Merge pull request #19 from wltrimbl/master

Changed uris to mg-rast.org

mg-rast-api-chapter.tex

@@ -16,12 +16,12 @@ \chapter{API --- The MG-RAST Application Programming Interface}
 \section{URLs}
 \begin{small}
 \begin{verbatim}
-http://api.metagenomics.anl.gov/
+https://api.mg-rast.org/
 \end{verbatim}
 \end{small} Further documentation, with a complete parameter listing for all resources available is at:
 \begin{small}
 \begin{verbatim}
-http://api.metagenomics.anl.gov/api.html
+https://api.mg-rast.org/api.html
 \end{verbatim}
 \end{small} Github repository of script tools, examples, and contributed code for using the MG-RAST API:
 \begin{small}
@@ -64,14 +64,14 @@ \section{Design and Implementation}
 Each query to the API is represented as a URI beginning with 
 \begin{small}
 \begin{verbatim}
-http://api.metagenomics.anl.gov/
+https://api.mg-rast.org/
 \end{verbatim}
 \end{small} and has a defined structure to pass the requests and parameters to the API server. These URI queries can be used from the command line, e.g. using curl, in a browser, or incorporated in a shell script or program.
 
 Each URI has the form:
 \begin{small}
 \begin{verbatim}
-http://api.metagenomics.anl.gov/{version}/{resourcepath}?{querystring}
+https://api.mg-rast.org/{version}/{resourcepath}?{querystring}
 \end{verbatim}
 \end{small} where
 
@@ -99,7 +99,7 @@ \section{Design and Implementation}
 For example, in:
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt
+https://api.mg-rast.org/1/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt
 \end{lstlisting}
 \end{small} the resource path 
 
@@ -129,26 +129,26 @@ \section{Design and Implementation}
 The auth\_key can be included in the query string like:
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt&auth_key=j6FNL61ekNarTgqupMma6eMx5
+https://api.mg-rast.org/1/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt&auth_key=j6FNL61ekNarTgqupMma6eMx5
 \end{lstlisting}
 \end{small} or in a request using curl like:
 \begin{small}
 \begin{lstlisting}
-curl -X GET -H "auth: j6FNL61ekNarTgqupMma6eMx5" "http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt"
+curl -X GET -H "auth: j6FNL61ekNarTgqupMma6eMx5" "https://api.mg-rast.org/1/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt"
 \end{lstlisting}
 \end{small} Note that for the curl command the quotes are necessary for the query to be passed to the API correctly.
 
 If an optional parameter passed through the query string has a list of values only the first will be used. When multiple values are required, e.g. for multiple md5 checksum values, they can be passed to the API like:
 \begin{small}
 \begin{lstlisting}
-curl -X POST -d '{"data":["000821a2e2f63df1a3873e4b280002a8","15bf1950bd9867099e72ea6516e3d602"]}' "http://api.metagenomics.anl.gov//m5nr/md5"
+curl -X POST -d '{"data":["000821a2e2f63df1a3873e4b280002a8","15bf1950bd9867099e72ea6516e3d602"]}' "https://api.mg-rast.org//m5nr/md5"
 \end{lstlisting}
 \end{small}
 
 In some cases, the data requested is in the form of a list with a large number of entries. In these cases the `limit' and `offset' parameters can be used to step through the list, e.g.
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/1/project?order=name&limit=20&offset=100
+https://api.mg-rast.org/1/project?order=name&limit=20&offset=100
 \end{lstlisting}
 \end{small} will limit the number of entries returned to 20 with an offset of 100. If these parameters are not provided default values of \texttt{limit=10} and \texttt{offset=0} are used. The returned JSON structure will contain the `next' and `prev' (previous) URIs to simplify stepping through the list.
 
@@ -199,28 +199,28 @@ \section{Examples}
 \textbf{annotation}
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4440036.3?type=function&filter=protease&source=Subsystems
+https://api.mg-rast.org/1/annotation/sequence/mgm4440036.3?type=function&filter=protease&source=Subsystems
 \end{lstlisting}
 \end{small} Retrieve the reads from a metagenome with ID mgm4440036.3 which were annotated as  protease in SEED Subsystems.
 
 \item
 \textbf{download}
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/1/download/mgm4447943.3
+https://api.mg-rast.org/1/download/mgm4447943.3
 \end{lstlisting}
 \end{small} Retrieve information formatted as a JSON object about all the files available for download for metagenome mgm4447943.3 with information about the files and sequence statistics where applicable. Each file listed has a URL included which can be used to download the file, e.g.
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/1/download/mgm4447943.3?file=650.1
+https://api.mg-rast.org/1/download/mgm4447943.3?file=650.1
 \end{lstlisting}
 \end{small} will download the protein.sims file containing the BLAT similarities.
 
 \item
 \textbf{inbox}
 \begin{small}
 \begin{lstlisting}
-curl -X POST -H "auth: auth_key" -F "[email protected]" "http://api.metagenomics.anl.gov/1/inbox"
+curl -X POST -H "auth: auth_key" -F "[email protected]" "https://api.mg-rast.org/1/inbox"
 \end{lstlisting}
 \end{small}
 Upload the file 'sequences.fastq' to your inbox. This API call requires user authentication using the auth\_key described above. It can not be used in a browser, but needs to be run from the command line or from a script.
@@ -229,7 +229,7 @@ \section{Examples}
 \textbf{matrix}
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/matrix/organism?group_level=family&source=SEED&evalue=5&id=mgm4440442.5&id=mgm4440026.3
+https://api.mg-rast.org/matrix/organism?group_level=family&source=SEED&evalue=5&id=mgm4440442.5&id=mgm4440026.3
 \end{lstlisting}
 \end{small}
 Retrieve the taxonomic abundance profile on family level for 2 metagenomes based on SEED assignments with an evalue cutoff of 1e-5.
@@ -238,61 +238,61 @@ \section{Examples}
 \textbf{metagenome}
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/1/metagenome/mgm4440026.3
+https://api.mg-rast.org/1/metagenome/mgm4440026.3
 \end{lstlisting}
 \end{small} List analysis submission parameters and other details for a metagenome.
 \newline
 The metagenome resource can also be used to search metadata, function and taxonomy.  
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/metagenome?function=dnaA&organism=coli&biome=marine&match=all&order=created
+https://api.mg-rast.org/metagenome?function=dnaA&organism=coli&biome=marine&match=all&order=created
 \end{lstlisting}
 \end{small} This call will find all marine metagenomes with reads annotated as dnaA and have taxonomic assignment containing the text `coli', the results will be ordered based on creation date for the metagenome.
 
 \item
 \textbf{project}
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/project/mgp31?verbosity=full
+https://api.mg-rast.org/project/mgp31?verbosity=full
 \end{lstlisting}
 \end{small} Retrieve available information about the project with ID mgp31.
 
 \item
 \textbf{sample}
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/1/sample/mgs12326?verbosity=full
+https://api.mg-rast.org/1/sample/mgs12326?verbosity=full
 \end{lstlisting}
 \end{small} Retrieve available information about individual samples, including IDs and metadata.
 
 \item
 \textbf{metadata}
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov//metadata/template
+https://api.mg-rast.org//metadata/template
 \end{lstlisting}
 \end{small} Retrieve the static template for metadata object relationships and types used by MG-RAST.
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov//metadata/export/mgp128
+https://api.mg-rast.org//metadata/export/mgp128
 \end{lstlisting}
 \end{small} Retrieve all metadata for project mgp128.
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/metadata/cv
+https://api.mg-rast.org/metadata/cv
 \end{lstlisting}
 \end{small} Retrieve a set of lists of all our controlled metadata terms, including the ontologies.
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/metadata/ontology?name=biome&version=2013-04-27
+https://api.mg-rast.org/metadata/ontology?name=biome&version=2013-04-27
 \end{lstlisting}
 \end{small} Retrieve a more detailed list (with relationships) for a specific version of the ontology.
 
 \item
 \textbf{m5nr}
 \begin{small}
 \begin{lstlisting}
-http://api.metagenomics.anl.gov/1/m5nr/md5/ffc62262a18b38671c3e337150ef535f?source=SwissProt
+https://api.mg-rast.org/1/m5nr/md5/ffc62262a18b38671c3e337150ef535f?source=SwissProt
 \end{lstlisting}
 \end{small} Retrieve the UniProt ID for a given sequence identifier.
 

mg-rast-api-examples.tex

@@ -83,7 +83,7 @@ \section{Download and translate similarities into different namespaces e.g. SEED
 
 \textbf{Example:}
 \begin{lstlisting}
-m5nr-tools.pl --api "http://api.metagenomics.anl.gov/1" --option annotation --source RefSeq --md5 0b95101ffea9396db4126e4656460ce5,068792e95e38032059ba7d9c26c1be78,0b96c92ce600d8b2427eedbc221642f1
+m5nr-tools.pl --api "https://api.mg-rast.org/1" --option annotation --source RefSeq --md5 0b95101ffea9396db4126e4656460ce5,068792e95e38032059ba7d9c26c1be78,0b96c92ce600d8b2427eedbc221642f1
 \end{lstlisting}
 
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