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        "description": "=============\nISPYB MONITOR\n=============\n\nThis plugin contains a monitor to send data to an ISPyB database, so having a working ISPyB database is required.\nBelow we summarize the steps taken to test this plugin if you don't already have ISPyB.\n\n=====\nSetup\n=====\n\n- **Install 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=10.3\n\n- **Fix root login**: check if you can log in as root to mysql ( ``$mysql -u root -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.\n\n- **Log in as root**:\n\n.. code-block::\n\n    $mysql -u root -p\n\n- **Set log_bin_trust_function_creators**:\n\n.. code-block::\n\n    MariaDB [(none)]> set global log_bin_trust_function_creators=ON;\n    Query OK, 0 rows affected (0.000 sec)\n\n\n- **Create DB**:\n\n.. code-block::\n\n    MariaDB [(none)]> create database ispyb;\n    Query OK, 1 row affected (0.000 sec)\n\n- **Create user for DB**: Grant privileges to your user on ispyb database we just created. See https://stackoverflow.com/questions/5016505/grant-all-privileges-on-database . Here we create a user username that can log in without password.\n\n.. code-block::\n\n    MariaDB [(none)]> CREATE USER username;\n    MariaDB [(none)]> CREATE USER username@\u2019localhost\u2019;\n    MariaDB [(none)]> use ispyb\n    MariaDB [(ispyb)]> GRANT ALL PRIVILEGES ON ispyb.* to username@'localhost';\n    MariaDB [(ispyb)]> grant all privileges on ispyb.* to username@'%';\n\n- **Add schemas**: Clone this repository and follow steps to add schemas https://github.com/DiamondLightSource/ispyb-database\n\n- **Create a config file**: based on https://github.com/DiamondLightSource/ispyb-api/blob/master/conf/config.example.cfg\n\n.. code-block::\n\n    [ispyb_mysql_sp]\n    user = username\n    pw =\n    host = localhost\n    port = 3306\n    db = ispyb\n\n- **Set ISPYB_CONFIG**: you can do it in the terminal where you will launch Scipion doing ``export ISPYB_CONFIG=path/to/ispyb.cfg`` or set it in the variables section of ~/.config/scipion/scipion.conf)\n\n.. code-block::\n\n    [VARIABLES]\n    SCIPION_NOTES_PROGRAM =\n    SCIPION_NOTES_ARGS =\n    SCIPION_NOTES_FILE = notes.txt\n    SCIPION_NOTIFY = False\n    ISPYB_CONFIG=/path/to/ispyb.conf\n\n- **Install this plugin:**\n\n.. code-block::\n\n    scipion installp -p scipion-em-ispyb\n\nAlternatively, in devel mode:\n\n.. code-block::\n\n    scipion installp -p local/path/to/scipion-em-ispyb --devel\n\n\n============\nRun and test\n============\n\n- **Run 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 use **cm14451-2** as the visit.\n\n- **ISPyB import error**: If the monitor fails because it can\u2019t import bz2, we need to install in our system libbz2-dev and re-install Scipion:\n\n.. code-block::\n\n    sudo apt-get install libbz2-dev\n    rm -rf software/lib/*\n    rm -rf software/include/*\n    rm software/bin/*\n    scipion install -j 8\n\n- **Check the data in the ISPyB database**:\n\n.. code-block::\n\n    MariaDB [ispyb]> select micrographFullPath, movieId, totalMotion from MotionCorrection;\n    +--------------------------------------------------------------+---------+-------------+\n    | micrographFullPath                                           | movieId | totalMotion |\n    +--------------------------------------------------------------+---------+-------------+\n    | Runs/000615_ProtMotionCorr/extra/movie000001_aligned_mic.mrc |       1 |     1.96068 |\n    | Runs/000615_ProtMotionCorr/extra/movie000002_aligned_mic.mrc |       2 |     3.57892 |\n    | Runs/000615_ProtMotionCorr/extra/movie000003_aligned_mic.mrc |       3 |     2.17066 |\n    | Runs/000615_ProtMotionCorr/extra/movie000004_aligned_mic.mrc |       4 |     1.96068 |\n    | Runs/000615_ProtMotionCorr/extra/movie000005_aligned_mic.mrc |       5 |     3.57892 |\n    | Runs/000615_ProtMotionCorr/extra/movie000006_aligned_mic.mrc |       6 |     2.17066 |\n    | Runs/000615_ProtMotionCorr/extra/movie000007_aligned_mic.mrc |       7 |     1.96068 |\n    | Runs/000615_ProtMotionCorr/extra/movie000008_aligned_mic.mrc |       8 |     3.57892 |\n    | Runs/000615_ProtMotionCorr/extra/movie000009_aligned_mic.mrc |       9 |     2.17066 |",
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