Add DSpace submit functionality

Why these changes are being introduced:
The core functionality of this app is to create new items with associated bitstreams in DSpace based on the messages retrieved from an input SQS queue. This commit adds the functionality to do so, along with some necessary functionality around configuration and secrets handling.

How this addresses that need:
* Adds a submission module with a Submission class that can be
  instantiated from an SQS message, with methods to facilitate creating
  a DSpace item with bitstreams and generating both success and error
  result messages
* Updates the sqs module process function to use the new submission
  module
* Adds an smm module with an SSM class that handles retrieving secrets
  from AWS Systems Manager Parameter Store
* Adds a config module that configures the application based on env
  (set by the WORKSPACE env variable)
* Adds and updates relevant tests, including adding a conftest.py and
  fixtures
* Updates Dockerfile and setup.py to reflect new dependencies

Additional changes in this commit:
* Adds logging throughout the app with logging configuration set by the
  root logger
* Adds pytest-cov and updates make test command to create a coverage
  report
* Updates .gitignore

Side effects of this change:
* For the app to work in staging and production environments, the
  WORKSPACE and SSM_PATH env variables must be set and the application
  must have an IAM role with access to SSM. This has been handled in a
  separate ticket, just noting it here (also added this info to the
  README).

Relevant ticket(s):
* https://mitlibraries.atlassian.net/browse/ETD-398
* https://mitlibraries.atlassian.net/browse/ETD-407

.gitignore

@@ -127,3 +127,5 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+.DS_Store

Dockerfile

@@ -9,6 +9,8 @@ ENV PIP_NO_CACHE_DIR yes
 WORKDIR /app
 RUN pip install --no-cache-dir --upgrade pip pipenv
 
+RUN apt-get update && apt-get upgrade -y && apt-get install -y git
+
 COPY Pipfile* /
 RUN pipenv install --system --clear --deploy
 

Makefile

@@ -39,7 +39,7 @@ isort: ## isort your imports, so you don't have to
 	pipenv run isort . --diff
 
 test: ## runs pytest
-	pipenv run pytest
+	pipenv run pytest --cov=submitter
 
 coveralls: test
 	pipenv run coveralls

Pipfile

@@ -6,6 +6,8 @@ name = "pypi"
 [packages]
 click = "*"
 boto3 = "*"
+smart-open = "*"
+dspace-python-client = {ref = "0.1.0", git = "https://github.com/mitlibraries/dspace-python-client.git"}
 
 [dev-packages]
 flake8 = "*"
@@ -15,6 +17,9 @@ bandit = "*"
 moto = {extras = ["s3", "sqs"], version = "*"}
 pytest = "*"
 coveralls = "*"
+requests-mock = "*"
+pytest-cov = "*"
+pytest-env = "*"
 
 [requires]
 python_version = "3.9"

README.md

@@ -37,4 +37,4 @@ make dist
 docker run submitter:latest --
 ```
 
-note: the application requires being run in an environment with Roles based access to the AWS resources.
+note: the application requires being run in an environment with Roles based access to the AWS resources. in addition, the environment must have WORKSPACE and SSM_PATH variables set according to stage and prod conventions.