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Now able to use local keycloak instance with Qiita via Docker
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‎Images/qiita/Dockerfile‎

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@@ -34,8 +34,8 @@ RUN pip install \
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coverage
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#Clone the Qiita Repo
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RUN git clone -b master https://github.com/qiita-spots/qiita.git
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#RUN git clone -b master https://github.com/qiita-spots/qiita.git
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RUN git clone -b auth_oidc https://github.com/jlab/qiita.git
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#We need to install necessary dependencies
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#as well as some extra dependencies for psycopg2 to work
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#Configuring the Qiita Config to run inside the container
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RUN sed -i 's/BASE_URL = https:\/\/localhost:8383/BASE_URL = https:\/\/localhost:21174\//' qiita/qiita_core/support_files/config_test.cfg
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RUN sed -i 's/\/home\/runner\/work\/qiita\/qiita\//\/qiita\//' qiita/qiita_core/support_files/config_test.cfg
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#RUN sed -i 's/BASE_URL = https:\/\/localhost:8383/BASE_URL = https:\/\/localhost:21174\//' qiita/qiita_core/support_files/config_test.cfg
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#RUN sed -i 's/\/home\/runner\/work\/qiita\/qiita\//\/qiita\//' qiita/qiita_core/support_files/config_test.cfg
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COPY config_qiita_oidc.cfg .
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RUN chmod 777 config_qiita_oidc.cfg
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#Copy Bash Script to run Qiita to the container
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COPY start_qiita.sh .

‎Images/qiita/config_qiita_oidc.cfg‎

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# WARNING!!!! DO NOT MODIFY THIS FILE
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# IF YOU NEED TO PROVIDE YOUR OWN CONFIGURATION, COPY THIS FILE TO A NEW
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# LOCATION AND EDIT THE COPY
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# -----------------------------------------------------------------------------
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# Copyright (c) 2014--, The Qiita Development Team.
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#
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# Distributed under the terms of the BSD 3-clause License.
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#
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# The full license is in the file LICENSE, distributed with this software.
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# -----------------------------------------------------------------------------
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# ------------------------------ Main settings --------------------------------
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[main]
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# Change to FALSE in a production system
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TEST_ENVIRONMENT = TRUE
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# Absolute path to the directory where log files are saved. If not given, no
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# log file will be created
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LOG_DIR =
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# Whether studies require admin approval to be made available
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REQUIRE_APPROVAL = True
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# Base URL: DO NOT ADD TRAILING SLASH
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BASE_URL = https://localhost:21174
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# Download path files
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UPLOAD_DATA_DIR = /qiita/qiita_db/support_files/test_data/uploads/
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# Working directory path
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WORKING_DIR = /qiita/qiita_db/support_files/test_data/working_dir/
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# Maximum upload size (in Gb)
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MAX_UPLOAD_SIZE = 100
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# Path to the base directory where the data files are going to be stored
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BASE_DATA_DIR = /qiita/qiita_db/support_files/test_data/
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# Valid upload extension, comma separated. Empty for no uploads
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VALID_UPLOAD_EXTENSION = fastq,fastq.gz,txt,tsv,sff,fna,qual
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# The script used to start the qiita environment, if any
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# used to spawn private CLI to a cluster
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QIITA_ENV = source activate qiita
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# Script used for launching private Qiita tasks
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PRIVATE_LAUNCHER = qiita-private-launcher
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# Script used for launching plugins
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PLUGIN_LAUNCHER = qiita-plugin-launcher
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# Plugins configuration directory
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PLUGIN_DIR =
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# Webserver certificate file paths
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CERTIFICATE_FILE =
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KEY_FILE =
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# The value used to secure cookies used for user sessions. A suitable value can
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# be generated with:
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#
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# python -c "from base64 import b64encode;\
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# from uuid import uuid4;\
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# print b64encode(uuid4().bytes + uuid4().bytes)"
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COOKIE_SECRET = SECRET
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# The value used to secure JWTs for delegated permission artifact download.
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JWT_SECRET = SUPER_SECRET
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# Address a user should write to when asking for help
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HELP_EMAIL = foo@bar.com
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# The email address, Qiita sends internal notifications to a sys admin
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SYSADMIN_EMAIL = jeff@bar.com
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# ----------------------------- SMTP settings -----------------------------
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[smtp]
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# The hostname to connect to
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# Google: smtp.google.com
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HOST = localhost
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# The port to connect to the database
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# Google: 587
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PORT = 25
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# SSL needed (True or False)
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# Google: True
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SSL = False
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# The user name to connect with
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USER =
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# The user password to connect with
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PASSWORD =
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# The email to have messages sent from
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EMAIL = example@domain.com
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# ----------------------------- Redis settings --------------------------------
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[redis]
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HOST = localhost
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PORT = 7777
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PASSWORD =
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# The redis database you will use, redis has a max of 16.
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# Qiita should have its own database
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DB = 13
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# ----------------------------- Postgres settings -----------------------------
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[postgres]
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# The user name to connect to the database
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USER = postgres
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# The administrator user, which can be used to create/drop environments
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ADMIN_USER = postgres
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# The database to connect to
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DATABASE = qiita_test
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# The host where the database lives on
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HOST = localhost
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# The port to connect to the database
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PORT = 5432
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# The password to use to connect to the database
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PASSWORD = postgres
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# The postgres password for the admin_user
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ADMIN_PASSWORD = postgres
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# ----------------------------- Job Scheduler Settings -----------------------------
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[job_scheduler]
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# The email address of the submitter of jobs
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JOB_SCHEDULER_JOB_OWNER = user@somewhere.org
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# The number of seconds to wait between successive calls
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JOB_SCHEDULER__POLLING_VALUE = 15
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# Hard upper-limit on concurrently running validator jobs
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JOB_SCHEDULER_PROCESSING_QUEUE_COUNT = 2
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# ----------------------------- EBI settings -----------------------------
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[ebi]
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# The user to use when submitting to EBI
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EBI_SEQ_XFER_USER = Webin-41528
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# Password for the above user
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EBI_SEQ_XFER_PASS =
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# URL of EBI's FASP site
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EBI_SEQ_XFER_URL = webin.ebi.ac.uk
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# URL of EBI's HTTPS dropbox
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# live submission URL
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#EBI_DROPBOX_URL = https://www.ebi.ac.uk/ena/submit/drop-box/submit/
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# testing URL
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EBI_DROPBOX_URL = https://www-test.ebi.ac.uk/ena/submit/drop-box/submit/
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# The name of the sequencing center to use when doing EBI submissions
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EBI_CENTER_NAME = qiita-test
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# This string (with an underscore) will be prefixed to your EBI submission and
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# study aliases
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EBI_ORGANIZATION_PREFIX = example_organization
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# ----------------------------- VAMPS settings -----------------------------
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[vamps]
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# general info to submit to vamps
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USER = user
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PASSWORD = password
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URL = https://vamps.mbl.edu/mobe_workshop/getfile.php
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# ----------------------------- Portal settings -----------------------------
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[portal]
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# Portal the site is working under
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PORTAL = QIITA
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# Portal subdirectory
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PORTAL_DIR =
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# Full path to portal styling config file
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PORTAL_FP =
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# The center latitude of the world map, shown on the Stats map.
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# Defaults to 40.01027 (Boulder, CO, USA)
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STATS_MAP_CENTER_LATITUDE =
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# The center longitude of the world map, shown on the Stats map.
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# Defaults to -105.24827 (Boulder, CO, USA)
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STATS_MAP_CENTER_LONGITUDE =
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# ----------------------------- iframes settings ---------------------------
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[iframe]
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# The real world QIIMP will always need to be accessed with https because Qiita
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# runs on https too
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QIIMP = https://localhost:8898/
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# --------------------- External Identity Provider settings --------------------
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# user authentication happens per default within Qiita, i.e. when a user logs in,
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# the stored password hash and email address is compared against what a user
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# just provided. You might however, use an external identity provider (IdP) to
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# authenticate the user like
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# google: https://developers.google.com/identity/protocols/oauth2 or
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# github: https://docs.github.com/en/apps/oauth-apps/building-oauth-apps/authorizing-oauth-apps or
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# self hosted keycloak: https://www.keycloak.org/
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# Thus, you don't have to deal with user verification, reset passwords, ...
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# Authorization (i.e. if the authorized user is allowed to use Qiita or which
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# user level he/she gets assigned is an independent process. You can even use
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# multiple independent external identity providers!
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# Qiita currently only support the "open ID connect" protocol with the implicit flow.
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# Each identity provider comes as its own config section [oidc_foo] and needs
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# to specify the following five fields:
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#
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# Typical identity provider manage multiple "realms" and specific "clients" per realm
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# You need to contact your IdP and register Qiita as a new "client". The IdP will
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# provide you with the correct values.
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#
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# The authorization protocol requires three steps to obtain user information:
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# 1) you identify as the correct client and ask the IdP for a request code
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# You have to forward the user to the login page of your IdP. To let the IdP
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# know how to come back to Qiita, you need to provide a redirect URL
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# 2) you exchange the code for a user token
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# 3) you obtain information about the user for the obtaines user token
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# Typically, each step is implemented as a separate URL endpoint
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#
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# To activate IdP: comment out the following config section
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[oidc_localkeycloak]
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# client ID for Qiita as registered at your Identity Provider of choice
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CLIENT_ID = qiita
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# client secret to verify Qiita as the correct client. Not all IdPs require
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# a client secret!
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CLIENT_SECRET = VrZOw326Pej0mFtlHi3fFu6plQeRs1CB
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# redirect URL (end point in your Qiita instance), to which the IdP redirects
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# after user types in his/her credentials. If you don't want to change code in
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# qiita_pet/webserver.py the URL must follow the pattern:
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# base_URL/auth/login_OIDC/foo where foo is the name of this config section
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# without the oidc_ prefix!
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REDIRECT_ENDPOINT = /auth/login_OIDC/localkeycloak
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# URL for step 1: obtain code
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AUTHORIZE_URL = http://localhost:8080/realms/qiita_realm/protocol/openid-connect/auth
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# URL for step 2: obtain user token
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ACCESS_TOKEN_URL = http://localhost:8080/realms/qiita_realm/protocol/openid-connect/token
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# URL for step 3: obtain user infos
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USERINFO_URL = http://localhost:8080/realms/qiita_realm/protocol/openid-connect/userinfo
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# a speaking label for the Identity Provider. Section name is used if empty.
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LABEL = localhost

‎Images/qiita/start_qiita.sh‎

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redis-server --daemonize yes --port 7777
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redis-server --daemonize yes --port 6379
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export QIITA_CONFIG_FP="./config_qiita_oidc.cfg"
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#building the database without ontologies
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qiita-env make --no-load-ontologies
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‎README.md‎

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3. Build docker image `docker build . -f qiita/Dockerfile -t qiita`
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4. Move to folder containing compose file `cd ../..`
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5. Run docker compose `docker compose up`
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6. To stop: Run `docker compose down`
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- Use `docker compose down --volumes`if you wish to remove the database volume as well.
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6. Open `http://localhost:21174`
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7. To stop: Run `docker compose down qiita qiita-db`
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- Use `docker compose down --volumes`if you wish to remove the database volume as well.
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### IF YOU WANT TO USE LOCAL KEYCLOAK:
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1. Clone repository
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2. Run `docker compose up keycloak_web keycloakdb`
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3. Open `http://localhost:8080`, login admin pw admin
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4. Configure Qiita as a service, create a user
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5. Edit `config_qiita_oidc.cfg` to fit your local Keycloak configuration.
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6. Open a new terminal, move into Image Folder `cd Images/qiita`
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7. Build docker image `docker build . -f qiita/Dockerfile -t qiita`
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8. Move to folder containing compose file `cd ../..`
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9. Run docker compose `docker compose up qiita qiita-db`
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10. Open `http://localhost:21174`

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