From cccf8184bd29a1edee180e90d56fbf6209e66cfb Mon Sep 17 00:00:00 2001
From: Elizabeth Seiver <elizabeth.seiver@gmail.com>
Date: Wed, 18 May 2016 14:09:01 -0700
Subject: [PATCH] Updated documentation to reflect new file structure

Resulting from directory change here: https://github.com/lagotto/lagotto/commit/b645a572c532d6550bf0f8da0cc40b577362f4af
---
 docs/ads.md                 | 2 +-
 docs/ads_fulltext.md        | 2 +-
 docs/bitbucket.md           | 2 +-
 docs/bmc_fulltext.md        | 2 +-
 docs/citeulike.md           | 2 +-
 docs/copernicus.md          | 2 +-
 docs/crossref.md            | 2 +-
 docs/datacite.md            | 2 +-
 docs/datacite_data.md       | 2 +-
 docs/dataone_counter.md     | 2 +-
 docs/dataone_usage.md       | 2 +-
 docs/europe_pmc.md          | 2 +-
 docs/europe_pmc_data.md     | 2 +-
 docs/europe_pmc_fulltext.md | 2 +-
 docs/facebook.md            | 2 +-
 docs/github.md              | 2 +-
 docs/mendeley.md            | 2 +-
 docs/nature.md              | 2 +-
 docs/nature_opensearch.md   | 2 +-
 docs/openedition.md         | 2 +-
 docs/orcid.md               | 2 +-
 docs/plos_fulltext.md       | 2 +-
 docs/pmc.md                 | 2 +-
 docs/pmceurope.md           | 2 +-
 docs/pmceuropedata.md       | 2 +-
 docs/pubmed.md              | 2 +-
 docs/reddit.md              | 2 +-
 docs/researchblogging.md    | 2 +-
 docs/roadmap.md             | 2 +-
 docs/scienceseeker.md       | 2 +-
 docs/scopus.md              | 2 +-
 docs/sources.md             | 2 +-
 docs/twitter_search.md      | 2 +-
 docs/wikipedia.md           | 2 +-
 docs/wordpress.md           | 2 +-
 35 files changed, 35 insertions(+), 35 deletions(-)

diff --git a/docs/ads.md b/docs/ads.md
index 83ce457..882f9b3 100644
--- a/docs/ads.md
+++ b/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).
diff --git a/docs/ads_fulltext.md b/docs/ads_fulltext.md
index 589ae3b..a955332 100644
--- a/docs/ads_fulltext.md
+++ b/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).
diff --git a/docs/bitbucket.md b/docs/bitbucket.md
index 9b00082..6743d9b 100644
--- a/docs/bitbucket.md
+++ b/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).
diff --git a/docs/bmc_fulltext.md b/docs/bmc_fulltext.md
index 579fe99..7d81d7a 100644
--- a/docs/bmc_fulltext.md
+++ b/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).
diff --git a/docs/citeulike.md b/docs/citeulike.md
index 669f095..758a100 100644
--- a/docs/citeulike.md
+++ b/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).
diff --git a/docs/copernicus.md b/docs/copernicus.md
index 88e46fe..1de037d 100644
--- a/docs/copernicus.md
+++ b/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)
diff --git a/docs/crossref.md b/docs/crossref.md
index 4040983..da8ede1 100644
--- a/docs/crossref.md
+++ b/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)
diff --git a/docs/datacite.md b/docs/datacite.md
index e3c7a1d..1d0b312 100644
--- a/docs/datacite.md
+++ b/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)
diff --git a/docs/datacite_data.md b/docs/datacite_data.md
index dc3377c..d1f52a0 100644
--- a/docs/datacite_data.md
+++ b/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)
diff --git a/docs/dataone_counter.md b/docs/dataone_counter.md
index ad5a39b..14368d0 100644
--- a/docs/dataone_counter.md
+++ b/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/)
diff --git a/docs/dataone_usage.md b/docs/dataone_usage.md
index 1a5712f..87afefc 100644
--- a/docs/dataone_usage.md
+++ b/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/)
diff --git a/docs/europe_pmc.md b/docs/europe_pmc.md
index ee71d32..11cb8db 100644
--- a/docs/europe_pmc.md
+++ b/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)
diff --git a/docs/europe_pmc_data.md b/docs/europe_pmc_data.md
index f262613..192aefb 100644
--- a/docs/europe_pmc_data.md
+++ b/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)
diff --git a/docs/europe_pmc_fulltext.md b/docs/europe_pmc_fulltext.md
index e6397c7..7cc986a 100644
--- a/docs/europe_pmc_fulltext.md
+++ b/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)
diff --git a/docs/facebook.md b/docs/facebook.md
index 5205547..d9453fe 100644
--- a/docs/facebook.md
+++ b/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)
diff --git a/docs/github.md b/docs/github.md
index 64b1285..bbcba74 100644
--- a/docs/github.md
+++ b/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).
diff --git a/docs/mendeley.md b/docs/mendeley.md
index 598a3ad..aa4acb1 100644
--- a/docs/mendeley.md
+++ b/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/)
diff --git a/docs/nature.md b/docs/nature.md
index 8881a94..a9c0049 100644
--- a/docs/nature.md
+++ b/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/)
diff --git a/docs/nature_opensearch.md b/docs/nature_opensearch.md
index d863074..6e8c599 100644
--- a/docs/nature_opensearch.md
+++ b/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/)
diff --git a/docs/openedition.md b/docs/openedition.md
index 58208d4..e658707 100644
--- a/docs/openedition.md
+++ b/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).
diff --git a/docs/orcid.md b/docs/orcid.md
index 913eb7f..b6469c4 100644
--- a/docs/orcid.md
+++ b/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)
diff --git a/docs/plos_fulltext.md b/docs/plos_fulltext.md
index ca79363..8a2cbea 100644
--- a/docs/plos_fulltext.md
+++ b/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).
diff --git a/docs/pmc.md b/docs/pmc.md
index 84400b0..ac5f618 100644
--- a/docs/pmc.md
+++ b/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)
diff --git a/docs/pmceurope.md b/docs/pmceurope.md
index 1deaddc..9607dc4 100644
--- a/docs/pmceurope.md
+++ b/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)
diff --git a/docs/pmceuropedata.md b/docs/pmceuropedata.md
index 5bde1d0..bef4652 100644
--- a/docs/pmceuropedata.md
+++ b/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)
diff --git a/docs/pubmed.md b/docs/pubmed.md
index 03c4f3f..5ca4408 100644
--- a/docs/pubmed.md
+++ b/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/)
diff --git a/docs/reddit.md b/docs/reddit.md
index 18a7fcb..980c7a2 100644
--- a/docs/reddit.md
+++ b/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)
diff --git a/docs/researchblogging.md b/docs/researchblogging.md
index 1894771..01c15f3 100644
--- a/docs/researchblogging.md
+++ b/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)
diff --git a/docs/roadmap.md b/docs/roadmap.md
index eab8689..10cda08 100644
--- a/docs/roadmap.md
+++ b/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
 
diff --git a/docs/scienceseeker.md b/docs/scienceseeker.md
index 58ccd4f..01ed8af 100644
--- a/docs/scienceseeker.md
+++ b/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)
diff --git a/docs/scopus.md b/docs/scopus.md
index fe5e885..065a238 100644
--- a/docs/scopus.md
+++ b/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)
diff --git a/docs/sources.md b/docs/sources.md
index 70afc8b..5e602ff 100644
--- a/docs/sources.md
+++ b/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).
diff --git a/docs/twitter_search.md b/docs/twitter_search.md
index 4cbb792..f473db7 100644
--- a/docs/twitter_search.md
+++ b/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/)
diff --git a/docs/wikipedia.md b/docs/wikipedia.md
index ab04831..63296c1 100644
--- a/docs/wikipedia.md
+++ b/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)
diff --git a/docs/wordpress.md b/docs/wordpress.md
index 56f9840..e1cb2b5 100644
--- a/docs/wordpress.md
+++ b/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/)