Merge pull request #80 from c3g/copy-editing

fixed a few typos, some wording / stylistic changes

chord_metadata_service/phenopackets/models.py

@@ -112,7 +112,7 @@ def __str__(self):
 class Procedure(models.Model):
     """
     Class to represent a clinical procedure performed on an individual
-    (subject) in oder to extract a biosample
+    (subject) in order to extract a biosample
 
     FHIR: Procedure
     """

docs/conf.py

@@ -21,8 +21,8 @@
 # -- Project information -----------------------------------------------------
 
 project = 'Metadata service'
-copyright = '2020, Ksenia Zaytseva, David Lougheed, Simon Chenard'
-author = 'Ksenia Zaytseva, David Lougheed, Simon Chenard'
+copyright = '2020, Ksenia Zaytseva, David Lougheed, Simon Chénard'
+author = 'Ksenia Zaytseva, David Lougheed, Simon Chénard'
 
 # The full version, including alpha/beta/rc tags
 release = '0.5.0'
@@ -53,4 +53,4 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ['_static']

docs/modules/installation.rst

@@ -14,9 +14,9 @@ Installation
 
     git submodule update --init
 
-3. Create and activate virtual environment
+3. Create and activate a virtual environment
 
-4. Cd to the main directory and install required packages:
+4. Move to the main directory and install required packages:
 
 .. code-block::
 
@@ -49,4 +49,4 @@ e.g. settings if running database on localhost, default port for PostgreSQL is 5
     python manage.py migrate
     python manage.py runserver
 
-8. Development server runs at :code:`localhost:8000`
+8. Development server runs at :code:`localhost:8000`

docs/modules/introduction.rst

@@ -19,8 +19,8 @@ Besides PostgreSQL the data can be indexed and queried in Elasticsearch.
 Architecture
 ------------
 
-Metadata Service contains several services that share one API.
-Services depend on each other and separated based on their scope.
+The Metadata Service contains several services that share one API.
+Services depend on each other and are separated based on their scope.
 
 **1. Patients service** handles anonymized individual’s data (e.g. individual id, sex, age or date of birth)
 
@@ -68,16 +68,16 @@ REST API highlights
 
 - Other available renderers:
 
-  - Currently the following classes can be retirved in FHIR format by appending :code:`?format=fhir`: Phenopackets, Individual, Biosample, PhenotypicFeature, HtsFile, Gene, Variants, Disease, Procedure.
+  - Currently the following classes can be retrieved in FHIR format by appending :code:`?format=fhir`: Phenopacket, Individual, Biosample, PhenotypicFeature, HtsFile, Gene, Variant, Disease, Procedure.
 
-  - JSON-LD context to schema.org provided for Dataset class in order to allow for a Google dataset search for Open Access Data: append :code:`?format=json-ld` when querying dataset endpoint.
+  - JSON-LD context to schema.org provided for the Dataset class in order to allow for a Google dataset search for Open Access Data: append :code:`?format=json-ld` when querying dataset endpoint.
 
-  - Dataset description can also be retrived in RDF format: append :code:`?format=rdf` when querying dataset endpoint.
+  - Dataset description can also be retrieved in RDF format: append :code:`?format=rdf` when querying the dataset endpoint.
 
 **Data ingest**
 
 Currently only the data that follow Phenopackets schema can be ingested.
-Ingest endpoint is :code:`/private/ingest` .
+Ingest endpoint is :code:`/private/ingest`.
 Example of POST request body:
 
 .. code-block::
@@ -118,15 +118,15 @@ Elasticsearch index (optional)
 ------------------------------
 
 Data in FHIR format can be indexed in Elasticsearch - this is optional.
-If an Elasticsearch instance is running on the server (so on :code:`localhost:9000`) these models will automatically be indexed on creation/update.
+If an Elasticsearch instance is running on the server (so on :code:`localhost:9000`) these models will be automatically indexed on creation/update.
 There are also two scripts provided to update these indexes all at once:
 
 .. code-block::
 
     python manage.py patients_build_index
     python manage.py phenopackets_build_index
 
-To query this information, here is an example request :
+Here is an example request for querying this information:
 
 .. code-block::