Merge branch 'develop'

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.1
+current_version = 0.6.0
 commit = True
 tag = True
 

.readthedocs.yml

@@ -3,11 +3,11 @@ formats:
     - epub
     - pdf
 
-requirements_file: requirements-docs.txt
+# requirements_file: requirements_dev.txt
 
 build:
     image: latest
 
 python:
     version: 3.6
-    # setup_py_install: true
+    # pip_install: true

.vscode/settings.json

@@ -2,6 +2,7 @@
     "peacock.color": "#eaca7f",
     "workbench.colorCustomizations": {
         "activityBar.background": "#f1dcab",
+        "activityBar.activeBackground": "#f1dcab",
         "activityBar.activeBorder": "#1ba47b",
         "activityBar.foreground": "#15202b",
         "activityBar.inactiveForeground": "#15202b99",

CHANGELOG.md

@@ -0,0 +1,61 @@
+# Change Log
+
+## [Unreleased](https://github.com/belbio/bel_api/tree/HEAD)
+
+[Full Changelog](https://github.com/belbio/bel_api/compare/v0.2.0...HEAD)
+
+**Closed issues:**
+
+- Refactor term completion [\#50](https://github.com/belbio/bel_api/issues/50)
+- Medline processing [\#46](https://github.com/belbio/bel_api/issues/46)
+
+## [v0.2.0](https://github.com/belbio/bel_api/tree/v0.2.0) (2018-01-21)
+[Full Changelog](https://github.com/belbio/bel_api/compare/v0.1.2...v0.2.0)
+
+## [v0.1.2](https://github.com/belbio/bel_api/tree/v0.1.2) (2018-01-08)
+[Full Changelog](https://github.com/belbio/bel_api/compare/v0.1.1...v0.1.2)
+
+## [v0.1.1](https://github.com/belbio/bel_api/tree/v0.1.1) (2018-01-08)
+**Fixed bugs:**
+
+- nested statements [\#35](https://github.com/belbio/bel_api/issues/35)
+- Ortholog bug - bad species\_id results in 500 error [\#25](https://github.com/belbio/bel_api/issues/25)
+
+**Closed issues:**
+
+- Allow setting custom canonical/decanonical targets [\#32](https://github.com/belbio/bel_api/issues/32)
+- Evaluate 204 instead of 404 [\#29](https://github.com/belbio/bel_api/issues/29)
+- Pluralize all routes [\#28](https://github.com/belbio/bel_api/issues/28)
+- Re-work Config.py [\#27](https://github.com/belbio/bel_api/issues/27)
+- Ortholog response [\#26](https://github.com/belbio/bel_api/issues/26)
+- Evaluate adding Swagger UI to Falcon [\#24](https://github.com/belbio/bel_api/issues/24)
+- Generate semantic classes using the YAML file [\#14](https://github.com/belbio/bel_api/issues/14)
+- Swap name/abbrev in yaml file [\#13](https://github.com/belbio/bel_api/issues/13)
+- BEL-LANG pop\(\) [\#12](https://github.com/belbio/bel_api/issues/12)
+- BEL-LANG Add label to subject/object [\#11](https://github.com/belbio/bel_api/issues/11)
+- BEL-LANG Add gene mod\_func [\#10](https://github.com/belbio/bel_api/issues/10)
+- Create namespace/annotation terminology files [\#9](https://github.com/belbio/bel_api/issues/9)
+- Create gene scaffold BEL statements [\#8](https://github.com/belbio/bel_api/issues/8)
+- Create orthology BEL statements [\#7](https://github.com/belbio/bel_api/issues/7)
+- Add LIC file to project root [\#5](https://github.com/belbio/bel_api/issues/5)
+- Add py.test skeleton [\#4](https://github.com/belbio/bel_api/issues/4)
+- Create Terminology JSON Schema [\#3](https://github.com/belbio/bel_api/issues/3)
+- Create API specification [\#1](https://github.com/belbio/bel_api/issues/1)
+
+**Merged pull requests:**
+
+- Bump elasticsearch from 5.4.0 to 6.0.0 [\#34](https://github.com/belbio/bel_api/pull/34) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump python-arango from 3.11.0 to 3.12.1 [\#30](https://github.com/belbio/bel_api/pull/30) ([dependabot[bot]](https://github.com/apps/dependabot))
+- updated schemas [\#22](https://github.com/belbio/bel_api/pull/22) ([wshayes](https://github.com/wshayes))
+- Updated nanopub jsonschema [\#21](https://github.com/belbio/bel_api/pull/21) ([wshayes](https://github.com/wshayes))
+- Bump PyJWT from 1.5.2 to 1.5.3 [\#20](https://github.com/belbio/bel_api/pull/20) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump falcon from 1.1.0 to 1.3.0rc2 [\#19](https://github.com/belbio/bel_api/pull/19) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump elasticsearch from 5.1.0 to 5.4.0 [\#18](https://github.com/belbio/bel_api/pull/18) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump gunicorn from 19.6.0 to 19.7.1 [\#16](https://github.com/belbio/bel_api/pull/16) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump PyJWT from 1.4.2 to 1.5.2 [\#15](https://github.com/belbio/bel_api/pull/15) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Added py.test skeleton/instructions [\#6](https://github.com/belbio/bel_api/pull/6) ([wshayes](https://github.com/wshayes))
+- Contribution guidelines [\#2](https://github.com/belbio/bel_api/pull/2) ([wshayes](https://github.com/wshayes))
+
+
+
+\* *This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)*

DEVELOPMENT.md

@@ -1,43 +1,25 @@
 # Development Notes
 
-## Developing
+## Run development tasks
 
-After going through the setup. You will be able to edit the bel and belapi code and see
-the changes made to the docker containers immediately. The belapi code is volume mounted
-into the /app directory of the docker container. The bel code is volume mounted into the
-python 3.6 package location for the install bel package.
+In order to run in the appropriate development environment, you need to run
+the following from the top-level directory with the docker-compose.yml file.
+This bel_operations docker instance includes all of the python modules needed
+for the main bel_api instance as well as additional python development modules
+such as py.test
 
-## Setup
 
-To get started:
+    docker-compose run bel_operations
 
-    bash <(curl -s https://raw.githubusercontent.com/belbio/bel_api/master/bin/setup_dev.sh)
+This will start a docker container with a python environment setup for testing, etc.
 
-Review configuration in the .env file and the conf directory files
+You may want to add the following to your .bash_aliases file
 
-Run:
+    alias belops="docker-compose run bel_operations"
 
-    docker-compose up -d
-
-## Docker info
-
-    # Follows logs for the belapi service
-    docker-compose logs -f bb_belapi
-
-Services:
-    bb_belapi - provides BEL API endpoint
-    bb_elasticsearch - used for terminology searches/term completion
-    bb_arangodb - [graph] database for terms, orthologies, etc
-    bb_celery_worker - queue/batch processing manager
-    bb_flower - Web GUI for celery
-    bb_rabbitmq - Message broker used for queues by celery
-    bb_traefik - reverse proxy to provide access to the docker services
-
-## Misc
-
-This will start docker containers needed to run everything.
-
-To make life easier on Macs using local DNS dev domains: https://medium.com/@williamhayes/local-dev-on-docker-fun-with-dns-85ca7d701f0a
+You can now run tests inside the bel_operations instance:
 
+    ./bin/runtests
 
+The bel_operations prompt will look like `api@<container_id>:/app$`
 

VERSION

@@ -1 +1 @@
-0.5.1
+0.6.0

app/__version__.py

@@ -1,2 +1,2 @@
-__version__ = "0.5.1"
+__version__ = "0.6.0"
 __name__ = "BELBIO API"

app/common/celery.py

@@ -5,9 +5,6 @@
 
 import bel.setup_logging
 
-from structlog import get_logger
-log = get_logger()
-
 CELERY_BROKER = os.environ.get('CELERY_BROKER')
 CELERY_BACKEND = os.environ.get('CELERY_BACKEND')
 

app/common/mail.py

@@ -1,4 +1,4 @@
-import requests
+from bel.utils import http_client
 
 from bel.Config import config
 
@@ -13,6 +13,6 @@ def send_mail(mail_to: str, subject: str, msg: str, mail_from: str = config['bel
         "text": msg,
     }
 
-    request = requests.post(f"{config['bel_api']['mail']['api']}/messages", auth=('api', config['secrets']['bel_api']['mail']['api_key']), data=data)
+    request = http_client.post(f"{config['bel_api']['mail']['api']}/messages", auth=('api', config['secrets']['bel_api']['mail']['api_key']), data=data)
     return request
 

app/main.py

@@ -1,16 +1,24 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
+""" BEL API
+
+   isort:skip_file
+"""
+
 import os
 import sys
 
+import gevent.monkey
+gevent.monkey.patch_all()
+
 import bel.lang.bel_specification
 # import logging
 # import logging.config
 # # from pythonjsonlogger import jsonlogger
 import bel.setup_logging
 import falcon
-import gevent.monkey
+
 # TODO - figure out how to run logging setup and belspec once on startup rather than
 #        every time a worker is initialized (moved bel.lang.bel_specification.update_specifications to bel/__init__.py)
 import structlog
@@ -39,7 +47,9 @@
                              TermEquivalentsResource, TermResource,
                              TermsResource, TermTypesResource)
 
-gevent.monkey.patch_all()
+# import logging_tree
+# from logging_tree import printout
+# printout()
 
 
 # Setup logging

app/resources/belspec.py

@@ -10,53 +10,53 @@
 
 log = structlog.getLogger(__name__)
 
-belspec_dir = config["bel"]["lang"]["specifications"]
+belspec_dir = config['bel']['lang']['specifications']
 
 
 class BelSpecResource(object):
-    def on_get(self, req, resp, version=""):
+
+    def on_get(self, req, resp, version=''):
 
         versions = bel.lang.bel_specification.get_bel_versions()
         if version:
             if version not in versions:
-                description = f"No BEL Specification found for {version}"
-                resp.media = {"title": "No BEL Spec found", "message": description}
+                description = f'No BEL Specification found for {version}'
+                resp.media = {'title': 'No BEL Spec found', 'message': description}
                 resp.status = falcon.HTTP_404
 
-            version_underscores = version.replace(".", "_")
-            fn = f"{belspec_dir}/bel_v{version_underscores}.yaml"
-            with open(fn, "r") as f:
-                belspec = yaml.load(f, Loader=yaml.SafeLoader)
+            version_underscores = version.replace('.', '_')
+            fn = f'{belspec_dir}/bel_v{version_underscores}.yaml'
+            with open(fn, 'r') as f:
+                belspec = yaml.load(f)
 
-            resp.media = {"belspec": belspec, "versions": versions}
+            resp.media = {'belspec': belspec, 'versions': versions}
             resp.status = falcon.HTTP_200
         else:
-            resp.media = {"versions": versions}
+            resp.media = {'versions': versions}
             resp.status = falcon.HTTP_200
 
     def on_put(self, req, resp):
         """Save BEL Spec onto server"""
 
-        force = req.get_param("force", False)
-        belspec = req.media["belspec"]
-        fn_version = belspec["version"].replace(".", "_")
+        belspec = req.media['belspec']
+        fn_version = belspec['version'].replace('.', '_')
 
-        fn = f"{belspec_dir}/bel_v{fn_version}.yaml"
-        with open(fn, "w") as f:
+        fn = f'{belspec_dir}/bel_v{fn_version}.yaml'
+        with open(fn, 'w') as f:
             yaml.dump(belspec, f, indent=2)
 
-        bel.lang.bel_specification.update_specifications(force=force)
+        bel.lang.bel_specification.update_specifications()
 
         resp.status = falcon.HTTP_204
 
     def on_delete(self, req, resp, version):
         """Delete version on server"""
 
-        fn_version = version.replace(".", "_")
-        yaml_fn = f"{belspec_dir}/bel_v{fn_version}.yaml"
-        json_fn = f"{belspec_dir}/bel_v{fn_version}.json"
-        ebnf_fn = f"{belspec_dir}/bel_v{fn_version}.ebnf"
-        parser_fn = f"{belspec_dir}/bel_v{fn_version}_parser.py"
+        fn_version = version.replace('.', '_')
+        yaml_fn = f'{belspec_dir}/bel_v{fn_version}.yaml'
+        json_fn = f'{belspec_dir}/bel_v{fn_version}.json'
+        ebnf_fn = f'{belspec_dir}/bel_v{fn_version}.ebnf'
+        parser_fn = f'{belspec_dir}/bel_v{fn_version}_parser.py'
 
         if os.path.exists(yaml_fn):
             os.remove(yaml_fn)
@@ -68,14 +68,15 @@ def on_delete(self, req, resp, version):
             os.remove(parser_fn)
 
         # Update versions file
-        version_fn = f"{belspec_dir}/versions.json"
-        with open(version_fn, "r") as f:
+        version_fn = f'{belspec_dir}/versions.json'
+        with open(version_fn, 'r') as f:
             versions = json.load(f)
 
         versions = [v for v in versions if v != version]
 
-        with open(version_fn, "w") as f:
+        with open(version_fn, 'w') as f:
             json.dump(versions, f, indent=4)
 
         resp.status = falcon.HTTP_200
-        resp.media = {"versions": versions}
+        resp.media = {'versions': versions}
+