spiritumduo / spiritumduo Goto Github PK
View Code? Open in Web Editor NEWImproving clinical pathways in an open source and modular fashion
License: MIT License
Improving clinical pathways in an open source and modular fashion
License: MIT License
return
to use the defaults to see what happened ....env
file would be gooddocker
containers built.return
to use the defaults to see what happened ...prod
build of the script I would parse the email entry and ensure only a valid email address was supplied.env
file does not work AND saying "no" does not work either! (at base).env
files in the other locations doesn't work either, but you can successfully say "No" this time.docker
containers built.return
to use the defaults to see what happened ...yarn
port is blocked which prevents a successful build ...sd-postgres
password authentication failing), 10 (a consequence of 8?)git
, docker
& docker-compose
installednginx
.env
file ... Eg. 6. nginx/.env.example
at the top of the section. The description is covered later.node
modulesvpn
and I had an issue resolving https://registry.yarnpkg.com/. It manifested with this error:Step 4/5 : RUN yarn install --development --silent
---> Running in e87d9f47b409
warning Pattern ["@apollo/client@latest"] is trying to unpack in the same destination "/usr/local/share/.cache/yarn/v6/npm-@apollo-client-3.5.5-ce331403ee5f099e595430890f9b510c8435c932-integrity/node_modules/@apollo/client" as pattern ["@apollo/client@>=2.0.0"]. This could result in non-deterministic behavior, skipping.
error An unexpected error occurred: "https://registry.yarnpkg.com/babel-loader/-/babel-loader-8.1.0.tgz: getaddrinfo ENOTFOUND registry.yarnpkg.com".
The command '/bin/sh -c yarn install --development --silent' returned a non-zero code: 1
Unable to find image 'sd-frontend:latest' locally
docker: Error response from daemon: pull access denied for sd-frontend, repository does not exist or may require 'docker login': denied: requested access to the resource is denied.
See 'docker run --help'.
vpn
it ran fine BUT a log of warnings, which might be concerning. [If you could fix the errors good, but I suspect resolving the dependencies is nigh on impossible ...docker-compose.dev.yml
docker-compose.dev.yml
file from the docker-compose-dev.yml.example
file. See below. (Or I was confused. Could be both. I note it because I experienced it ...)docker-compose -f docker-compose.dev.yml up -d --build
created an error. To address need to say at the beginning to copy and rename docker-compose.dev.yml.example
to docker-compose.dev.yml
. E.g.docker-compose
file by running: cp docker-compose.dev.yml.example docker-compose.dev.yml
NB Reviewing the instructions again I see that this step was covered in Configure docker-compose.dev.yml
section. So, for whatever reason I missed it which could mean a bunch of things -- like it was late and I am tired and/or the documentation could be clearer.
Had an initial failure because there had been no instruction to create a .env
file in the nginx
section.
docker exec -ti sd-backend bash -c "chmod +x ./bin/container-migrate-alembic && ./bin/container-migrate-alembic"
and
docker exec -ti sd-pseudotie bash -c "chmod +x ./bin/container-migrate-alembic && ./bin/container-migrate-alembic"
Still get an error that database does not exist. I note that there is an instruction that the containers need to be running before the database can be migrated, without instructions as to get them running. I believe that this would be a good idea, or some instruction as to check that they are.
Furthermore, the containers are running so not sure what is going on, and there is a reboot-loop for the sd-nginx-dev
container, so there is an issue there. i.e. it keeps restarting.
Error reproduced below:
docker exec -ti sd-backend bash -c "chmod +x ./bin/container-migrate-alembic && ./bin/container-migrate-alembic"
/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/base.py:299: SAWarning: Can't validate argument 'native_enum'; can't locate any SQLAlchemy dialect named 'native'
util.warn(
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2336, in _wrap_pool_connect
return fn()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 304, in unique_connection
return _ConnectionFairy._checkout(self)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 778, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 495, in checkout
rec = pool._do_get()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/impl.py", line 241, in _do_get
return self._create_connection()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 309, in _create_connection
return _ConnectionRecord(self)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 440, in __init__
self.__connect(first_connect_check=True)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 661, in __connect
pool.logger.debug("Error on connect(): %s", e)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
compat.raise_(
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
raise exception
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 656, in __connect
connection = pool._invoke_creator(self)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/strategies.py", line 114, in connect
return dialect.connect(*cargs, **cparams)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 508, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/usr/local/lib/python3.9/site-packages/psycopg2/__init__.py", line 122, in connect
conn = _connect(dsn, connection_factory=connection_factory, **kwasync)
psycopg2.OperationalError: FATAL: database "spiritum_duo" does not exist
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/bin/alembic", line 8, in <module>
sys.exit(main())
File "/usr/local/lib/python3.9/site-packages/alembic/config.py", line 588, in main
CommandLine(prog=prog).main(argv=argv)
File "/usr/local/lib/python3.9/site-packages/alembic/config.py", line 582, in main
self.run_cmd(cfg, options)
File "/usr/local/lib/python3.9/site-packages/alembic/config.py", line 559, in run_cmd
fn(
File "/usr/local/lib/python3.9/site-packages/alembic/command.py", line 227, in revision
script_directory.run_env()
File "/usr/local/lib/python3.9/site-packages/alembic/script/base.py", line 563, in run_env
util.load_python_file(self.dir, "env.py")
File "/usr/local/lib/python3.9/site-packages/alembic/util/pyfiles.py", line 92, in load_python_file
module = load_module_py(module_id, path)
File "/usr/local/lib/python3.9/site-packages/alembic/util/pyfiles.py", line 108, in load_module_py
spec.loader.exec_module(module) # type: ignore
File "<frozen importlib._bootstrap_external>", line 850, in exec_module
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
File "alembic/env.py", line 89, in <module>
run_migrations_online()
File "alembic/env.py", line 77, in run_migrations_online
with connectable.connect() as connection:
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2263, in connect
return self._connection_cls(self, **kwargs)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 104, in __init__
else engine.raw_connection()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2369, in raw_connection
return self._wrap_pool_connect(
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2339, in _wrap_pool_connect
Connection._handle_dbapi_exception_noconnection(
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1583, in _handle_dbapi_exception_noconnection
util.raise_(
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
raise exception
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2336, in _wrap_pool_connect
return fn()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 304, in unique_connection
return _ConnectionFairy._checkout(self)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 778, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 495, in checkout
rec = pool._do_get()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/impl.py", line 241, in _do_get
return self._create_connection()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 309, in _create_connection
return _ConnectionRecord(self)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 440, in __init__
self.__connect(first_connect_check=True)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 661, in __connect
pool.logger.debug("Error on connect(): %s", e)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
compat.raise_(
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
raise exception
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 656, in __connect
connection = pool._invoke_creator(self)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/strategies.py", line 114, in connect
return dialect.connect(*cargs, **cparams)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 508, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/usr/local/lib/python3.9/site-packages/psycopg2/__init__.py", line 122, in connect
conn = _connect(dsn, connection_factory=connection_factory, **kwasync)
sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) FATAL: database "spiritum_duo" does not exist
(Background on this error at: http://sqlalche.me/e/13/e3q8)
/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/base.py:299: SAWarning: Can't validate argument 'native_enum'; can't locate any SQLAlchemy dialect named 'native'
util.warn(
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2336, in _wrap_pool_connect
return fn()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 304, in unique_connection
return _ConnectionFairy._checkout(self)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 778, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 495, in checkout
rec = pool._do_get()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/impl.py", line 241, in _do_get
return self._create_connection()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 309, in _create_connection
return _ConnectionRecord(self)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 440, in __init__
self.__connect(first_connect_check=True)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 661, in __connect
pool.logger.debug("Error on connect(): %s", e)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
compat.raise_(
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
raise exception
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 656, in __connect
connection = pool._invoke_creator(self)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/strategies.py", line 114, in connect
return dialect.connect(*cargs, **cparams)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 508, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/usr/local/lib/python3.9/site-packages/psycopg2/__init__.py", line 122, in connect
conn = _connect(dsn, connection_factory=connection_factory, **kwasync)
psycopg2.OperationalError: FATAL: database "spiritum_duo" does not exist
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/bin/alembic", line 8, in <module>
sys.exit(main())
File "/usr/local/lib/python3.9/site-packages/alembic/config.py", line 588, in main
CommandLine(prog=prog).main(argv=argv)
File "/usr/local/lib/python3.9/site-packages/alembic/config.py", line 582, in main
self.run_cmd(cfg, options)
File "/usr/local/lib/python3.9/site-packages/alembic/config.py", line 559, in run_cmd
fn(
File "/usr/local/lib/python3.9/site-packages/alembic/command.py", line 320, in upgrade
script.run_env()
File "/usr/local/lib/python3.9/site-packages/alembic/script/base.py", line 563, in run_env
util.load_python_file(self.dir, "env.py")
File "/usr/local/lib/python3.9/site-packages/alembic/util/pyfiles.py", line 92, in load_python_file
module = load_module_py(module_id, path)
File "/usr/local/lib/python3.9/site-packages/alembic/util/pyfiles.py", line 108, in load_module_py
spec.loader.exec_module(module) # type: ignore
File "<frozen importlib._bootstrap_external>", line 850, in exec_module
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
File "alembic/env.py", line 89, in <module>
run_migrations_online()
File "alembic/env.py", line 77, in run_migrations_online
with connectable.connect() as connection:
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2263, in connect
return self._connection_cls(self, **kwargs)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 104, in __init__
else engine.raw_connection()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2369, in raw_connection
return self._wrap_pool_connect(
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2339, in _wrap_pool_connect
Connection._handle_dbapi_exception_noconnection(
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1583, in _handle_dbapi_exception_noconnection
util.raise_(
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
raise exception
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2336, in _wrap_pool_connect
return fn()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 304, in unique_connection
return _ConnectionFairy._checkout(self)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 778, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 495, in checkout
rec = pool._do_get()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/impl.py", line 241, in _do_get
return self._create_connection()
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 309, in _create_connection
return _ConnectionRecord(self)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 440, in __init__
self.__connect(first_connect_check=True)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 661, in __connect
pool.logger.debug("Error on connect(): %s", e)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
compat.raise_(
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
raise exception
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 656, in __connect
connection = pool._invoke_creator(self)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/strategies.py", line 114, in connect
return dialect.connect(*cargs, **cparams)
File "/usr/local/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 508, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/usr/local/lib/python3.9/site-packages/psycopg2/__init__.py", line 122, in connect
conn = _connect(dsn, connection_factory=connection_factory, **kwasync)
sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) FATAL: database "spiritum_duo" does not exist
(Background on this error at: http://sqlalche.me/e/13/e3q8)
install.md
install.md
does not pass markdownlint
on VSCode
. LOTS of errors.## Overview //TODO @jcf54 can you check that this section is corrent?
Line 3 in ed0adf0
Line 21 in da2391b
Line 22 in 1352d15
test
//TODO @jcf54 What would this be for Windows and Linux
Line 22 in ed0adf0
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We are working to build community through open source technology. NB: members must have two-factor auth.
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