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next version #48

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143 changes: 73 additions & 70 deletions developer-guide/20-User interface/02-api.md
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Expand Up @@ -7,76 +7,79 @@ slug: /web-ui-api
### All endpoints

```
Endpoint Methods Rule
--------------------------------------- ------- -------------------------------------------------------------------------
able_to_install_plugins_from_ui GET /api/allow_ui_installs
create_or_update_new_calibrations PUT /api/calibrations
get_available_calibrations_type_by_unit GET /api/calibrations/<pioreactor_unit>
get_available_calibrations_of_type GET /api/calibrations/<pioreactor_unit>/<calibration_type>
get_calibration_by_name GET /api/calibrations/<pioreactor_unit>/<calibration_type>/<calibration_name>
patch_calibrations PATCH /api/calibrations/<pioreactor_unit>/<calibration_type>/<calibration_name>
get_current_calibrations_of_type GET /api/calibrations/<pioreactor_unit>/<calibration_type>/current
get_configs GET /api/configs
get_config GET /api/configs/<filename>
update_config PATCH /api/configs/<filename>
get_automation_contrib GET /api/contrib/automations/<automation_type>
get_charts_contrib GET /api/contrib/charts
create_experiment_profile POST /api/contrib/experiment_profiles
get_experiment_profiles GET /api/contrib/experiment_profiles
get_experiment_profile GET /api/contrib/experiment_profiles/<filename>
delete_experiment_profile DELETE /api/contrib/experiment_profiles/<filename>
get_job_contrib GET /api/contrib/jobs
get_experiments GET /api/experiments
create_experiment POST /api/experiments
delete_experiment DELETE /api/experiments/<experiment>
update_experiment PATCH /api/experiments/<experiment>
get_logs GET /api/experiments/<experiment>/logs
get_media_rates GET /api/experiments/<experiment>/media_rates
get_fallback_time_series GET /api/experiments/<experiment>/time_series/<data_source>/<column>
get_growth_rates GET /api/experiments/<experiment>/time_series/growth_rates
get_od_readings GET /api/experiments/<experiment>/time_series/od_readings
get_od_readings_filtered GET /api/experiments/<experiment>/time_series/od_readings_filtered
get_temperature_readings GET /api/experiments/<experiment>/time_series/temperature_readings
get_unit_labels GET /api/experiments/<experiment>/unit_labels
upsert_unit_labels PUT /api/experiments/<experiment>/unit_labels
get_logs_for_unit_and_experiment GET /api/experiments/<experiment>/units/<unit>/logs
get_list_of_workers_for_experiment GET /api/experiments/<experiment>/workers
add_worker_to_experiment PUT /api/experiments/<experiment>/workers
remove_workers_from_experiment DELETE /api/experiments/<experiment>/workers
remove_worker_from_experiment DELETE /api/experiments/<experiment>/workers/<pioreactor_unit>
stop_worker_in_experiment POST /api/experiments/<experiment>/workers/<worker>/stop
stop_all_in_experiment POST /api/experiments/<experiment>/workers/stop
get_experiments_worker_assignments GET /api/experiments/assignment_count
get_latest_experiment GET /api/experiments/latest
export_datasets POST /api/export_datasets
get_historical_config_for GET /api/historical_configs/<filename>
get_historical_media_used GET /api/historical_media
get_historical_organisms_used GET /api/historical_organisms
is_local_access_point_active GET /api/is_local_access_point_active
install_plugin POST /api/plugins/install
get_installed_plugins GET /api/plugins/installed
get_plugin GET /api/plugins/installed/<filename>
uninstall_plugin POST /api/plugins/uninstall
setup_worker_pioreactor POST /api/setup_worker_pioreactor
reboot_unit POST /api/units/<unit>/reboot
shutdown_unit POST /api/units/<unit>/shutdown
update_app POST /api/update_app
update_app_from_release_archive POST /api/update_app_from_release_archive
update_app_to_develop POST /api/update_app_to_develop
upload POST /api/upload
get_app_version GET /api/versions/app
get_ui_version GET /api/versions/ui
get_list_of_workers GET /api/workers
add_worker PUT /api/workers
delete_worker DELETE /api/workers/<pioreactor_unit>
get_worker GET /api/workers/<pioreactor_unit>
get_experiment_assignment_for_worker GET /api/workers/<pioreactor_unit>/experiment
change_worker_status PUT /api/workers/<pioreactor_unit>/is_active
run_job_on_unit PATCH /api/workers/<unit>/experiments/<experiment>/jobs/<job>/run
stop_job_on_unit PATCH /api/workers/<unit>/jobs/<job>/stop
get_workers_and_experiment_assignments GET /api/workers/assignments
static GET /static/<path:filename>

Endpoint Methods Rule
--------------------------------------- ----------- -------------------------------------------------------------------------
able_to_install_plugins_from_ui GET /api/allow_ui_installs
create_or_update_new_calibrations PUT /api/calibrations
get_available_calibrations_type_by_unit GET /api/calibrations/<pioreactor_unit>
get_available_calibrations_of_type GET /api/calibrations/<pioreactor_unit>/<calibration_type>
get_calibration_by_name GET /api/calibrations/<pioreactor_unit>/<calibration_type>/<calibration_name>
patch_calibrations PATCH /api/calibrations/<pioreactor_unit>/<calibration_type>/<calibration_name>
get_current_calibrations_of_type GET /api/calibrations/<pioreactor_unit>/<calibration_type>/current
get_custer_time GET /api/cluster_time
set_cluster_time POST /api/cluster_time
get_configs GET /api/configs
get_config GET /api/configs/<filename>
update_config PATCH /api/configs/<filename>
get_automation_contrib GET /api/contrib/automations/<automation_type>
get_charts_contrib GET /api/contrib/charts
create_experiment_profile POST /api/contrib/experiment_profiles
edit_experiment_profile PATCH /api/contrib/experiment_profiles
get_experiment_profiles GET /api/contrib/experiment_profiles
get_experiment_profile GET /api/contrib/experiment_profiles/<filename>
delete_experiment_profile DELETE /api/contrib/experiment_profiles/<filename>
get_job_contrib GET /api/contrib/jobs
get_experiments GET /api/experiments
create_experiment POST /api/experiments
delete_experiment DELETE /api/experiments/<experiment>
update_experiment PATCH /api/experiments/<experiment>
get_logs GET /api/experiments/<experiment>/logs
get_media_rates GET /api/experiments/<experiment>/media_rates
get_fallback_time_series GET /api/experiments/<experiment>/time_series/<data_source>/<column>
get_growth_rates GET /api/experiments/<experiment>/time_series/growth_rates
get_od_readings GET /api/experiments/<experiment>/time_series/od_readings
get_od_readings_filtered GET /api/experiments/<experiment>/time_series/od_readings_filtered
get_temperature_readings GET /api/experiments/<experiment>/time_series/temperature_readings
get_unit_labels GET /api/experiments/<experiment>/unit_labels
upsert_unit_labels PUT /api/experiments/<experiment>/unit_labels
get_list_of_workers_for_experiment GET /api/experiments/<experiment>/workers
add_worker_to_experiment PUT /api/experiments/<experiment>/workers
remove_workers_from_experiment DELETE /api/experiments/<experiment>/workers
remove_worker_from_experiment DELETE /api/experiments/<experiment>/workers/<pioreactor_unit>
stop_all_in_experiment POST /api/experiments/<experiment>/workers/stop
get_experiments_worker_assignments GET /api/experiments/assignment_count
get_latest_experiment GET /api/experiments/latest
export_datasets POST /api/export_datasets
get_historical_config_for GET /api/historical_configs/<filename>
get_historical_media_used GET /api/historical_media
get_historical_organisms_used GET /api/historical_organisms
is_local_access_point_active GET /api/is_local_access_point_active
install_plugin POST /api/plugins/install
get_installed_plugins GET /api/plugins/installed
get_plugin GET /api/plugins/installed/<filename>
uninstall_plugin POST /api/plugins/uninstall
reboot_unit POST /api/units/<pioreactor_unit>/reboot
shutdown_unit POST /api/units/<pioreactor_unit>/shutdown
update_app POST /api/update_app
update_app_from_release_archive POST /api/update_app_from_release_archive
update_app_to_develop POST /api/update_app_to_develop
upload POST /api/upload
get_app_version GET /api/versions/app
get_ui_version GET /api/versions/ui
get_list_of_workers GET /api/workers
add_worker PUT /api/workers
delete_worker DELETE /api/workers/<pioreactor_unit>
get_worker GET /api/workers/<pioreactor_unit>
get_experiment_assignment_for_worker GET /api/workers/<pioreactor_unit>/experiment
run_job_on_unit PATCH, POST /api/workers/<pioreactor_unit>/experiments/<experiment>/jobs/<job>/run
stop_job_on_unit PATCH /api/workers/<pioreactor_unit>/experiments/<experiment>/jobs/<job>/stop
update_job_on_unit PATCH /api/workers/<pioreactor_unit>/experiments/<experiment>/jobs/<job>/update
get_logs_for_unit_and_experiment GET /api/workers/<pioreactor_unit>/experiments/<experiment>/logs
stop_all_jobs_on_worker POST /api/workers/<pioreactor_unit>/experiments/<experiment>/stop
change_worker_status PUT /api/workers/<pioreactor_unit>/is_active
get_workers_and_experiment_assignments GET /api/workers/assignments
setup_worker_pioreactor POST /api/workers/setup
static GET /static/<path:filename>
```

From `python3 -m flask --debug --app main routes -s rule`
37 changes: 37 additions & 0 deletions ...ng your Pioreactor/04-Experiment Profiles/02-create-edit-experiment-profiles.md
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Expand Up @@ -181,6 +181,43 @@ common:
target_rpm: ${{ ::stirring:target_rpm + 10 * ::od_reading:od1.od }}
```

### The `when` action

The `when` action is used to trigger an actions(s) _the first time_ the condition is satisfied. For example, you could start a chemostat when the OD rises above a threshold, or turn off heating when the temperature exceed some threshold, or log a message when some condition is met.

The `when` action has a few required fields:

- `condition`: this is an expression (see above) that when evaluated to `true`, will execute the `actions`
- `actions`: this is a list of `actions` to run when the expression evaluates to true.

For example, the following section would start a chemostat when the OD reading is greater than 2.0 in all workers:

```yaml
common:
jobs:
od_reading:
actions:
- type: start
dosing_control:
actions:
- type: when
condition: ${{::od_reading:od1.od > 2.0}}
hours_elapsed: 0
actions:
- type: start
hours_elapsed: 0
options:
automation_name: chemostat
volume: 0.6
duration: 10


```

The `hours_elapsed` works like an other action: it'll only start to check after `hours_elapsed` hours have occurred since the start of execution.

After the condition is met, the actions run, and the condition is never checked again. The `when` is said to be _exhausted_.


### The `repeat` action

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6 changes: 3 additions & 3 deletions ...tending your Pioreactor/04-Experiment Profiles/10-experiment-profiles-schema.md
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Expand Up @@ -4,7 +4,7 @@ slug: /experiment-profiles-schema
---


Below is a schema for experiment profiles. We also do a run-time check
Below is a schema for experiment profiles. We also do a run-time check.

```yaml
# Main structure of the experiment profile
Expand All @@ -26,7 +26,7 @@ common:
jobs:
<job_name>:
actions:
- type: <string> # Type of action: "start", "pause", "resume", "stop", "update", or "log"
- type: <string> # Type of action: "start", "pause", "resume", "stop", "update", "repeat", "when", or "log"
hours_elapsed: <float> # Time when the action is scheduled (in hours after experiment start)
# Options for the action (optional)
# If type is 'log', a 'message' parameter is required here
Expand All @@ -44,7 +44,7 @@ pioreactors:
jobs:
<job_name>:
actions:
- type: <string> # Type of action: "start", "pause", "resume", "stop", or "update"
- type: <string> # Type of action: "start", "pause", "resume", "stop", "update", "repeat", "when", or "log"
hours_elapsed: <float> # Time when the action is scheduled (in hours after experiment start)
# Optional 'if' directive for conditional execution of actions
if: <string> # Can be an expression
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