

@@ -171,4 +171,4 @@ Number of forks and stars for Github repos.
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/github.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/github.rb).

docs/mendeley.md

@@ -122,7 +122,7 @@ Mendeley uses OAuth2 authentication, we automatically obtain the access token us
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/mendeley.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/mendeley.rb).
 
 ## Further Documentation
 * [Mendeley API Documentation](http://dev.mendeley.com/methods/)

docs/nature.md

@@ -104,7 +104,7 @@ Nature Blogs is a science blog aggregator. Since May 1st 2013 API keys are [no l
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/nature.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/nature.rb).
 
 ## Further Documentation
 * [Nature Blogs API Documentation](http://www.nature.com/developers/documentation/api-references/blogs-api/)

docs/nature_opensearch.md

@@ -507,7 +507,7 @@ Search the Nature.com corpus for scholarly works using their [OpenSearch](http:/
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/nature_opensearch.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/nature_opensearch.rb).
 
 ## Further Documentation
 * [Nature.com Developers OpenSearch API](http://www.nature.com/developers/documentation/api-references/opensearch-api/)

docs/openedition.md

@@ -79,4 +79,4 @@ title: "OpenEdition"
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/openedition.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/openedition.rb).

docs/orcid.md

@@ -168,7 +168,7 @@ ORCID is a persistent author identifier for connecting research and researchers.
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/orcid.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/orcid.rb).
 
 ## Further Documentation
 * [Searching with the ORCID API](http://support.orcid.org/knowledgebase/articles/132354-searching-with-the-public-api)

docs/plos_fulltext.md

@@ -82,4 +82,4 @@ Search the fulltext content of PLOS articles for scholarly works.
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/plos_fulltext.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/plos_fulltext.rb).

docs/pmc.md

@@ -102,7 +102,7 @@ When installing the source, the CouchDB database for PMC has to be created with
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/pmc.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/pmc.rb).
 
 ## Further Documentation
 * [PubMed Central usage stats](http://www.ncbi.nlm.nih.gov/pmc/about/faq/#q26)

docs/pmceurope.md

@@ -340,7 +340,7 @@ Europe PubMed Central ([Europe PMC](http://europepmc.org/)) is an archive of lif
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/pmc_europe.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/pmc_europe.rb).
 
 ## API Documentation
 * [PMC Europe RESTful Web Service](http://europepmc.org/RestfulWebService)

docs/pmceuropedata.md

@@ -243,7 +243,7 @@ Europe PubMed Central ([Europe PMC](http://europepmc.org/)) is an archive of lif
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/pmc_europe_data.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/pmc_europe_data.rb).
 
 ## API Documentation
 * [PMC Europe RESTful Web Service](http://europepmc.org/RestfulWebService)

docs/pubmed.md

@@ -70,7 +70,7 @@ title: "PubMed Central"
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/pub_med.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/pub_med.rb).
 
 ## API Documentation
 * [PubMed Central citation data](http://www.pubmedcentral.nih.gov/utils/)

docs/reddit.md

@@ -204,7 +204,7 @@ title: "Reddit"
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/reddit.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/reddit.rb).
 
 ## Further Documentation
 * [Reddit API Documentation](http://www.reddit.com/dev/api)

docs/researchblogging.md

@@ -124,7 +124,7 @@ Research Blogging is a science blog aggregator.
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/researchblogging.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/researchblogging.rb).
 
 ## Further Documentation
 * [Research Blogging website](http://researchblogging.org)

docs/roadmap.md

@@ -36,7 +36,7 @@ All API responses from external sources should go through the new push API to ma
 
 ### Rewrite F1000 source as internal agent
 
-Once we have separated out the agent functionality from sources in we can start rewriting our existing sources to more efficiently collect events from external sources. The [F1000 source](https://github.com/lagotto/lagotto/blob/master/app/models/sources/f1000.rb) is a good starting point, and the new agent should parse the F1000 XML file and then deposit the payload in the new push API. We can consider packaging the internal agent as Ruby gem if the functionality is decoupled enough.
+Once we have separated out the agent functionality from sources in we can start rewriting our existing sources to more efficiently collect events from external sources. The [F1000 source](https://github.com/lagotto/lagotto/blob/master/app/models/agents/f1000.rb) is a good starting point, and the new agent should parse the F1000 XML file and then deposit the payload in the new push API. We can consider packaging the internal agent as Ruby gem if the functionality is decoupled enough.
 
 ### Add generic webmention endpoint
 

docs/scienceseeker.md

@@ -232,7 +232,7 @@ title: "ScienceSeeker"
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/science_seeker.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/science_seeker.rb).
 
 ## Further Documentation
 * [ScienceSeeker API](http://scienceseeker.org/api)

docs/scopus.md

@@ -130,7 +130,7 @@ title: Scopus
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/scopus.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/scopus.rb).
 
 ## Further Documentation
 * [Scopus Cited-by Linking](http://www.developers.elsevier.com/cms/scopus-citedby-retrieval)

docs/sources.md

@@ -265,4 +265,4 @@ Most sources return information about each individual event (citation, bookmark,
 </table>
 
 ## Creating a new source
-Basically, each of the APIs that the ALM application is calling will be defined as a **source**. The ALM application provides a number of services to each source to help it get what it needs. Note the samples provided at [http://github.com/lagotto/lagotto/tree/master/app/models/sources](http://github.com/lagotto/lagotto/tree/master/app/models/sources).
+Basically, each of the APIs that the ALM application is calling will be defined as a **source**. The ALM application provides a number of services to each source to help it get what it needs. Note the samples provided at [http://github.com/lagotto/lagotto/tree/master/app/models/agents](http://github.com/lagotto/lagotto/tree/master/app/models/sources).

docs/twitter_search.md

@@ -386,7 +386,7 @@ The rate-limits for application-only authentication and search are 450 requests
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/twitter_search.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/twitter_search.rb).
 
 ## Further Documentation
 * [Twitter Developer Documentation](https://dev.twitter.com/)

docs/wikipedia.md

@@ -113,7 +113,7 @@ We would for example use `en.wikipedia.org` as `HOST` in the `API URL` below. We
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/wikipedia.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/wikipedia.rb).
 
 ## Further Documentation
 * [Mediawiki API Documentation](http://www.mediawiki.org/wiki/API:Main_page)

docs/wordpress.md

@@ -141,7 +141,7 @@ Wordpress.com is a blog hosting platform by the makers of the Wordpress blogging
 ```
 
 ## Source Code
-The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/sources/wordpress.rb).
+The source code is available [here](https://github.com/lagotto/lagotto/blob/master/app/models/agents/wordpress.rb).
 
 ## Further Documentation
 * [WordPress.com Search](http://en.support.wordpress.com/wordpresscom-search/)