Add SampleTab Api documentation

docs/exportdata.rst

@@ -0,0 +1,37 @@
+###############################
+Exporting data from ISA formats
+###############################
+
+We have provided a number of modules that allow you to export data from ISA formats to formats for well-known
+databases or services.
+
+----------------------------------
+Exporting ISA content to SampleTab
+----------------------------------
+To export metadata from SampleTab files (e.g. for EBI BioSamples database), you can do the following to export a
+ISA-Tab to SampleTab:
+
+.. code-block:: python
+
+    from isatools.convert import isatab2sampletab
+    with open('your/path/to/i_investigation.txt', 'r') as input_investigation_file:
+        with open('your/path/to/sampletab.txt', 'w') as output_sampletab_file:
+            isatab2sampletab.convert(input_investigation_file, output_sampletab_file)
+
+To export an ISA JSON file to SampleTab, you can do:
+
+.. code-block:: python
+
+    from isatools.convert import isatab2sampletab
+    with open('your/path/to/i_investigation.txt', 'r') as input_investigation_file:
+        with open('your/path/to/sampletab.txt', 'w') as output_sampletab_file:
+            isatab2sampletab.convert(input_investigation_file, output_sampletab_file)
+
+You can also dump SampleTab content directly from ISA Python objects:
+
+.. code-block:: python
+
+    from isatools import sampletab
+    with open('your/path/to/sampletab.txt', 'w') as output_sampletab:
+        # Note: ISA would be a previously loaded or constructed root Investigation object
+        sampletab.dump(ISA, output_sampletab)

docs/importdata.rst

@@ -99,4 +99,34 @@ tool from https://github.com/ISA-tools/mzml2isa and can be run as follows:
 .. code-block:: python
 
     from isatools.convert import mzml2isa
-    mzml2isa.convert('your/path/to/mzml/files/', 'tmp/', "My Study ID")
+    mzml2isa.convert('your/path/to/mzml/files/', 'tmp/', "My Study ID")
+
+
+--------------------------
+Importing SampleTab to ISA
+--------------------------
+To import metadata from SampleTab files (e.g. from EBI BioSamples database), you can do the following to import a
+SampleTab to ISA-Tab:
+
+.. code-block:: python
+
+    from isatools.convert import sampletab2isatab
+    with open('your/path/to/sampletab.txt', 'r') as input_sampletab:
+        sampletab2isatab.convert(input_sampletab, 'tmp/')
+
+To import a SampleTab to ISA JSON, you can do:
+
+.. code-block:: python
+
+    from isatools.convert import sampletab2json
+    with open('your/path/to/sampletab.txt', 'r') as input_sampletab:
+        with open('your/path/to/myjson.json', 'w') as output_json:'
+            sampletab2json.convert(input_sampletab, output_json)
+
+You can also load SampleTab content directly into ISA Python objects:
+
+.. code-block:: python
+
+    from isatools import sampletab
+    with open('your/path/to/sampletab.txt', 'r') as input_sampletab:
+        ISA = sampletab.load(input_sampletab)

docs/index.rst

@@ -19,6 +19,7 @@ flexible way to build and use ISA content, as well as provide utility functions
 #. :doc:`Downloading files stored in Github </github>`
 #. :doc:`Validating ISA-Tab and ISA JSON </validation>`
 #. :doc:`Importing data in ISA formats </importdata>`
+#. :doc:`Exporting data in ISA formats </exportdata>`
 #. :doc:`Known Issues </knownissues>`
 
 License
@@ -43,4 +44,5 @@ This code is licensed under the `CPAL License <https://raw.githubusercontent.com
    Downloading files stored in Github <github>
    Validating ISA-Tab and ISA JSON <validation>
    Importing data in ISA formats <importdata>
+   Exporting data from ISA formats <exportdata>
    Known Issues <knownissues>