12.8. CamCOPS command-line tools¶
12.8.1. camcops_server¶
The camcops_server command is the main interface to the CamCOPS server.
Options (output from camcops_server --allhelp):
USAGE: camcops_server [-h] [--allhelp] [--version] [-v] [--no_log]
{docs,demo_camcops_config,demo_supervisor_config,demo_apache_config,upgrade_db,dev_upgrade_db,dev_downgrade_db,dev_add_dummy_data,show_db_title,show_db_schema,merge_db,create_db,ddl,reindex,check_index,make_superuser,reset_password,enable_user,export,show_export_queue,crate_dd,cris_dd,serve_cherrypy,serve_gunicorn,serve_pyramid,convert_athena_icd_snomed_to_xml,launch_workers,launch_scheduler,launch_monitor,housekeeping,purge_jobs,dev_cli,list_tasks}
...
CamCOPS server, created by Rudolf Cardinal; version 2.4.20.
Use 'camcops_server <COMMAND> --help' for more detail on each command.
OPTIONS:
-h, --help show this help message and exit
--allhelp show help for all commands and exit
--version show program's version number and exit
-v, --verbose Be verbose
--no_log Disable log (stderr) entirely.
COMMANDS:
Valid CamCOPS commands are as follows.
{docs,demo_camcops_config,demo_supervisor_config,demo_apache_config,upgrade_db,dev_upgrade_db,dev_downgrade_db,dev_add_dummy_data,show_db_title,show_db_schema,merge_db,create_db,ddl,reindex,check_index,make_superuser,reset_password,enable_user,export,show_export_queue,crate_dd,cris_dd,serve_cherrypy,serve_gunicorn,serve_pyramid,convert_athena_icd_snomed_to_xml,launch_workers,launch_scheduler,launch_monitor,housekeeping,purge_jobs,dev_cli,list_tasks}
Specify one command.
docs Launch the main documentation (CamCOPS manual)
demo_camcops_config
Print a demo CamCOPS config file
demo_supervisor_config
Print a demo 'supervisor' config file for CamCOPS
demo_apache_config Print a demo Apache config file section for CamCOPS
upgrade_db Upgrade database to most recent version (via Alembic)
dev_upgrade_db (DEVELOPER OPTION ONLY.) Upgrade a database to a
specific revision.
dev_downgrade_db (DEVELOPER OPTION ONLY.) Downgrades a database to a
specific revision. May DESTROY DATA.
dev_add_dummy_data (DEVELOPER OPTION ONLY.) Populates the database with a
set of dummy patients and tasks for testing.
show_db_title Show database title
show_db_schema Show the database schema as PlantUML +/- PNG
merge_db Merge in data from an old or recent CamCOPS database
create_db Create CamCOPS database from scratch (AVOID; use the
upgrade facility instead)
ddl Print database schema (data definition language; DDL)
reindex Recreate task index
check_index Check index validity (exit code 0 for OK, 1 for bad)
make_superuser Make superuser, or give superuser status to an
existing user
reset_password Reset a user's password
enable_user Re-enable a locked user account
export Trigger pending exports
show_export_queue View outbound export queue (without sending)
crate_dd Make draft data dictionary for CRATE anonymisation
tool
cris_dd Make draft data dictionary for CRIS anonymisation tool
serve_cherrypy Start web server via CherryPy
serve_gunicorn Start web server via Gunicorn (not available under
Windows)
serve_pyramid Start test web server via Pyramid (single-thread,
single-process, HTTP-only; for development use only)
convert_athena_icd_snomed_to_xml
Fetch SNOMED-CT codes for ICD-9-CM and ICD-10 from the
Athena OHDSI data set (https://athena.ohdsi.org/) and
write them to the CamCOPS XML format
launch_workers Launch Celery workers, for background processing
launch_scheduler Launch Celery Beat scheduler, to schedule background
jobs
launch_monitor Launch Celery Flower monitor, to monitor background
jobs
housekeeping Run housekeeping tasks (remove stale sessions, etc.)
purge_jobs Purge any outstanding background (back-end, worker)
jobs
dev_cli Developer command-line interface, with config loaded
as 'config'.
list_tasks List supported tasks.
===============================================================================
Help for command 'docs'
===============================================================================
USAGE: camcops_server docs [-h] [-v]
Launch the main documentation (CamCOPS manual)
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
===============================================================================
Help for command 'demo_camcops_config'
===============================================================================
USAGE: camcops_server demo_camcops_config [-h] [-v] [--docker]
Print a demo CamCOPS config file
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--docker Use settings for Docker (default: False)
===============================================================================
Help for command 'demo_supervisor_config'
===============================================================================
USAGE: camcops_server demo_supervisor_config [-h] [-v]
Print a demo 'supervisor' config file for CamCOPS
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
===============================================================================
Help for command 'demo_apache_config'
===============================================================================
USAGE: camcops_server demo_apache_config [-h] [-v] [--path PATH]
Print a demo Apache config file section for CamCOPS
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--path PATH Path where CamCOPS should appear on the server e.g. 'camcops'
for https://example.com/camcops (default: )
===============================================================================
Help for command 'upgrade_db'
===============================================================================
USAGE: camcops_server upgrade_db [-h] [-v] --config CONFIG [--show_sql_only]
[--no_reindex]
Upgrade database to most recent version (via Alembic)
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--show_sql_only Show SQL only (to stdout); don't execute it (default:
False)
--no_reindex Don't recreate the task index (default: False)
REQUIRED NAMED ARGUMENTS:
--config CONFIG Configuration file (default: None)
===============================================================================
Help for command 'dev_upgrade_db'
===============================================================================
USAGE: camcops_server dev_upgrade_db [-h] [-v] --config CONFIG
--destination_db_revision
DESTINATION_DB_REVISION [--show_sql_only]
(DEVELOPER OPTION ONLY.) Upgrade a database to a specific revision.
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--destination_db_revision DESTINATION_DB_REVISION
The target database revision (default: None)
--show_sql_only Show SQL only (to stdout); don't execute it (default:
False)
REQUIRED NAMED ARGUMENTS:
--config CONFIG Configuration file (default: None)
===============================================================================
Help for command 'dev_downgrade_db'
===============================================================================
USAGE: camcops_server dev_downgrade_db [-h] [-v] --config CONFIG
--destination_db_revision
DESTINATION_DB_REVISION
[--confirm_downgrade_db]
[--show_sql_only]
(DEVELOPER OPTION ONLY.) Downgrades a database to a specific revision. May
DESTROY DATA.
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--destination_db_revision DESTINATION_DB_REVISION
The target database revision (default: None)
--confirm_downgrade_db
Must specify this too, as a safety measure (default:
False)
--show_sql_only Show SQL only (to stdout); don't execute it (default:
False)
REQUIRED NAMED ARGUMENTS:
--config CONFIG Configuration file (default: None)
===============================================================================
Help for command 'dev_add_dummy_data'
===============================================================================
USAGE: camcops_server dev_add_dummy_data [-h] [-v] --config CONFIG
[--confirm_add_dummy_data]
(DEVELOPER OPTION ONLY.) Populates the database with a set of dummy patients
and tasks for testing.
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--confirm_add_dummy_data
Must specify this too, as a safety measure (default:
False)
REQUIRED NAMED ARGUMENTS:
--config CONFIG Configuration file (default: None)
===============================================================================
Help for command 'show_db_title'
===============================================================================
USAGE: camcops_server show_db_title [-h] [-v] [--config CONFIG]
Show database title
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
===============================================================================
Help for command 'show_db_schema'
===============================================================================
USAGE: camcops_server show_db_schema [-h] [-v] [--config CONFIG]
[--schemastem SCHEMASTEM] [--make_image]
[--java JAVA] [--plantuml PLANTUML]
[--height_width_limit HEIGHT_WIDTH_LIMIT]
[--java_memory_limit_mb JAVA_MEMORY_LIMIT_MB]
Show the database schema as PlantUML +/- PNG
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default:
None)
--schemastem SCHEMASTEM
Stem for output filenames (for schema diagrams);
'.plantuml' and '.png' are appended (default: schema)
--make_image Create a PNG image (impractically large!) (default:
False)
--java JAVA Java executable (for schema diagrams) (default: java)
--plantuml PLANTUML PlantUML Java .jar file (for schema diagrams)
(default: plantuml.jar)
--height_width_limit HEIGHT_WIDTH_LIMIT
Maximum image height/width in pixels (default: 20000)
--java_memory_limit_mb JAVA_MEMORY_LIMIT_MB
Java virtual machine memory limit in Mb (default:
2048)
===============================================================================
Help for command 'merge_db'
===============================================================================
USAGE: camcops_server merge_db [-h] [-v] --config CONFIG
[--report_every REPORT_EVERY] [--echo]
[--dummy_run] [--info_only]
[--default_group_id DEFAULT_GROUP_ID]
[--default_group_name DEFAULT_GROUP_NAME] --src
SRC --whichidnum_map WHICHIDNUM_MAP
--groupnum_map GROUPNUM_MAP
Merge in data from an old or recent CamCOPS database
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--report_every REPORT_EVERY
Report progress every n rows (default: 10000)
--echo Echo SQL to source database (default: False)
--dummy_run Perform a dummy run only; do not alter destination
database (default: False)
--info_only Show table information only; don't do any work
(default: False)
--default_group_id DEFAULT_GROUP_ID
Default group ID (integer) to apply to old records
without one. If none is specified, a new group will be
created for such records. (default: None)
--default_group_name DEFAULT_GROUP_NAME
If default_group_id is not specified, use this group
name. The group will be looked up if it exists, and
created if not. (default: None)
REQUIRED NAMED ARGUMENTS:
--config CONFIG Configuration file (default: None)
--src SRC Source database (specified as an SQLAlchemy URL). The
contents of this database will be merged into the
database specified in the config file. (default: None)
--whichidnum_map WHICHIDNUM_MAP
Map to convert ID number types, in the format
'from_a:to_a,from_b:to_b,...', where all values are
integers. (default: None)
--groupnum_map GROUPNUM_MAP
Map to convert group numbers, in the format
'from_a:to_a,from_b:to_b,...', where all values are
integers. (default: None)
===============================================================================
Help for command 'create_db'
===============================================================================
USAGE: camcops_server create_db [-h] [-v] --config CONFIG --confirm_create_db
Create CamCOPS database from scratch (AVOID; use the upgrade facility instead)
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
REQUIRED NAMED ARGUMENTS:
--config CONFIG Configuration file (default: None)
--confirm_create_db Must specify this too, as a safety measure (default:
False)
===============================================================================
Help for command 'ddl'
===============================================================================
USAGE: camcops_server ddl [-h] [-v] [--config CONFIG] [--dialect DIALECT]
Print database schema (data definition language; DDL)
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
--dialect DIALECT SQL dialect (options: firebird, mssql, mysql, oracle,
postgresql, sqlite, sybase) (default: mysql)
===============================================================================
Help for command 'reindex'
===============================================================================
USAGE: camcops_server reindex [-h] [-v] [--config CONFIG]
Recreate task index
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
===============================================================================
Help for command 'check_index'
===============================================================================
USAGE: camcops_server check_index [-h] [-v] [--config CONFIG] [--show_all_bad]
Check index validity (exit code 0 for OK, 1 for bad)
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
--show_all_bad Show all bad index entries (rather than stopping at the
first) (default: False)
===============================================================================
Help for command 'make_superuser'
===============================================================================
USAGE: camcops_server make_superuser [-h] [-v] [--config CONFIG]
[--username USERNAME]
[--password PASSWORD]
Make superuser, or give superuser status to an existing user
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default:
None)
--username USERNAME Username of superuser to create/promote (if omitted,
you will be asked to type it in) (default: None)
--password PASSWORD Password of superuser to create (if omitted, you will
be asked to type it in) (default: None)
===============================================================================
Help for command 'reset_password'
===============================================================================
USAGE: camcops_server reset_password [-h] [-v] [--config CONFIG]
[--username USERNAME]
Reset a user's password
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default:
None)
--username USERNAME Username to change password for (if omitted, you will
be asked to type it in) (default: None)
===============================================================================
Help for command 'enable_user'
===============================================================================
USAGE: camcops_server enable_user [-h] [-v] [--config CONFIG]
[--username USERNAME]
Re-enable a locked user account
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default:
None)
--username USERNAME Username to enable (if omitted, you will be asked to
type it in) (default: None)
===============================================================================
Help for command 'export'
===============================================================================
USAGE: camcops_server export [-h] [-v] [--config CONFIG]
[--recipients [RECIPIENTS ...]]
[--all_recipients] [--disable_task_index]
[--schedule_via_backend]
Trigger pending exports
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default:
None)
--recipients [RECIPIENTS ...]
Export recipients (as named in config file) (default:
None)
--all_recipients Use all recipients (default: False)
--disable_task_index Disable use of the task index (for debugging only)
(default: False)
--schedule_via_backend
Export tasks as a background job (default: False)
===============================================================================
Help for command 'show_export_queue'
===============================================================================
USAGE: camcops_server show_export_queue [-h] [-v] [--config CONFIG]
[--recipients [RECIPIENTS ...]]
[--all_recipients]
[--disable_task_index] [--pretty]
[--debug_show_fhir]
[--debug_fhir_include_docs]
View outbound export queue (without sending)
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default:
None)
--recipients [RECIPIENTS ...]
Export recipients (as named in config file) (default:
None)
--all_recipients Use all recipients (default: False)
--disable_task_index Disable use of the task index (for debugging only)
(default: False)
--pretty Pretty (but slower) formatting for tasks (default:
False)
--debug_show_fhir Show FHIR output for tasks (default: False)
--debug_fhir_include_docs
(If --debug_show_fhir) Included FHIR documents? Large.
(default: False)
===============================================================================
Help for command 'crate_dd'
===============================================================================
USAGE: camcops_server crate_dd [-h] [-v] [--config CONFIG] --filename FILENAME
--recipient RECIPIENT
Make draft data dictionary for CRATE anonymisation tool
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default:
None)
--filename FILENAME Output filename (data dictionary to write) (default:
None)
--recipient RECIPIENT
Export recipient (as named in config file) (default:
None)
===============================================================================
Help for command 'cris_dd'
===============================================================================
USAGE: camcops_server cris_dd [-h] [-v] [--config CONFIG] --filename FILENAME
--recipient RECIPIENT
Make draft data dictionary for CRIS anonymisation tool
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default:
None)
--filename FILENAME Filename of data dictionary to write (default: None)
--recipient RECIPIENT
Export recipient (as named in config file) (default:
None)
===============================================================================
Help for command 'serve_cherrypy'
===============================================================================
USAGE: camcops_server serve_cherrypy [-h] [-v] [--config CONFIG]
Start web server via CherryPy
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
===============================================================================
Help for command 'serve_gunicorn'
===============================================================================
USAGE: camcops_server serve_gunicorn [-h] [-v] [--config CONFIG]
Start web server via Gunicorn (not available under Windows)
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
===============================================================================
Help for command 'serve_pyramid'
===============================================================================
USAGE: camcops_server serve_pyramid [-h] [-v] [--config CONFIG]
Start test web server via Pyramid (single-thread, single-process, HTTP-only;
for development use only)
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
===============================================================================
Help for command 'convert_athena_icd_snomed_to_xml'
===============================================================================
USAGE: camcops_server convert_athena_icd_snomed_to_xml [-h] [-v]
[--config CONFIG]
--athena_concept_tsv_filename
ATHENA_CONCEPT_TSV_FILENAME
--athena_concept_relationship_tsv_filename
ATHENA_CONCEPT_RELATIONSHIP_TSV_FILENAME
--icd9_xml_filename
ICD9_XML_FILENAME
--icd10_xml_filename
ICD10_XML_FILENAME
Fetch SNOMED-CT codes for ICD-9-CM and ICD-10 from the Athena OHDSI data set
(https://athena.ohdsi.org/) and write them to the CamCOPS XML format
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default:
None)
--athena_concept_tsv_filename ATHENA_CONCEPT_TSV_FILENAME
Path to CONCEPT.csv file from Athena download
(default: None)
--athena_concept_relationship_tsv_filename ATHENA_CONCEPT_RELATIONSHIP_TSV_FILENAME
Path to CONCEPT_RELATIONSHIP.csv file from Athena
download (default: None)
--icd9_xml_filename ICD9_XML_FILENAME
Filename of ICD-9-CM/SNOMED-CT XML file to write
(default: None)
--icd10_xml_filename ICD10_XML_FILENAME
Filename of ICD-10/SNOMED-CT XML file to write
(default: None)
===============================================================================
Help for command 'launch_workers'
===============================================================================
USAGE: camcops_server launch_workers [-h] [-v] [--config CONFIG]
Launch Celery workers, for background processing
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
===============================================================================
Help for command 'launch_scheduler'
===============================================================================
USAGE: camcops_server launch_scheduler [-h] [-v] [--config CONFIG]
Launch Celery Beat scheduler, to schedule background jobs
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
===============================================================================
Help for command 'launch_monitor'
===============================================================================
USAGE: camcops_server launch_monitor [-h] [-v] [--config CONFIG]
[--address ADDRESS] [--port PORT]
Launch Celery Flower monitor, to monitor background jobs
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
--address ADDRESS Address to use for Flower (default: 127.0.0.1)
--port PORT Port to use for Flower (default: 5555)
===============================================================================
Help for command 'housekeeping'
===============================================================================
USAGE: camcops_server housekeeping [-h] [-v] [--config CONFIG]
Run housekeeping tasks (remove stale sessions, etc.)
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
===============================================================================
Help for command 'purge_jobs'
===============================================================================
USAGE: camcops_server purge_jobs [-h] [-v] [--config CONFIG]
Purge any outstanding background (back-end, worker) jobs
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
===============================================================================
Help for command 'dev_cli'
===============================================================================
USAGE: camcops_server dev_cli [-h] [-v] [--config CONFIG]
Developer command-line interface, with config loaded as 'config'.
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
===============================================================================
Help for command 'list_tasks'
===============================================================================
USAGE: camcops_server list_tasks [-h] [-v] [--config CONFIG]
List supported tasks.
OPTIONS:
-h, --help show this help message and exit
-v, --verbose Be verbose (default: False)
--config CONFIG Configuration file (if not specified, the environment
variable CAMCOPS_CONFIG_FILE is checked) (default: None)
12.8.2. camcops_server_meta¶
The camcops_server_meta tool allows you to run CamCOPS over multiple
CamCOPS configuration files/databases. It’s less useful than it was, because
the dominant mode of “one database per research group” has been replaced by the
concept of “a single database with group-level security”.
Options:
USAGE: camcops_server_meta [-h] --filespecs FILESPECS [FILESPECS ...]
[--ccargs [CCARGS ...]] [--python PYTHON]
[--camcops CAMCOPS] [-d] [-v]
cc_command
Run commands across multiple CamCOPS databases
POSITIONAL ARGUMENTS:
cc_command Main command to pass to CamCOPS
OPTIONS:
-h, --help show this help message and exit
--filespecs FILESPECS [FILESPECS ...]
List of CamCOPS config files (wildcards OK)
--ccargs [CCARGS ...]
List of CamCOPS arguments, to which '--' will be
prefixed
--python PYTHON Python interpreter (default: /path/to/python)
--camcops CAMCOPS CamCOPS server executable (default:
/path/to/camcops/server/camcops_server.py)
-d, --dummyrun Dummy run (show filenames only)
-v, --verbose Verbose
12.8.3. camcops_fetch_snomed_codes¶
Subject to you having the necessary permissions, and access to a SNOMED CT REST API server, this tool will help you find SNOMED CT codes relevant to CamCOPS. See SNOMED CT coding and SNOMED CT licensing.
Options:
usage: camcops_fetch_snomed_codes [-h] [--allhelp] [--url URL]
[--edition EDITION] [--release RELEASE]
[--language LANGUAGE]
[--rate_limit_hz RATE_LIMIT_HZ] [--verbose]
{test,fetch} ...
Fetch SNOMED CT codes from a SNOMED CT Snapshot REST API provider
options:
-h, --help show this help message and exit
--allhelp show help for all commands and exit
--url URL URL (protocol, host, API root path) for SNOMED-CT API
(default: https://termbrowser.nhs.uk/sct-browser-
api/snomed)
--edition EDITION SNOMED CT edition (default: uk-edition)
--release RELEASE Snomed release identifier (version) (default:
v20210929)
--language LANGUAGE Language (default: english)
--rate_limit_hz RATE_LIMIT_HZ
Maximum number of requests per second (default: 1)
--verbose Be verbose (default: False)
commands:
{test,fetch} Specify one command. Use 'camcops_fetch_snomed_codes
<command> --help' for more help
test Run tests. If you specify no arguments, default tests
will be run.
fetch Fetch data relevant to CamCOPS and write to XML
===============================================================================
Help for command 'test'
===============================================================================
USAGE: camcops_fetch_snomed_codes test [-h] [--concept_id [CONCEPT_ID ...]]
[--term [TERM ...]]
[--semantic_area SEMANTIC_AREA]
OPTIONS:
-h, --help show this help message and exit
--concept_id [CONCEPT_ID ...]
For tests: Concept ID(s) to test (default: None)
--term [TERM ...] For tests: Term(s) to test (default: None)
--semantic_area SEMANTIC_AREA
For tests: semantic area to restrict to (default:
None)
===============================================================================
Help for command 'fetch'
===============================================================================
USAGE: camcops_fetch_snomed_codes fetch [-h] [--outfile OUTFILE]
[--continue_on_error]
OPTIONS:
-h, --help show this help message and exit
--outfile OUTFILE XML filename to write (default:
camcops_tasks_snomed.xml)
--continue_on_error Carry on despite errors (default: False)
12.8.4. camcops_backup_mysql_database¶
This simple tool uses MySQL to dump a MySQL database to a .SQL file (from which you can restore it), and names the file according to the name of the database plus a timestamp.
Options:
usage: camcops_backup_mysql_database [-h]
[--max_allowed_packet MAX_ALLOWED_PACKET]
[--mysqldump MYSQLDUMP]
[--username USERNAME]
[--password PASSWORD]
[--with_drop_create_database]
[--output_dir OUTPUT_DIR] [--verbose]
databases [databases ...]
Back up a specific MySQL database. The resulting filename has the format
'<DATABASENAME>_<DATETIME><SUFFIX>.sql', where <DATETIME> is of the ISO-8601
format '%Y%m%dT%H%M%S' and <SUFFIX> is either blank or
'_with_drop_create_database'. A typical filename is therefore
'mydb_20190415T205524.sql'.
positional arguments:
databases Database(s) to back up
options:
-h, --help show this help message and exit
--max_allowed_packet MAX_ALLOWED_PACKET
Maximum size of buffer (default: 1GB)
--mysqldump MYSQLDUMP
mysqldump executable (default: mysqldump)
--username USERNAME MySQL user (default: root)
--password PASSWORD MySQL password (AVOID THIS OPTION IF POSSIBLE; VERY
INSECURE; VISIBLE TO OTHER PROCESSES; if you don't use
it, you'll be prompted for the password) (default:
None)
--with_drop_create_database
Include DROP DATABASE and CREATE DATABASE commands,
and append a suffix to the output filename as above
(default: False)
--output_dir OUTPUT_DIR
Output directory (if not specified, current directory
will be used) (default: None)
--verbose Verbose output (default: False)