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2023-08-28 11:06:24 +02:00
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README.md
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@ -43,7 +43,7 @@ In case of installation from source, so different location of the code and conda
## Configuration files<a name="config"></a>
### BEAM_ENERGY.txt
This file should contain a beam energy values (in eV). There must be one line with the default values and (optionally) it's possible to define beam energy values, different from defaults for specific runs(scans). Example:
This file should contain a beam energy values (in eV). There must be one line with the default value and it's possible to define beam energy values, different from defaults for specific runs(scans). Example:
> $ cat BEAM_ENERGY.txt
>
> DEFAULT 11330.0
@ -75,7 +75,7 @@ this file contains indexing parameters used by crystfel.
**HINT** - in case several proteins are used during expertiment, it's possible to define different indexing parameters for each of them: in case run_index.<cell_name>.sh file is present - indexing parameters from that file will be used to process <cell_name> protein sample, if not present(default) - run_index.sh parameters are used
## Google Authentication (optional)<a name="google-api"></a>
## Google Authentication<a name="google-api"></a>
ap can fill automatically google spreadsheet with different information. This is done using google-api and one need to have api-keys created and allowed for the corresponding spreadsheet (logbook). To create keys, few steps needs to be done first:
- [enable API access for a project](https://docs.gspread.org/en/v5.10.0/oauth2.html#enable-api-access-for-a-project)
@ -119,23 +119,22 @@ this file contains indexing parameters used by crystfel.
runs with the <cell_name>=lyso will be indexed using lyso.cell file, while for the <cell_name>=chim - indexing will be done twice, using chim.cell and chim.cell_alternative files (and results of both indexing will be filled in logbook)
* (optional, if filling is requested)
* create (an empty) google spreadsheet
* create (an empty) google spreadsheet
* create (several distinct) credentials files (see section [google authentication](#google-api) how to create service accounts and keys if not done before) and store them with the names in the config directory (it's important to have file with name credentials.json and have few(3 is enough) with names credentials-1.json, credentials-2.json...):
* create (several distinct) credentials files (see section [google authentication](#google-api) how to create service accounts and keys if not done before) and store them with the names in the config directory (it's important to have file with name credentials.json and have few(3 is enough) with names credentials-1.json, credentials-2.json...):
> $ ls res/ap/credentials*json
>
>credentials.json credentials-1.json credentials-2.json credentials-3.json
***RECOMMENDATION*** - use/generate new credentials files for each beamtime to not expose experiment information
* give write access to the google spreadsheet to the service-accounts (recommended) or give full editor access to all who know url of the logbook(quicker, but not recommended action). To find e-mails of the service accounts:
* give write access to the google spreadsheet to the service-accounts (recommended) or give full editor access to all who know url of the logbook(quicker, but not recommended action). To find e-mails of the service accounts:
> $ grep client_email credentials*json
* edit env_setup.sh file to fill URL_TO_GOOGLE_SPREADSHEET(https://...) to the LOGBOOK variable
* edit env_setup.sh file to fill URL_TO_GOOGLE_SPREADSHEET(https://...) to the LOGBOOK variable
* setup/prepare spreadsheet for automatic filling:
* setup/prepare spreadsheet for automatic filling:
> $ . ./env_setup.sh
>
> $ python /sf/jungfrau/applications/ap/ap/update-spreadsheet.py --setup --url ${LOGBOOK}