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Requirements
============
python 3 >= 3.7
Initial steps
=============
1. Install docker-compose
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}
4. Get the Yafits archive (https://zenodo.org/record/3696974#.Ya-L633ftdB)
5. Untar the archive in a directory
6. Go in the newly created directory
7. Copy yafits.bashrc.dist in .yafits.bashrc
8. Fill .yafits.bashrc configuration file according to your needs ( the file is self-documented )
By default the application will use 3 ports :
* 3022 for the UI
* 4252 for the fits file server
* 30000 for the spectral lines server
Installation without spectroscopic data
========================================
1. Start from Initial step -> 8
2. Check that ./yafits scripts is executable
3. Execute ./yafits buildrun
Installation with spectroscopic data
====================================
1. Start from Initial step -> 8
2. Download spectroscopic data zip files
3. Moves them in YAFITS_HOME/spectro/mongo-seed/data
4. Comment/Uncomment content of YAFITS_HOME/spectro/mongo-seed/Dockerfile
```
# example where only local.json file is enabled
# metadata is required
COPY ./data/local.json.zip /local.json.zip
#COPY ./data/cdms.json.zip /cdms.json.zip
#COPY ./data/jpl.json.zip /jpl.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/metadata.json.zip /metadata.json.zip
RUN unzip /local.json.zip
#RUN unzip /cdms.json.zip
#RUN unzip /jpl.json.zip
#RUN unzip /ISM_cdms.json.zip
#RUN unzip /ISM_CSM_cdms.json.zip
RUN unzip /metadata.json.zip
RUN rm /local.json.zip
#RUN rm /cdms.json.zip
#RUN rm /jpl.json.zip
#RUN rm /ISM_cdms.json.zip
#RUN rm /ISM_CSM_cdms.json.zip
RUN rm /metadata.json.zip
```
4. Comment/Uncomment content of YAFITS_HOME/spectro/mongo-seed/import.sh
```
# example where only local.json file is enabled
# metadata is required
# removes old databases
mongo spectroscopy --eval "db.dropDatabase()"
# import available json files
#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 ismcsm --file /ISM_CSM_cdms.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 metadata --file /metadata.json
# create indexes
#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.ismcsm.createIndex({sourcefile: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({frequency:1})"
#mongo --host mongodb spectroscopy --eval "db.cdms.createIndex({sourcefile:1})"
#mongo --host mongodb spectroscopy --eval "db.cdms.createIndex({frequency:1})"
```
5. Go back to YAFITS_HOME
6. Execute ./yafits updatespectro
Running the application in background
======================================
1. Execute nohup ./yafits buildrun & ( same goes for updatespectro option )
Stopping the application
========================
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
Requirements
============
python 3 >= 3.7
Initial steps
=============
1. Install docker-compose
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}
4. Get the Yafits archive (https://zenodo.org/record/3696974#.Ya-L633ftdB)
5. Untar the archive in a directory
6. Go in the newly created directory
7. Copy yafits.bashrc.dist in .yafits.bashrc
8. Fill .yafits.bashrc configuration file according to your needs ( the file is self-documented )
By default the application will use 3 ports :
* 3022 for the UI
* 4252 for the fits file server
* 30000 for the spectral lines server
Installation without spectroscopic data
========================================
1. Start from Initial step -> 8
2. Check that ./yafits scripts is executable
3. Execute ./yafits buildrun
Installation with spectroscopic data
====================================
1. Start from Initial step -> 8
2. Download spectroscopic data zip files
3. Moves them in YAFITS_HOME/spectro/mongo-seed/data
4. Comment/Uncomment content of YAFITS_HOME/spectro/mongo-seed/Dockerfile
```
# example where only local.json file is enabled
# metadata is required
COPY ./data/local.json.zip /local.json.zip
#COPY ./data/cdms.json.zip /cdms.json.zip
#COPY ./data/jpl.json.zip /jpl.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/metadata.json.zip /metadata.json.zip
RUN unzip /local.json.zip
#RUN unzip /cdms.json.zip
#RUN unzip /jpl.json.zip
#RUN unzip /ISM_cdms.json.zip
#RUN unzip /ISM_CSM_cdms.json.zip
RUN unzip /metadata.json.zip
RUN rm /local.json.zip
#RUN rm /cdms.json.zip
#RUN rm /jpl.json.zip
#RUN rm /ISM_cdms.json.zip
#RUN rm /ISM_CSM_cdms.json.zip
RUN rm /metadata.json.zip
```
4. Comment/Uncomment content of YAFITS_HOME/spectro/mongo-seed/import.sh
```
# example where only local.json file is enabled
# metadata is required
# removes old databases
mongo spectroscopy --eval "db.dropDatabase()"
# import available json files
#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 ismcsm --file /ISM_CSM_cdms.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 metadata --file /metadata.json
# create indexes
#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.ismcsm.createIndex({sourcefile: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({frequency:1})"
#mongo --host mongodb spectroscopy --eval "db.cdms.createIndex({sourcefile:1})"
#mongo --host mongodb spectroscopy --eval "db.cdms.createIndex({frequency:1})"
```
5. Go back to YAFITS_HOME
6. Execute ./yafits updatespectro
Running the application in background
======================================
1. Execute nohup ./yafits buildrun & ( same goes for updatespectro option )
Stopping the application
========================
1. Execute ./yafits down