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Changes to be committed: modified: README.md new file: docs/dockerDeployment.md new file: docs/faq.md new file: docs/localDeployment.md new file: docs/productionDeployment.md
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‎README.md‎

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@@ -12,126 +12,6 @@ The service definitions are for deployment on a server exposed ot the internet.
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- [Docker deployment](docs/dockerDeployment.md) [WIP]
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- [FAQ and trouble shooting](docs/faq.md)
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Clone the repository
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git clone https://github.com/biocompute-objects/bco_api
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cd bco_api
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Make sure you are on the desired branch (Check for latest branch):
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git switch 22.05
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Enter the repository, create a virtual environment, and install the required packages
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pyenv local 3.10.6
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python3 -m venv env
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source env/bin/activate
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python -m pip install -r requirements.txt
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(You can use python3.9 if you’d like, but since you’re in the virtual environment you created python points to python3.9)
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Modify the Config files:
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Check/Edit the server.conf file
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This is the main server configuration file for the BCO API. (most of these values will NOT need to be changed for local deployment)
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vim bco_api/bco_api/server.conf
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Production and publishing flags NOTE: Valid values are True or False (note the capitalization).
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[PRODUCTION]
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production=False
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DB Version
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[VERSION]
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version=22.01
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Is this a publish-only server?
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[PUBLISHONLY]
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publishonly=False
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Security settings: Create a key for an anonymous public user.
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[KEYS]
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anon=627626823549f787c3ec763ff687169206626149
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Which host names do you want to associate with the server? Note: the local hostname (i.e. 127.0.0.1) should come at the end.
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[HOSTNAMES]
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prod_names=test.portal.biochemistry.gwu.edu,127.0.0.1
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names=127.0.0.1:8000,127.0.0.1
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Give the human-readable hostnames
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[HRHOSTNAME]
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hrnames=BCO Server (Default)
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The public hostname of the server (i.e. the one to make requests to)
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[PUBLICHOSTNAME]
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prod_name=https://test.portal.biochemistry.gwu.edu
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name=http://127.0.0.1:8000
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Who gets to make requests?
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[REQUESTS_FROM]
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portal=https://test.portal.biochemistry.gwu.edu
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local_development_portal=http://127.0.0.1:3000,http://localhost:3000
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public=true
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Namings: How do you want to name your objects?
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[OBJECT_NAMING]
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prod_root_uri=https://test.portal.biochemistry.gwu.edu
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root_uri=http://127.0.0.1:8000
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prod_uri_regex=root_uri/prefix_(\d+)/(\d+).(\d+)
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uri_regex=root_uri/prefix_(\d+)/(\d+).(\d+)
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**Requests ** Where are the request templates defined?
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[REQUESTS]
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folder=../api/request_definitions/
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Where are the validation templates defined?
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[VALIDATIONS]
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folder=../api/validation_definitions/
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Set up DB
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cd bco_api/bco_api
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Option #1: Use existing DB
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Copy the dev db
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cp ../admin_only/db.sqlite3.dev db.sqlite3
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superusername: bco_api_user
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password: testing123
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Make Migrations
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python3 manage.py migrate
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Option #2: Create a new DB
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Make Migrations
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python3 manage.py migrate
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Create a super user for the API:
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python3 manage.py createsuperuser
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Then follow the prompts
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Then: Do a quick check to make sure the server can run
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Start the server
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python3 manage.py runserver 8000
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Make sure API is accessible via web browser.
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[YOU WEB HOST HERE]/api/admin/
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EX: http://localhost:8000/api/admin/
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If it worked you should be able to login using the SuperUser credentials you created above
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Log in with the superuser credentials you created or imported
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If you copied over the existing dbs you should be able to log in with any of the crednetials listed in /portal_userdb/server/admin/users.tsv
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Otherwise you will have to register a new user.
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## Issues and BCODB Development

‎docs/dockerDeployment.md‎

Whitespace-only changes.

‎docs/faq.md‎

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‎docs/localDeployment.md‎

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# BCODB Local Deployment
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## Clone the repository
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```
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git clone https://github.com/biocompute-objects/bco_api
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```
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**Make sure you are on the desired branch (Check for latest branch):**
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```
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git switch [DESIRED BRANCH TAG]
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```
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## Enter the repository, create a virtual environment, and install the required packages
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```
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cd bco_api
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pyenv local 3.10.6
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python3 -m venv env
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source env/bin/activate
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python -m pip install -r requirements.txt
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```
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(You can use python3 if you’d like, but since you’re in the virtual environment you created python points to python3.10.6)
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## Modify the Config files:
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Check/Edit the server.conf file
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This is the main server configuration file for the BCO API. (most of these values will NOT need to be changed for local deployment)
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vim bco_api/bco_api/server.conf
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Production and publishing flags NOTE: Valid values are True or False (note the capitalization).
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[PRODUCTION]
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production=False
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DB Version
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[VERSION]
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version=22.01
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Is this a publish-only server?
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[PUBLISHONLY]
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publishonly=False
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Security settings: Create a key for an anonymous public user.
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[KEYS]
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anon=627626823549f787c3ec763ff687169206626149
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Which host names do you want to associate with the server? Note: the local hostname (i.e. 127.0.0.1) should come at the end.
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[HOSTNAMES]
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prod_names=test.portal.biochemistry.gwu.edu,127.0.0.1
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names=127.0.0.1:8000,127.0.0.1
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Give the human-readable hostnames
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[HRHOSTNAME]
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hrnames=BCO Server (Default)
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The public hostname of the server (i.e. the one to make requests to)
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[PUBLICHOSTNAME]
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prod_name=https://test.portal.biochemistry.gwu.edu
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name=http://127.0.0.1:8000
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Who gets to make requests?
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[REQUESTS_FROM]
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portal=https://test.portal.biochemistry.gwu.edu
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local_development_portal=http://127.0.0.1:3000,http://localhost:3000
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public=true
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Namings: How do you want to name your objects?
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[OBJECT_NAMING]
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prod_root_uri=https://test.portal.biochemistry.gwu.edu
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root_uri=http://127.0.0.1:8000
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prod_uri_regex=root_uri/prefix_(\d+)/(\d+).(\d+)
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uri_regex=root_uri/prefix_(\d+)/(\d+).(\d+)
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**Requests ** Where are the request templates defined?
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[REQUESTS]
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folder=../api/request_definitions/
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Where are the validation templates defined?
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[VALIDATIONS]
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folder=../api/validation_definitions/
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Set up DB
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cd bco_api/bco_api
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Option #1: Use existing DB
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Copy the dev db
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cp ../admin_only/db.sqlite3.dev db.sqlite3
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superusername: bco_api_user
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password: testing123
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Make Migrations
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python3 manage.py migrate
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Option #2: Create a new DB
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Make Migrations
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python3 manage.py migrate
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Create a super user for the API:
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python3 manage.py createsuperuser
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Then follow the prompts
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Then: Do a quick check to make sure the server can run
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Start the server
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python3 manage.py runserver 8000
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Make sure API is accessible via web browser.
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[YOU WEB HOST HERE]/api/admin/
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EX: http://localhost:8000/api/admin/
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If it worked you should be able to login using the SuperUser credentials you created above
123+
124+
Log in with the superuser credentials you created or imported
125+
126+
If you copied over the existing dbs you should be able to log in with any of the crednetials listed in /portal_userdb/server/admin/users.tsv
127+
128+
Otherwise you will have to register a new user.

‎docs/productionDeployment.md‎

Whitespace-only changes.

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