diff --git a/README.md b/README.md index eb9e865..74e045f 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,6 @@ Runs on files produced by [sf-daq](https://github.com/paulscherrerinstitute/sf_d # Table of Contents * [Installation](#installation) -* [Google Authentication](#google-api) * [Usage](#usage) * [Before beamtime](#usage1) * [During beamtime](#usage2) @@ -16,6 +15,7 @@ Runs on files produced by [sf-daq](https://github.com/paulscherrerinstitute/sf_d * [pausing indexing](#usage2_pause) * [After beamtime](#usage3) * [Configuration files](#config) +* [Google Authentication](#google-api) ## Description Automatic Processing tool checks for the new files/runs produced by sf-daq and runs automatically workload (currently - indexing (by crystfel)) and fills logbook (google spreadsheet) with information with some daq parameters from the sf-daq and processing. @@ -42,7 +42,7 @@ Needed conda environment can be sourced/used from the common place. In case new gspread numpy matplotlib ``` -In case of installation from source, so different location of the code and conda environment - change correspondingly lines in [env_setup.sh](#config_env_setup) file +In case of installation from source, so different location of the code or conda environment - change correspondingly lines in [env_setup.sh](#config_env_setup) file ## Google Authentication @@ -208,6 +208,11 @@ 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..sh file is present - indexing parameters from that file will be used to process protein sample, if not present(default) - run_index.sh parameters are used +## Google Authentication + + 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) +- [create (*hint* - do several for same project) service accounts](https://docs.gspread.org/en/v5.10.0/oauth2.html#for-bots-using-service-account) (steps 1-4) ## Roadmap @@ -218,4 +223,6 @@ this file contains indexing parameters used by crystfel. ## Authors and acknowledgment Automatic Processing tool was made in 2018 by Karol Nass and Dmitry Ozerov. +Automatic processing pipeline is described in "*Nass, K. et al. Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser. IUCrJ 8, 905–920 (2021).*" This paper can be referenced in case usage of automatic pipeline was helpful in beamtime. +