Compound Data Tool is a fancy and useful CLI application which allows you to:
- download summary information about compounds from open API resources
- show the summary information in a fancy way from the local storage
Common user use-case starting with the actualizing procedure. When the user wants to actualize local compound information from the Open Public API. For that purpose, use actualize sub-command. For example, command for actualization of ATP compound will looks like:
$ cdt actualize --full ATP
-----------------------------------------------------------------------------------
| name | value |
|---------------------------------------------------------------------------------|
| compound | ATP |
| name | ADENOSINE-5'-TRIPHOSPHATE |
| formula | C10 H16 N5 O13 P3 |
| inchi | InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(1 |
| | 7)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2- |
| | 4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,1 |
| | 9,20)/t4-,6-,7-,10-/m1/s1 |
| inchi_key | ZKHQWZAMYRWXGA-KQYNXXCUSA-N |
| smiles | c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O) |
| | O)O)N |
| cross_links_count | 22 |
-----------------------------------------------------------------------------------
By specifying --full option you will be able to see the full information which gets into local database without any cuts. By default you will see only cut values (which are longer then 13 characters)
After actualizing the information you will be able to retreive compound summary by execution:
cdt show --full ATPOption --full is working in the same manner as described before and you'll get the same result as for actualize plus the updated field which contains information about when that entity was updated.
Another useful command provides you an information about locally stored compound summary:
$ cdt ls
-------------------------------------
| name | updated_at |
|------+----------------------------|
| ATP | 2022-07-05T13:19:46.995453 |
| 18W | 2022-07-05T13:25:06.095516 |
-------------------------------------
For list of supported compounds use supported sub-command. For example:
$ cdt supported
Next compounds are supported by cdt:
ADP
ATP
STI
ZID
DPM
XP9
18W
29P
In case you would like to get rid of some specific compound summary, use remove sub-command. For example:
$ cdt remove ATP
Compound ATP succesfully removed.
Below section describe how to run cdt in Docker containers using docker-compose.
⚠️ All below commands are running from the project root directory
- git
- Docker
- docker-compose
Verified at versions:
$ docker --version
Docker version 20.10.17, build 100c701
$ docker-compose --version
Docker Compose version v2.3.4Checkout the code:
# checkout
git clone git@github.com:drnk/pyforge3.git pyforge3 && cd pyforge3Build and run configured containers from the root project directory (where docker-compose.yml file located)
# build and run
docker-compose -p pyforge3 build && docker-compose -p pyforge3 up -dRun the pyforge3_cli container
docker run --network=pyforge3_appnetwork --env-file=.env.dev -it pyforge3_cliFrom the container you are able to use cdt tool:
app@be94926f743d:/usr/src/app$ cdt --help
Usage: cdt [OPTIONS] COMMAND [ARGS]...
Compound-data-tool or CDT is a command line tool allows you to actualize the
information about compounds.
Options:
-v, --verbose Enables verbose mode.
--version Show the version and exit.
--help Show this message and exit.
Commands: l
actualize Actualizing compound data from the open source APIs.
show
supported Information about supported compounds.
or another example with actualizing information:
app@be94926f743d:/usr/src/app$ cdt actualize 18W
-------------------------------------
| name | value |
|-----------------------------------|
| compound | 18W |
| name | 3-[(5Z)-5-... |
| formula | C20 H22 N2 O9 |
| inchi | InChI=1S/C... |
| inchi_key | MBSNQHZDAB... |
| smiles | Cc1c(c(c([... |
| cross_links_count | 2 |
-------------------------------------
app@be94926f743d:/usr/src/app$
For local development you have to obtain Postgres running instance. Update your local .env.dev file data.
Another (preferable) option is to run docker PostgreSQL image by:
docker-compose -p pyforge3 build && docker-compose -p pyforge3 up -dIn that way, connection to database will be established automatically if the PostgreSQL container is running in WSL.
It is highly recommended to use virtual environment for development purposes. Use pyenv or virtual-env or venv or what you like. Activate the environment and install the python packages via pip:
python -m pip install -U pip wheel setuptools && pip install -r services/app/requirements.dev.txtFor test running use:
pytest -vv -ra --cov=src --cov=storageFor convinient use of cdt tool from command line install it as a package:
pip install --editable services/appAfter that you are able to use cdt. For example:
cdt supportedFor troubleshooting and debugging purposes it is possible to obtain the logs of cdt.
By default, the application logs are writing to the console.log file in the root folder of the project.
If you a lazy person and like the hardcore, check the -v/--verboose option of command line. By setting it immediate after cdt token you will receive the DEBUG level logs into the STDOUT. This is switched off by default. For example:
3$ cdt -v supported
2022-07-05 16:34:44,053 INFO sqlalchemy.engine.Engine select pg_catalog.version()
2022-07-05 16:34:44,053 INFO sqlalchemy.engine.Engine [raw sql] {}
2022-07-05 16:34:44,055 INFO sqlalchemy.engine.Engine select current_schema()
2022-07-05 16:34:44,055 INFO sqlalchemy.engine.Engine [raw sql] {}
2022-07-05 16:34:44,056 INFO sqlalchemy.engine.Engine show standard_conforming_strings
2022-07-05 16:34:44,056 INFO sqlalchemy.engine.Engine [raw sql] {}
2022-07-05 16:34:44,058 INFO sqlalchemy.engine.Engine select relname from pg_class c join pg_namespace n on n.oid=c.relnamespace where pg_catalog.pg_table_is_visible(c.oid) and relname=%(name)s
2022-07-05 16:34:44,058 INFO sqlalchemy.engine.Engine [generated in 0.00031s] {'name': 'compounds_summary'}
2022-07-05 16:34:44,061 - [root] - [DEBUG] - COMMAND supported()
Next compounds are supported by cdt:
ADP
ATP
STI
ZID
DPM
XP9
18W
29P
$