Bug fixes and performance improvements (uc-cdis#5)

* chore(graphene) upgrade to 2.0.1
* chore(travis): Pull in Rudy's PR for codacy coverage
* chore(swagger): Add swagger file

.codacy.yml

@@ -0,0 +1,5 @@
+---
+coverage:
+  enabled: true
+exclude_paths:
+  - 'tests/**' 

.travis.yml

@@ -1,47 +1,26 @@
-sudo: false
 dist: trusty
-group: deprecated-2017Q2
+sudo: false
 language: python
 
 python:
   - "2.7"
 
 cache:
-  # pip: true  # We have overridden the default install step, caching manually
-  # ref: <https://docs.travis-ci.com/user/caching/#Arbitrary-directories>
-  - directories:
-      - /home/travis/virtualenv/python2.7.9/lib/python2.7/site-packages
-      - $HOME/.pip-cache
+  - pip
   - apt
 
 addons:
   postgresql: '9.4'
-  # fix for scipy inside SurvivalPy
-  apt:
-    packages:
-    - libatlas-dev
-    - libatlas-base-dev
-    - liblapack-dev
-    - gfortran
 
 services:
   - elasticsearch
 
 before_install:
   # bust only the the part of the cache that we are frequently changing
-  - pip uninstall --yes psqlgraph gdcdictionary gdcdatamodel || true
-
-  # fix for scipy inside SurvivalPy
-  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - conda update --yes conda
+  - pip uninstall --yes gdcdictionary gdcdatamodel || true
 
 # command to install dependencies
 install:
-  # fix for scipy inside SurvivalPy
-  - conda install --yes python=$TRAVIS_PYTHON_VERSION pip numpy scipy nose future
-
   - pip install -r requirements.txt
   - pip install -r dev-requirements.txt
 
@@ -53,10 +32,10 @@ before_script:
 
 # command to run tests
 script:
-- |
-  set -e
-  PYTHONPATH=. py.test -vv tests/system_test.py tests/graphql/test_graphql.py
-  set +e
+  - py.test -vv --cov=peregrine --cov-report xml tests/system_test.py tests/graphql/test_graphql.py
+
+after_script:
+  - python-codacy-coverage -r coverage.xml
 
 env:
   global:

README.md

@@ -1,3 +1,21 @@
-## Peregrine
-Query interface to get insights into data in Gen3 Commons Edit
-Add topics
+# Peregrine
+
+[![Build Status](https://travis-ci.org/uc-cdis/peregrine.svg?branch=master)](https://travis-ci.org/uc-cdis/peregrine)
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/f6128183864d4e5da5093eb72a3c9c97)](https://www.codacy.com/app/uc-cdis/peregrine?utm_source=github.com&utm_medium=referral&utm_content=uc-cdis/peregrine&utm_campaign=Badge_Grade)
+[![Codacy Badge](https://api.codacy.com/project/badge/Coverage/f6128183864d4e5da5093eb72a3c9c97)](https://www.codacy.com/app/uc-cdis/peregrine?utm_source=github.com&utm_medium=referral&utm_content=uc-cdis/peregrine&utm_campaign=Badge_Coverage)
+
+Query interface to get insights into data in Gen3 Commons
+
+## Setup
+
+```bash
+# Install requirements.
+pip install -r requirements.txt
+```
+
+## API Documentation
+
+[OpenAPI documentation available here.](http://petstore.swagger.io/?url=https://raw.githubusercontent.com/uc-cdis/peregrine/master/openapis/swagger.yaml)
+
+YAML file for the OpenAPI documentation is found in the `openapi` folder (in
+the root directory); see the README in that folder for more details.

dev-requirements.txt

@@ -4,11 +4,12 @@ lockfile==0.10.2
 coverage==3.7.1
 mock==1.0.1
 pytest-flask==0.8.1
+pytest-cov==2.5.1
+codacy-coverage
 moto==0.4.5
 Sphinx==1.3.1
 sphinxcontrib-httpdomain==1.3.0
--e git+https://[email protected]/NCI-GDC/signpost.git@c5d499936943e71eefe2ec4b3d4ced6ac48f35c0#egg=signpost
+-e git+https://[email protected]/NCI-GDC/signpost.git@c8e2aa5ff572c808cba9b522b64f7b497e79c524#egg=signpost
 -e git+https://[email protected]/uc-cdis/[email protected]#egg=cdisutilstest
 -e git+https://[email protected]/uc-cdis/[email protected]#egg=flask_postgres_session
 -e git+https://[email protected]/uc-cdis/sheepdog.git@53cb3a5d69d04a3daf0cdf00957151813fcccac4#egg=sheepdog
--e git+https://[email protected]/uc-cdis/[email protected]#egg=storageclient

openapis/README.md

@@ -0,0 +1,17 @@
+# TL;DR
+
+[Swagger](https://swagger.io/getting-started-with-swagger-i-what-is-swagger/) specification of Peregrine's REST API
+
+## Swagger Tools
+
+Use swagger's editor to update swagger.yaml and swagger.json using one of the following:
+* [online editor](https://editor.swagger.io/) 
+* [Docker image](https://hub.docker.com/r/swaggerapi/swagger-editor/) - `docker run -d -p 80:8080 swaggerapi/swagger-editor`
+* or pull the editor code from [github](https://github.com/swagger-api/swagger-editor), and `npm start` an editor locally.
+
+Publish API documentation with the [swagger-ui](https://github.com/swagger-api/swagger-ui) - also easily launched with docker: `docker run -p 80:8080 -e SWAGGER_JSON=/foo/swagger.json -v /bar:/foo swaggerapi/swagger-ui` 
+
+## OpenAPI Spec
+
+The swagger definition format has been open sourced as the OpenAPI Specification administered by the Linux Foundation.  As of writing this the latest spec defining the structure and elements of a swagger.yaml file is [version 3](https://github.com/OAI/OpenAPI-Specification/blob/master/versions/3.0.0.md).
+

openapis/swagger.yaml

@@ -0,0 +1,142 @@
+swagger: '2.0'
+info:
+  title: Peregrine OpenAPI Specification
+  version: 0.1.0
+  description: >-
+    GraphQL search microservice for CDIS Gen 3 data commons. Code is available
+    on [GitHub](https://github.com/uc-cdis/peregrine).
+  termsOfService: 'http://cdis.uchicago.edu/terms/'
+  contact:
+    email: [email protected]
+  license:
+    name: Apache 2.0
+    url: 'http://www.apache.org/licenses/LICENSE-2.0.html'
+host: example.domain
+basePath: /
+tags:
+  - name: graphql
+    description: GraphQL Queries
+  - name: system
+    description: System endpoints
+schemes:
+  - https
+paths:
+  /graphql:
+    post:
+      tags:
+        - graphql
+      summary: Perform a GraphQL Query
+      description: >-
+        Perform a graphql query over the data commons given a query, variables,
+        and name.
+      consumes:
+        - application/json
+      produces:
+        - application/json
+      parameters:
+        - in: body
+          name: body
+          description: The GraphQL query and parameters
+          required: true
+          schema:
+            $ref: '#/definitions/QueryInputInfo'
+      responses:
+        '200':
+          description: successful operation
+          schema:
+            $ref: '#/definitions/QueryOutputRef'
+        '400':
+          description: Invalid input
+        '403':
+          description: Invalid authorization token
+  /getschema:
+    get:
+      tags:
+        - graphql
+      summary: Returns the data dictionary schema json
+      description: >-
+        The data dictionary for the data commons is internally converted from
+        yaml files to json. This endpoint returns the json schema for the
+        dictionary for use in generating queries.
+      produces:
+        - application/json
+      responses:
+        '200':
+          description: successful operation
+          schema:
+            $ref: '#/definitions/SchemaOutputRef'
+  /_version:
+    get:
+      tags:
+        - system
+      summary: Returns the version of Peregrine
+      produces:
+        - application/json
+      responses:
+        '200':
+          description: successful operation
+          schema:
+            $ref: '#/definitions/VersionOutputRef'
+  /_status:
+    get:
+      tags:
+        - system
+      summary: Returns if Peregrine is healthy or not
+      description: >-
+        Health check endpoint which checks if Peregrine can connect to its
+        backing PostgreSQL datastore or not.
+      produces:
+        - application/text
+      responses:
+        '200':
+          description: Healthy
+        default:
+          description: Unhealthy
+definitions:
+  QueryInputInfo:
+    type: object
+    properties:
+      query:
+        type: string
+        description: the text of the GraphQL query
+      variables:
+        type: string
+        description: variables for the GraphQL query
+      operationName:
+        type: string
+        description: the name of the operation
+    example:
+      query: '{ project {project_id} }'
+      operationName: null
+      variables: null
+  QueryOutputRef:
+    type: object
+    properties:
+      data:
+        type: object
+        description: the results of the GraphQL query
+  SchemaOutputRef:
+    type: object
+    properties:
+      data:
+        type: object
+        description: the json schema for the data dictionary
+  VersionOutputRef:
+    type: object
+    properties:
+      commit:
+        type: string
+        description: the current git commit hash for this version
+      version:
+        type: string
+        description: the current git tag version
+      dictionary:
+        type: object
+        description: the version information for the data dictionary
+        properties:
+          commit:
+            type: string
+            description: the current git commit hash for the dictionary
+          version:
+            type: string
+            description: the current git tag version for the dictionary

peregrine/auth/__init__.py

@@ -69,8 +69,6 @@ def get_user_projects(self, user):
             .all()
         )
         return_res = {}
-        if not results:
-            raise AuthError("No project access")
         for item in results:
             dbgap_no, user_access = item
             return_res[dbgap_no] = user_access.privilege

peregrine/resources/submission/__init__.py

@@ -30,7 +30,7 @@ def get_open_project_ids():
             .filter(models.Project.availability_type.astext == "Open")
             .all()
         )
-    return [project['code'] for project in projects]
+        return [project['programs'][0]['name'] + '-' + project['code'] for project in projects]
 
 
 def set_read_access_projects():

peregrine/resources/submission/graphql/counts.py

@@ -58,14 +58,14 @@ def _queries():
             Query.schema(
                 args=ns.NodeSubclassQuery.get_node_query_args(cls),
                 name=NodeCountQuery._query_name(cls),
-                type=Int,
+                type=graphene.Int,
             )
             for cls in Node.get_subclasses()
         ] + [
             Query.schema(
                 args=transaction.TransactionLogQuery._args(),
                 name="_{}_count".format(transaction.TransactionLogQuery.name),
-                type=Int,
+                type=graphene.Int,
             )
         ]