📝 minor changes in RTD documentation

flask-data/smarter/docs/source/accessing/python.rst

@@ -26,7 +26,8 @@ urls. Eventually, we will transform data into a ``pandas`` DataFrame.
 Deal with data and pagination in python
 ---------------------------------------
 
-We can define some utility functions to deal with data and pagination:
+We can define some utility functions to deal with data and pagination. Those
+functions are general and can be used to access any endpoint of the SMARTER API:
 
 .. code-block:: python
 
@@ -83,7 +84,7 @@ Read data with Python
 ---------------------
 
 Now we can read data from the API using the functions we defined before. We can
-get the data from the API and transform it into a pandas DataFrame. We can define
+get the data from the API and transform it into a ``pandas.DataFrame`` by creating
 a custom function in order to call the API with different parameters:
 
 .. code-block:: python
@@ -97,7 +98,7 @@ a custom function in order to call the API with different parameters:
       return pd.json_normalize(results)
 
 By calling the function ``get_smarter_datasets`` we can get the data from the API
-and transform it into a pandas DataFrame to collect all the *datasets* object from
+and transform it into a ``pandas.DataFrame`` to collect all the *datasets* object from
 the *Dataset* endpoint. Similarly, we can define a function to get the data from the
 *Breed* endpoint:
 
@@ -113,7 +114,7 @@ the *Dataset* endpoint. Similarly, we can define a function to get the data from
 
 ``get_smarter_breeds`` and ``get_smarter_datasets`` functions can be used to return
 all the SMARTER *datasets* and *breeds*. However you can pass additional parameters to
-the endpoint using the ``params`` parameter (which can be a dictionary or a list
+the endpoints using the ``params`` parameter (which can be a dictionary or a list
 of tuples, when specifying the same parameter multiple times). For
 example, you could retrieve all goats breeds using the ``species`` option:
 

flask-data/smarter/docs/source/accessing/r.rst

@@ -219,7 +219,7 @@ endpoints relying on parameters:
       query = list(breed_code = "LNR")
    )
 
-As for the breed example, we can refine our query, for example by selecting
+We can refine our query, for example by selecting
 Landrace goat samples which have a locations (GPS coordinates) and phenotypes
 defined (mind to the double ``_`` in ``locations__exists`` and
 ``phenotype__exists``):

flask-data/smarter/docs/source/index.rst

@@ -9,8 +9,8 @@ Welcome to SMARTER-backend's documentation!
 This documentation describes how to install and interact with the SMARTER database
 backend. Briefly, the SMARTER database created and maintained with the
 `SMARTER-database <https://github.com/cnr-ibba/SMARTER-database>`_ project is
-made accessible to SMARTER partners using this API. This API is the same used
-by the `SMARTER-frontend <https://github.com/cnr-ibba/SMARTER-frontend>`_ in
+made accessible to the community using this API. This API is the same used
+by the `SMARTER-frontend <https://webserver.ibba.cnr.it/smarter/>`_ in
 order to access and browse SMARTER data using a web browser.
 
 SMARTER-backend is a `flask-API <https://flask.palletsprojects.com/en/2.0.x/>`_
@@ -24,10 +24,7 @@ the data they need using a `PLINK <https://zzz.bwh.harvard.edu/plink/>`_ command
 Documentation is organized as following: in :ref:`Introduction` we describe what
 SMARTER-backend is and we provide general information. In :ref:`Backend installation`
 we describe how to install a local instance of SMARTER-backend. Then in
-:ref:`Accessing SMARTER-backend` we describe how to programmatically access to data
-or how to inspect data using applications like `Postman <https://www.postman.com/>`_
-or `Talend Api Tester <https://chrome.google.com/webstore/detail/talend-api-tester-free-ed/aejoelaoggembcahagimdiliamlcdmfm>`_
-google-chrome extension.
+:ref:`Accessing SMARTER-backend` we describe how to programmatically access to data.
 
 .. toctree::
    :maxdepth: 2

flask-data/smarter/docs/source/installing.rst

@@ -26,9 +26,9 @@ official installation instructions for your operating system.
 Create a .env file
 ------------------
 
-Before running the application, you need to create a .env file in the root directory
+Before running the application, you need to create a ``.env`` file in the root directory
 of the project. This is required to set the environment variables needed by the
-application, like the database connection string. Create a .env file in the root
+application, like the database connection string. Create a ``.env`` file in the root
 directory of the project with the following content:
 
 .. code-block:: bash

flask-data/smarter/docs/source/introduction.rst

@@ -111,7 +111,10 @@ supported, ``GET`` and ``POST``:
 More precisely, SMARTER data through the SMARTER-backend are read-only and
 ``GET`` and ``POST`` method are allowed in order to retrieve any type of SMARTER
 data object from the API. ``POST`` method are required to submit complex queries
-by providing a payload to certain endpoints.
+by providing a payload to certain endpoints, for example to retrieve samples
+relying on GPS data. For a detailed list of the available endpoints and the
+HTTP methods they support, please refer to the
+`swagger documentation <https://webserver.ibba.cnr.it/smarter-api/docs/>`_ available.
 
 Status codes
 ------------