Metadata-Version: 1.0
Name: scipion-em-ispyb
Version: 1.0.0a0
Summary: ISPyB monitor for scipion
Home-page: https://github.com/scipion-em/scipion-em-ispyb
Author: I2PC
Author-email: scipion@cnb.csic.es
License: UNKNOWN
Description: =============
        ISPYB MONITOR
        =============
        
        This 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.
        
        =====
        Setup
        =====
        
        - **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
        
        - **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.
        
        - **Log in as root**:
        
        .. code-block::
        
            $mysql -u root -p
        
        - **Set log_bin_trust_function_creators**:
        
        .. code-block::
        
            MariaDB [(none)]> set global log_bin_trust_function_creators=ON;
            Query OK, 0 rows affected (0.000 sec)
        
        
        - **Create DB**:
        
        .. code-block::
        
            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. See https://stackoverflow.com/questions/5016505/grant-all-privileges-on-database . Here we create a user username that can log in without password.
        
        .. code-block::
        
            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 schemas https://github.com/DiamondLightSource/ispyb-database
        
        - **Create a config file**: based on https://github.com/DiamondLightSource/ispyb-api/blob/master/conf/config.example.cfg
        
        .. code-block::
        
            [ispyb_mysql_sp]
            user = username
            pw =
            host = localhost
            port = 3306
            db = ispyb
        
        - **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)
        
        .. code-block::
        
            [VARIABLES]
            SCIPION_NOTES_PROGRAM =
            SCIPION_NOTES_ARGS =
            SCIPION_NOTES_FILE = notes.txt
            SCIPION_NOTIFY = False
            ISPYB_CONFIG=/path/to/ispyb.conf
        
        - **Install this plugin:**
        
        .. code-block::
        
            scipion installp -p scipion-em-ispyb
        
        Alternatively, in devel mode:
        
        .. code-block::
        
            scipion installp -p local/path/to/scipion-em-ispyb --devel
        
        
        ============
        Run and test
        ============
        
        - **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.
        
        - **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:
        
        .. code-block::
        
            sudo apt-get install libbz2-dev
            rm -rf software/lib/*
            rm -rf software/include/*
            rm software/bin/*
            scipion install -j 8
        
        - **Check the data in the ISPyB database**:
        
        .. code-block::
        
            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 |
        
        
        
Keywords: scipion cryoem imageprocessing scipion-1.2
Platform: UNKNOWN
