Updated documentation for db. Moved metadata scripts to install.

chipathlon/db.py

@@ -321,6 +321,7 @@ class MongoDB(object):
         :type accession: string
         :param file_type: The file type of the target sample.
         :type file_type: string
+        :returns: A tuple (valid, msg, data)
 
         Gets the associated sample based on accession number and file_type.
         For loading input files for workflows the file_type should be fastq
@@ -357,6 +358,7 @@ class MongoDB(object):
         :type experiment_accession: str
         :param file_type: File type of samples to grab usually fastq or bam
         :type file_type: str
+        :returns: A tuple (valid, msg, data)
 
         Validates and gets samples for the given experiment.  Experiments must
         have control and signal samples of the provided file_type to be

doc/source/db.rst

 MongoDB
 ==============
+The MongoDB class is used to manage all interactions with the encode data.
+The encode data is available from their website, and can be queried as json
+files using the following link:
+https://www.encodeproject.org/experiments/?format=json&limit=all
+From the list of experiments, we can extract all information for a particular
+experiment by requesting a url using the experiment accession:
+https://www.encodeproject.org/experiments/ENCSR000AHW/?format=json
+
+Each of these json files is used to load data into mongodb.  There is an
+enormous amount of metadata for each experiment that follows roughly the
+same format.  I recommend looking at some experiments to familiarize yourself
+with the experiment metadata.  For more information about how to create the
+mongodb database look at the :ref:`chip-meta-download` and
+:ref:`chip-meta-import` scripts.
+
 
 MongoDB Class
 ^^^^^^^^^^^^^^

doc/source/scripts.rst

@@ -7,3 +7,9 @@ chip-gen
 
 chip-create-run
 ^^^^^^^^^^^^^^^
+
+chip-meta-download
+^^^^^^^^^^^^^^^^^^^
+
+chip-meta-import
+^^^^^^^^^^^^^^^^^

setup.py

@@ -10,6 +10,8 @@ setup(
     },
     scripts = [
         "scripts/chip-gen",
-        "scripts/chip-create-run"
+        "scripts/chip-create-run",
+        "scripts/chip-meta-download",
+        "scripts/chip-meta-import"
     ]
 )