Cannot export data for <All Experiments>

Software User interface
1

Hi everyone,

I am trying to export the experimental data, and I can export individual experiment data without problem. However, when I use All Experiments option in the Export data section, I am keep getting this error log:

e[32m2023-10-13T02:30:50+0200 INFO [export_experiment_data] Starting export of tables: pioreactor_unit_activity_data, growth_rates, dosing_events, led_change_events, experiments, od_readings, od_readings_filtered, logs, alt_media_fractions, dosing_automation_settings, led_automation_settings, temperature_automation_settings, kalman_filter_outputs, stirring_rates, temperature_readings, pioreactor_unit_labels, led_automation_events, dosing_automation_events, temperature_automation_events, pwm_dcs, ir_led_intensities, pioreactor_unit_activity_data_rollup.e[0m Traceback (most recent call last): File “/usr/local/bin/pio”, line 8, in sys.exit(pio()) ^^^^^ File “/usr/local/lib/python3.11/dist-packages/click/core.py”, line 1157, in call return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File “/usr/local/lib/python3.11/dist-packages/click/core.py”, line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File “/usr/local/lib/python3.11/dist-packages/click/core.py”, line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File “/usr/local/lib/python3.11/dist-packages/click/core.py”, line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File “/usr/local/lib/python3.11/dist-packages/click/core.py”, line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File “/usr/local/lib/python3.11/dist-packages/click/core.py”, line 783, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File “/usr/local/lib/python3.11/dist-packages/pioreactor/actions/leader/export_experiment_data.py”, line 165, in click_export_experiment_data export_experiment_data(experiment, output, partition_by_unit, tables) File “/usr/local/lib/python3.11/dist-packages/pioreactor/actions/leader/export_experiment_data.py”, line 123, in export_experiment_data raise ValueError(“Experiment name should be provided.”) ValueError: Experiment name should be provided.

Perhaps, it is a simple mistake on my side. However, if you have any idea what can be the cause, I would appreciate the help!

In advance, thank you for your help!

2

Hi @sharknaro, hm, this might be a bug. Let me investigate further.

3

Are you trying to export pioreactor_unit_activity_data? Currently we don’t allow that without a chosen experiment, which seems silly for us to include, so let me further investigate why.

4

Hi Cameron,

Thanks for your quick response!

I am not sure if we are referring to the same thing, so I will look to it further and return back!

In the mean time, what we were trying to export was the experimental data generated by running a leader and worker. We had two experiments (EXP01 and EXP02) and I was trying to export all the data collected on these experiments. Hence, I selected all the boxes (e.g., LED, OD, Stirring…) and tried to export it for both of the experiments at the same time (so both EXP01 and EXP02). I though the option all experiments exports separate files of each experiment with the selected boxes, but I guess that is not the case as I can export each experiment data individually but not both at the same time.

5

In the latest version, 24.1.30, this should be fixed!

1 Like
6

other question, also about exportin data: so i want to take a look at my calibration curve i did a while back and typed in what was written in the pio docs:

image
image1090Ă—279 13.3 KB

sooo…how can i get to that data? or how can i export it otherwise? actually i would just like tot ake a look at the curve though

7

Hi @LeoKleym,

Did you try pio run od_calibration display ?

In case it got changed, you should try pio run --help and should be able to see the correct term you need to use to display the od calibration.

Once, the calibration is displayed you can copy paste the data between {} and save it in a .txt file to use later. For instance you can check Made a mistake, or want to change some data? section in this link which describes how you can change the calibration data if needed. Basically, you can do the same to save the calibration data and re-run it if needed.

Hope this answers your question.

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