updated documentation

README.md

@@ -6,14 +6,14 @@ Python client for the Open Targets REST API at targetvalidation.org
 
 Why should you use this client instead of the REST API directly?
 
+- Include wrappers for all public methods, with query validation
+- Tools for the most common calls (E.g. get data for a target gene symbol even if you do not know its Ensembl Gene Id)
+- Supports automatic retrieval of paginated results with an iterator pattern
+- Easily save query results as JSON, CSV or Excel file
 - Handles Authentication
 - Handles fair usage limits transparently
 - Follows HTTP cache as set by the REST API
 - Experimental HTTP2 support for better performance (beware the client library is in alpha)
-- Supports automatic retrieval of paginated results with an iterator pattern
-- Include wrappers for public methods
-- Tools for the most common calls (E.g. get data for a target gene symbol even if you do not know its Ensembl Gene Id)
-- Easily save query results as JSON, CSV or Excel file
 
 This client is supported for Python 3.5 and upper.
 Works on lower version (including python 2) on a best effort basis.
@@ -40,8 +40,7 @@ a_for_disease = ot.get_associations_for_disease('cancer')
 print(ot.get_association('ENSG00000157764-EFO_0005803')[0])
 
 e_for_target = ot.get_evidence_for_target('BRAF')
-for e in e_for_target:
-    print(e.to_json())
+print(e_for_target.to_json())
 
 e_for_disease = ot.get_evidence_for_disease('medulloblastoma')
 

docs/source/history.rst

@@ -3,6 +3,14 @@
 Changelog
 =========
 
+1.2.0b1
+---------------------
+
+- Added option to export data as JSON, csv, excel or pandas dataframe. (optional dependency for pandas and xlwt)
+- Fixed post calls and qutomatically switch to post for a large request
+
+
+
 1.2.0a2
 ---------------------
 

docs/source/index.rst

@@ -17,6 +17,7 @@ Main advantages of using the client versus querying the REST API directly
 - Include wrappers for all public methods, with query validation
 - Tools for the most common calls (E.g. get data for a target gene symbol even if you do not know its Ensembl Gene Id)
 - Supports automatic retrieval of paginated results with an iterator pattern
+- Easily save query results as JSON, CSV or Excel file
 - Handles Authentication
 - Handles fair usage limits transparently
 - Follows HTTP cache as set by the REST API

docs/source/tutorial.rst

@@ -39,10 +39,8 @@ get an association by id:
 get evidence for a target:
 ::
 
-    from opentargets.conn import result_to_json
     e_for_target = ot.get_evidence_for_target('BRAF')
-    for e in e_for_target:
-        print(result_to_json(e))
+    print(e_for_target.to_json())
 
 get evidence for a disease:
 ::
@@ -96,3 +94,19 @@ use incremental filter:
     10 ENSG00000157764-EFO_1000249 0.5555555555555556 Extramammary Paget Disease
     11 ENSG00000157764-Orphanet_774 0.21793721666666668 Hereditary hemorrhagic telangiectasia
 
+
+export a table with association score for each datasource into an excel file:
+::
+
+    >>> from opentargets import OpenTargetsClient
+    >>> client = OpenTargetsClient()
+    >>> response = client.get_associations_for_target('BRAF',
+    ...     fields=['association_score.datasource*',
+    ...             'association_score.overall',
+    ...             'target.gene_info.symbol',
+    ...             'disease.efo_info.*']
+    ...     )
+    >>> response
+    865 Results found | parameters: {'target': 'ENSG00000157764', 'fields': ['association_score.datasource*', 'association_score.overall', 'target.gene_info.symbol', 'disease.efo_info.label']}
+    >>> response.to_excel('BRAF_associated_diseases_by_datasource.xls')
+    >>>