Changes

Page history
Update Installation guide authored by Moreau Nicolas's avatar Moreau Nicolas
Hide whitespace changes
Inline Side-by-side
Installation-guide.md
View page @ 8ba03eae
Requirements Requirements
============ ============
python 3 >= 3.7 python 3 >= 3.7
Initial steps Initial steps
============= =============
1. Install docker-compose 1. Install docker-compose
2. Add the user that will run the command to the docker group (sudo usermod -aG docker ${USER}) 2. Add the user that will run the command to the docker group (sudo usermod -aG docker ${USER})
3. Start a new session or su - ${USER} 3. Start a new session or su - ${USER}
4. Get the Yafits archive (https://zenodo.org/record/3696974#.Ya-L633ftdB) 4. Get the Yafits archive (https://zenodo.org/record/3696974#.Ya-L633ftdB)
5. Untar the archive in a directory 5. Untar the archive in a directory
6. Go in the newly created directory 6. Go in the newly created directory
7. Copy yafits.bashrc.dist in .yafits.bashrc 7. Copy yafits.bashrc.dist in .yafits.bashrc
8. Fill .yafits.bashrc configuration file according to your needs ( the file is self-documented ) 8. Fill .yafits.bashrc configuration file according to your needs ( the file is self-documented )
By default the application will use 3 ports : By default the application will use 3 ports :
* 3022 for the UI * 3022 for the UI
* 4252 for the fits file server * 4252 for the fits file server
* 30000 for the spectral lines server * 30000 for the spectral lines server
Installation without spectroscopic data Installation without spectroscopic data
======================================== ========================================
1. Start from Initial step -> 8 1. Start from Initial step -> 8
2. Check that ./yafits scripts is executable 2. Check that ./yafits scripts is executable
3. Execute ./yafits buildrun 3. Execute ./yafits buildrun
Installation with spectroscopic data Installation with spectroscopic data
==================================== ====================================
1. Start from Initial step -> 8 1. Start from Initial step -> 8
2. Download spectroscopic data zip files 2. Download spectroscopic data zip files
3. Moves them in YAFITS_HOME/spectro/mongo-seed/data 3. Moves them in YAFITS_HOME/spectro/mongo-seed/data
4. Comment/Uncomment content of YAFITS_HOME/spectro/mongo-seed/Dockerfile 4. Comment/Uncomment content of YAFITS_HOME/spectro/mongo-seed/Dockerfile
``` ```
# example where only local.json file is enabled # example where only local.json file is enabled
# metadata is required # metadata is required
COPY ./data/local.json.zip /local.json.zip COPY ./data/local.json.zip /local.json.zip
#COPY ./data/cdms.json.zip /cdms.json.zip #COPY ./data/cdms.json.zip /cdms.json.zip
#COPY ./data/jpl.json.zip /jpl.json.zip #COPY ./data/jpl.json.zip /jpl.json.zip
#COPY ./data/ISM_cdms.json.zip /ISM_cdms.json.zip #COPY ./data/ISM_cdms.json.zip /ISM_cdms.json.zip
#COPY ./data/ISM_CSM_cdms.json.zip /ISM_CSM_cdms.json.zip #COPY ./data/ISM_CSM_cdms.json.zip /ISM_CSM_cdms.json.zip
COPY ./data/metadata.json.zip /metadata.json.zip COPY ./data/metadata.json.zip /metadata.json.zip
RUN unzip /local.json.zip RUN unzip /local.json.zip
#RUN unzip /cdms.json.zip #RUN unzip /cdms.json.zip
#RUN unzip /jpl.json.zip #RUN unzip /jpl.json.zip
#RUN unzip /ISM_cdms.json.zip #RUN unzip /ISM_cdms.json.zip
#RUN unzip /ISM_CSM_cdms.json.zip #RUN unzip /ISM_CSM_cdms.json.zip
RUN unzip /metadata.json.zip RUN unzip /metadata.json.zip
RUN rm /local.json.zip RUN rm /local.json.zip
#RUN rm /cdms.json.zip #RUN rm /cdms.json.zip
#RUN rm /jpl.json.zip #RUN rm /jpl.json.zip
#RUN rm /ISM_cdms.json.zip #RUN rm /ISM_cdms.json.zip
#RUN rm /ISM_CSM_cdms.json.zip #RUN rm /ISM_CSM_cdms.json.zip
RUN rm /metadata.json.zip RUN rm /metadata.json.zip
``` ```
4. Comment/Uncomment content of YAFITS_HOME/spectro/mongo-seed/import.sh 4. Comment/Uncomment content of YAFITS_HOME/spectro/mongo-seed/import.sh
``` ```
# example where only local.json file is enabled # example where only local.json file is enabled
# metadata is required # metadata is required
# removes old databases # removes old databases
mongo spectroscopy --eval "db.dropDatabase()" mongo spectroscopy --eval "db.dropDatabase()"
# import available json files # import available json files
#mongoimport --host mongodb --db spectroscopy --collection cdms --file /cdms.json #mongoimport --host mongodb --db spectroscopy --collection cdms --file /cdms.json
#mongoimport --host mongodb --db spectroscopy --collection ism --file /ISM_cdms.json #mongoimport --host mongodb --db spectroscopy --collection ism --file /ISM_cdms.json
#mongoimport --host mongodb --db spectroscopy --collection ismcsm --file /ISM_CSM_cdms.json #mongoimport --host mongodb --db spectroscopy --collection ismcsm --file /ISM_CSM_cdms.json
#mongoimport --host mongodb --db spectroscopy --collection jpl --file /jpl.json #mongoimport --host mongodb --db spectroscopy --collection jpl --file /jpl.json
mongoimport --host mongodb --db spectroscopy --collection local --file /local.json mongoimport --host mongodb --db spectroscopy --collection local --file /local.json
mongoimport --host mongodb --db spectroscopy --collection metadata --file /metadata.json mongoimport --host mongodb --db spectroscopy --collection metadata --file /metadata.json
# create indexes # create indexes
#mongo --host mongodb spectroscopy --eval "db.ism.createIndex({sourcefile:1})" #mongo --host mongodb spectroscopy --eval "db.ism.createIndex({sourcefile:1})"
#mongo --host mongodb spectroscopy --eval "db.ism.createIndex({frequency:1})" #mongo --host mongodb spectroscopy --eval "db.ism.createIndex({frequency:1})"
#mongo --host mongodb spectroscopy --eval "db.ismcsm.createIndex({sourcefile:1})" #mongo --host mongodb spectroscopy --eval "db.ismcsm.createIndex({sourcefile:1})"
#mongo --host mongodb spectroscopy --eval "db.ismcsm.createIndex({frequency:1})" #mongo --host mongodb spectroscopy --eval "db.ismcsm.createIndex({frequency:1})"
#mongo --host mongodb spectroscopy --eval "db.jpl.createIndex({sourcefile:1})" #mongo --host mongodb spectroscopy --eval "db.jpl.createIndex({sourcefile:1})"
#mongo --host mongodb spectroscopy --eval "db.jpl.createIndex({frequency:1})" #mongo --host mongodb spectroscopy --eval "db.jpl.createIndex({frequency:1})"
#mongo --host mongodb spectroscopy --eval "db.cdms.createIndex({sourcefile:1})" #mongo --host mongodb spectroscopy --eval "db.cdms.createIndex({sourcefile:1})"
#mongo --host mongodb spectroscopy --eval "db.cdms.createIndex({frequency:1})" #mongo --host mongodb spectroscopy --eval "db.cdms.createIndex({frequency:1})"
``` ```
5. Go back to YAFITS_HOME 5. Go back to YAFITS_HOME
6. Execute ./yafits updatespectro 6. Execute ./yafits updatespectro
Running the application in background Running the application in background
====================================== ======================================
1. Execute nohup ./yafits buildrun & ( same goes for updatespectro option ) 1. Execute nohup ./yafits buildrun & ( same goes for updatespectro option )
Stopping the application Stopping the application
======================== ========================
1. Execute ./yafits down 1. Execute ./yafits down
Performing tests
================
Running the tests
-----------------
1. Execute ./yafits test
This will generate a report file in the Yafits home directory
Configuring the tests
---------------------
The configuration is done through the .yafits.bashrc file.
```
# contains reference json files against which the tests will be performed
export YAFITS_REFDIR=/obs/partemix/yafits_tmp/REF
# contains the test json files
export YAFITS_OBJDIR=/obs/partemix/yafits_tmp/OBJ
# if true, a json data file will be created in YAFITS_OBJDIR for each opened data cube
export YAFITSV_TESTMODE=true
```
How does it work
----------------
All the files existing in YAFITS_REFDIR will be compared to the file with the same name in YAFITS_OBJDIR
The result of the comparison will be stored in a report file in the home directory of Yafits