Package: scipion-em-ispyb
ISPYB MONITORThis plugin contains a monitor to send data to an ISPyB database, so having a working ISPyB database is required.
Below we summarize the steps taken to test this plugin if you don’t already have ISPyB.SetupInstall MariaDB: Download choosing OS and version (recommended >=10.2), follow steps:https://downloads.mariadb.org/mariadb/repositories/#mirror=digitalocean-sfo&distro=Ubuntu&distro_release=xenial–ubuntu_xenial&version=10.3Fix root login: check if you can log in as root to mysql ($mysql-uroot-p).Skip this step if you log in successfully.If not, use the accepted answer on this link to fix your root login:https://askubuntu.com/questions/705458/ubuntu-15-10-mysql-error-1524-unix-socket.Log in as root:$mysql -u root -pSet log_bin_trust_function_creators:MariaDB [(none)]> set global log_bin_trust_function_creators=ON;
Query OK, 0 rows affected (0.000 sec)Create DB:MariaDB [(none)]> create database ispyb;
Query OK, 1 row affected (0.000 sec)Create user for DB: Grant privileges to your user on ispyb database we just created. Seehttps://stackoverflow.com/questions/5016505/grant-all-privileges-on-database. Here we create a user username that can log in without password.MariaDB [(none)]> CREATE USER username;
MariaDB [(none)]> CREATE USER username@’localhost’;
MariaDB [(none)]> use ispyb
MariaDB [(ispyb)]> GRANT ALL PRIVILEGES ON ispyb.* to username@'localhost';
MariaDB [(ispyb)]> grant all privileges on ispyb.* to username@'%';Add schemas: Clone this repository and follow steps to add schemashttps://github.com/DiamondLightSource/ispyb-databaseCreate a config file: based onhttps://github.com/DiamondLightSource/ispyb-api/blob/master/conf/config.example.cfg[ispyb_mysql_sp]
user = username
pw =
host = localhost
port = 3306
db = ispybSet ISPYB_CONFIG: you can do it in the terminal where you will launch Scipion doingexport ISPYB_CONFIG=path/to/ispyb.cfgor set it in the variables section of ~/.config/scipion/scipion.conf)[VARIABLES]
SCIPION_NOTES_PROGRAM =
SCIPION_NOTES_ARGS =
SCIPION_NOTES_FILE = notes.txt
SCIPION_NOTIFY = False
ISPYB_CONFIG=/path/to/ispyb.confInstall this plugin:scipion installp -p scipion-em-ispybAlternatively, in devel mode:scipion installp -p local/path/to/scipion-em-ispyb --develRun and testRun Scipion and the ISPyB monitor: you should now be able to find the ISPyB monitor in the list of available protocols of Scipion. Launch a workflow with one or all of the following protocols: import movies,movie  alignment, ctf estimation (TestStreamingWorkflow is a good candidate), and set them as the input of ISPyB Monitor. For test purposes, you can select “test” as the database in the dropdown menu at the bottom, and usecm14451-2as the visit.ISPyB import error: If the monitor fails because it can’t import bz2, we need to install in our system libbz2-dev and re-install Scipion:sudo apt-get install libbz2-dev
rm -rf software/lib/*
rm -rf software/include/*
rm software/bin/*
scipion install -j 8Check the data in the ISPyB database:MariaDB [ispyb]> select micrographFullPath, movieId, totalMotion from MotionCorrection;
+--------------------------------------------------------------+---------+-------------+
| micrographFullPath                                           | movieId | totalMotion |
+--------------------------------------------------------------+---------+-------------+
| Runs/000615_ProtMotionCorr/extra/movie000001_aligned_mic.mrc |       1 |     1.96068 |
| Runs/000615_ProtMotionCorr/extra/movie000002_aligned_mic.mrc |       2 |     3.57892 |
| Runs/000615_ProtMotionCorr/extra/movie000003_aligned_mic.mrc |       3 |     2.17066 |
| Runs/000615_ProtMotionCorr/extra/movie000004_aligned_mic.mrc |       4 |     1.96068 |
| Runs/000615_ProtMotionCorr/extra/movie000005_aligned_mic.mrc |       5 |     3.57892 |
| Runs/000615_ProtMotionCorr/extra/movie000006_aligned_mic.mrc |       6 |     2.17066 |
| Runs/000615_ProtMotionCorr/extra/movie000007_aligned_mic.mrc |       7 |     1.96068 |
| Runs/000615_ProtMotionCorr/extra/movie000008_aligned_mic.mrc |       8 |     3.57892 |
| Runs/000615_ProtMotionCorr/extra/movie000009_aligned_mic.mrc |       9 |     2.17066 |