Merge pull request #3 from tagbase/timezone_fix

Fix issue with Timzone and update from Swagger 2.0 to OpenAPI 3.0.0

.dockerignore

@@ -1,5 +1,5 @@
 .travis.yaml
-.swagger-codegen-ignore
+.openapi-generator-ignore
 README.md
 tox.ini
 git_push.sh

.gitignore

@@ -62,5 +62,3 @@ target/
 
 #Ipython Notebook
 .ipynb_checkpoints
-
-tagbase.log*

.openapi-generator/VERSION

@@ -0,0 +1 @@
+4.0.1

Dockerfile

@@ -19,4 +19,4 @@ EXPOSE 5433
 
 ENTRYPOINT ["python3"]
 
-CMD ["-m", "swagger_server"]
+CMD ["-m", "openapi_server"]

Dockerfile-tagbase

@@ -6,11 +6,16 @@ WORKDIR /usr/src/app
 COPY requirements.txt /usr/src/app/
 
 RUN apk update && \
+ apk upgrade && \
  apk add bash postgresql-libs && \
+ apk add --update tzdata && \
  apk add --virtual .build-deps gcc musl-dev postgresql-dev && \
  python3 -m pip install -r requirements.txt --no-cache-dir && \
  apk --purge del .build-deps
 
+RUN ln -fs /usr/share/zoneinfo/Etc/UTC /etc/localtime 
+#&& \ dpkg-reconfigure -f noninteractive tzdata
+
 RUN pip3 install --no-cache-dir -r requirements.txt
 
 COPY . /usr/src/app
@@ -19,4 +24,4 @@ EXPOSE 5433
 
 ENTRYPOINT ["python3"]
 
-CMD ["-m", "swagger_server"]
+CMD ["-m", "openapi_server"]

README.md

@@ -3,7 +3,8 @@
 ## Overview
 
 Tagbase is a [Flask](http://flask.pocoo.org/) application which provides HTTP endpoints for ingestion of 
-various files into the Tagbase SQL database.
+various files into the Tagbase SQL database. This project was autogenerated from the OpenAPI v3 specification
+which can be found at **openapi_server/openapi/openapi.yaml**
 
 
 ## Running with Docker
@@ -68,23 +69,23 @@ You will see the services graciously shutdown.
 
 **N.B.** The URI's below may alternate between ***localhost*** and ***0.0.0.0*** depending on whether your workstation is Windows (localhost) or Linux/Mac (0.0.0.0)
 
-Navigate to [http://localhost:5433/v1/tagbase/ui/](http://0.0.0.0:5433/v1/tagbase/ui/) 
+Navigate to [http://localhost:5433/v2/tagbase/ui/](http://0.0.0.0:5433/v2/tagbase/ui/) 
 to see the tagbase-server UI running. 
 **It will really help for you to read the API documentation provided in the Web Application.**
-Using the [eTUFF API](http://0.0.0.0:5433/v1/tagbase/ui/#!/Products/ingest_etuff_get), 
+Using the [eTUFF API](http://0.0.0.0:5433/v2/tagbase/ui/#!/Products/ingest_etuff_get), 
 you can execute the following commands to initiate a primitive test
 ingestion of some sample eTUFF-sailfish-117259.txt data present on the server.
 
 using curl...
 
 ```bash
-curl -X GET --header 'Accept: application/json' 'http://0.0.0.0:5433/v1/tagbase/ingest/etuff?granule_id=1234&file=file%3A%2F%2F%2Fusr%2Fsrc%2Fapp%2Fdata%2FeTUFF-sailfish-117259.txt'
+curl -X GET --header 'Accept: application/json' 'http://0.0.0.0:5433/v2/tagbase/ingest/etuff?granule_id=1234&file=file%3A%2F%2F%2Fusr%2Fsrc%2Fapp%2Fdata%2FeTUFF-sailfish-117259.txt'
 ```
 
 ...or using a Request URL
 
 ```bash
-http://0.0.0.0:5433/v1/tagbase/ingest/etuff?granule_id=1234&file=file%3A%2F%2F%2Fusr%2Fsrc%2Fapp%2Fdata%2FeTUFF-sailfish-117259.txt
+http://0.0.0.0:5433/v2/tagbase/ingest/etuff?granule_id=1234&file=file%3A%2F%2F%2Fusr%2Fsrc%2Fapp%2Fdata%2FeTUFF-sailfish-117259.txt
 ```
 
 **N.B.** The REST server is capable of ingesting data from many sources e.g. file, ftp, http and https.

git_push.sh

@@ -0,0 +1,52 @@
+#!/bin/sh
+# ref: https://help.github.com/articles/adding-an-existing-project-to-github-using-the-command-line/
+#
+# Usage example: /bin/sh ./git_push.sh wing328 openapi-pestore-perl "minor update"
+
+git_user_id=$1
+git_repo_id=$2
+release_note=$3
+
+if [ "$git_user_id" = "" ]; then
+    git_user_id="GIT_USER_ID"
+    echo "[INFO] No command line input provided. Set \$git_user_id to $git_user_id"
+fi
+
+if [ "$git_repo_id" = "" ]; then
+    git_repo_id="GIT_REPO_ID"
+    echo "[INFO] No command line input provided. Set \$git_repo_id to $git_repo_id"
+fi
+
+if [ "$release_note" = "" ]; then
+    release_note="Minor update"
+    echo "[INFO] No command line input provided. Set \$release_note to $release_note"
+fi
+
+# Initialize the local directory as a Git repository
+git init
+
+# Adds the files in the local repository and stages them for commit.
+git add .
+
+# Commits the tracked changes and prepares them to be pushed to a remote repository.
+git commit -m "$release_note"
+
+# Sets the new remote
+git_remote=`git remote`
+if [ "$git_remote" = "" ]; then # git remote not defined
+
+    if [ "$GIT_TOKEN" = "" ]; then
+        echo "[INFO] \$GIT_TOKEN (environment variable) is not set. Using the git credential in your environment."
+        git remote add origin https://github.com/${git_user_id}/${git_repo_id}.git
+    else
+        git remote add origin https://${git_user_id}:${GIT_TOKEN}@github.com/${git_user_id}/${git_repo_id}.git
+    fi
+
+fi
+
+git pull origin master
+
+# Pushes (Forces) the changes in the local repository up to the remote repository
+echo "Git pushing to https://github.com/${git_user_id}/${git_repo_id}.git"
+git push origin master 2>&1 | grep -v 'To https'
+

swagger_server/__main__.py → openapi_server/__main__.py

@@ -6,7 +6,7 @@
 #from flask_swagger_ui import get_swaggerui_blueprint
 from logging.handlers import RotatingFileHandler
 from logging import Formatter
-from swagger_server import encoder
+from openapi_server import encoder
 
 def main():
     handler = RotatingFileHandler('tagbase.log', maxBytes=10000, backupCount=10)
@@ -18,9 +18,9 @@ def main():
 
     logger = logging.getLogger('werkzeug')
     logger.addHandler(handler)
-    app = connexion.FlaskApp(__name__, specification_dir='./swagger/')
+    app = connexion.FlaskApp(__name__, specification_dir='./openapi/')
     app.app.json_encoder = encoder.JSONEncoder
-    app.add_api('swagger.yaml', arguments={'title': 'Tagbase API'})
+    app.add_api('openapi.yaml', arguments={'title': 'Tagbase API'})
 
     ## Uncomment the following code if you wish the swagger ui to be available at
     ## http://localhost:5433/api/docs/

swagger_server/controllers/products_controller.py → openapi_server/controllers/products_controller.py

@@ -8,9 +8,9 @@
 from time import time
 from tzlocal import get_localzone
 
-from swagger_server.models.error import Error
-from swagger_server.models.success import Success
-from swagger_server import util
+from openapi_server.models.error import Error  # noqa: E501
+from openapi_server.models.success import Success  # noqa: E501
+from openapi_server import util
 
 # Needed Python 2/3 urllib compatability
 try:
@@ -22,7 +22,6 @@
 
 from werkzeug.exceptions import InternalServerError
 
-
 def ingest_etuff_get(granule_id, file):
     """Get eTUFF file and execute ingestion.
 

openapi_server/controllers/security_controller_.py

@@ -0,0 +1,3 @@
+from typing import List
+
+

swagger_server/encoder.py → openapi_server/encoder.py

@@ -1,7 +1,7 @@
 from connexion.apps.flask_app import FlaskJSONEncoder
 import six
 
-from swagger_server.models.base_model_ import Model
+from openapi_server.models.base_model_ import Model
 
 
 class JSONEncoder(FlaskJSONEncoder):
@@ -10,7 +10,7 @@ class JSONEncoder(FlaskJSONEncoder):
     def default(self, o):
         if isinstance(o, Model):
             dikt = {}
-            for attr, _ in six.iteritems(o.swagger_types):
+            for attr, _ in six.iteritems(o.openapi_types):
                 value = getattr(o, attr)
                 if value is None and not self.include_nulls:
                     continue

swagger_server/models/__init__.py → openapi_server/models/__init__.py

@@ -3,5 +3,5 @@
 # flake8: noqa
 from __future__ import absolute_import
 # import models into model package
-from swagger_server.models.error import Error
-from swagger_server.models.success import Success
+from openapi_server.models.error import Error
+from openapi_server.models.success import Success

swagger_server/models/base_model_.py → openapi_server/models/base_model_.py

@@ -3,15 +3,15 @@
 import six
 import typing
 
-from swagger_server import util
+from openapi_server import util
 
 T = typing.TypeVar('T')
 
 
 class Model(object):
-    # swaggerTypes: The key is attribute name and the
+    # openapiTypes: The key is attribute name and the
     # value is attribute type.
-    swagger_types = {}
+    openapi_types = {}
 
     # attributeMap: The key is attribute name and the
     # value is json key in definition.
@@ -29,7 +29,7 @@ def to_dict(self):
         """
         result = {}
 
-        for attr, _ in six.iteritems(self.swagger_types):
+        for attr, _ in six.iteritems(self.openapi_types):
             value = getattr(self, attr)
             if isinstance(value, list):
                 result[attr] = list(map(

swagger_server/models/error.py → openapi_server/models/error.py

@@ -5,18 +5,18 @@
 
 from typing import List, Dict  # noqa: F401
 
-from swagger_server.models.base_model_ import Model
-from swagger_server import util
+from openapi_server.models.base_model_ import Model
+from openapi_server import util
 
 
 class Error(Model):
-    """NOTE: This class is auto generated by the swagger code generator program.
+    """NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
 
     Do not edit the class manually.
     """
 
-    def __init__(self, code: int=None, message: str=None, fields: str=None):  # noqa: E501
-        """Error - a model defined in Swagger
+    def __init__(self, code=None, message=None, fields=None):  # noqa: E501
+        """Error - a model defined in OpenAPI
 
         :param code: The code of this Error.  # noqa: E501
         :type code: int
@@ -25,7 +25,7 @@ def __init__(self, code: int=None, message: str=None, fields: str=None):  # noqa
         :param fields: The fields of this Error.  # noqa: E501
         :type fields: str
         """
-        self.swagger_types = {
+        self.openapi_types = {
             'code': int,
             'message': str,
             'fields': str
@@ -53,7 +53,7 @@ def from_dict(cls, dikt) -> 'Error':
         return util.deserialize_model(dikt, cls)
 
     @property
-    def code(self) -> int:
+    def code(self):
         """Gets the code of this Error.
 
 
@@ -63,7 +63,7 @@ def code(self) -> int:
         return self._code
 
     @code.setter
-    def code(self, code: int):
+    def code(self, code):
         """Sets the code of this Error.
 
 
@@ -74,7 +74,7 @@ def code(self, code: int):
         self._code = code
 
     @property
-    def message(self) -> str:
+    def message(self):
         """Gets the message of this Error.
 
 
@@ -84,7 +84,7 @@ def message(self) -> str:
         return self._message
 
     @message.setter
-    def message(self, message: str):
+    def message(self, message):
         """Sets the message of this Error.
 
 
@@ -95,7 +95,7 @@ def message(self, message: str):
         self._message = message
 
     @property
-    def fields(self) -> str:
+    def fields(self):
         """Gets the fields of this Error.
 
 
@@ -105,7 +105,7 @@ def fields(self) -> str:
         return self._fields
 
     @fields.setter
-    def fields(self, fields: str):
+    def fields(self, fields):
         """Sets the fields of this Error.