Merge pull request #27 from valeriupredoi/new_mass_download

Updated the download from mass tool

Author: ledm

Diff for: README.md

@@ -134,7 +134,7 @@ Multi-model comaprison report
 -----------------------------
 
 Once several models have been analysed using the time series analysis,
-their time development can be compared using the analysis_compare command:
+their time development can be compared using the `analysis_compare` command:
 ```
 analysis_compare recipe.yml
 ```
@@ -172,6 +172,38 @@ The optional arguments for each job are:
 A sample yaml exists in `input_yml/comparison_analysis_template.yml`,
 which can be adapted to additional analysis. 
 
+Download data from MASS
+-----------------------
+
+It's straightforward to download data from the Met Office
+Storage System, MASS.
+The bgcval2 tool `download_data_from mass` sets up the command and 
+outputs a script which you can run on Jasmin's mass-cli1 machine. 
+
+Note that the only place on CEDA-JASMIN you can download data  
+is the dedicated virtual machine, mass-cli1.jasmin.ac.uk.
+
+The recommended process is to generate the download script on an interactive node,
+like sci1 with the command:
+```
+download_from_mass jobID noMoo
+```
+Which will then create a script in the directory `mass_scripts`.
+The runtime flag `noMoo` stops the script from attempted to execute the script.
+
+From there, the user must log into the mass machine, and execute the script:
+```
+#from login1.jasmin.ac.uk:
+ssh -X mas-cli1
+cd bgcval2
+source mass_script/*.sh
+```
+
+Note that these scripts can also be automatically generated by 
+the `analysis_compare` command by including the 
+```
+do_mass_download: True 
+```
 
 Documentation
 =============

Diff for: bgcval2/analysis_compare.py

@@ -59,6 +59,8 @@
 from .timeseries import profileAnalysis
 from .timeseries import timeseriesPlots as tsp
 from bgcval2.analysis_timeseries import analysis_timeseries
+from bgcval2.download_from_mass import download_from_mass
+
 
 try:
     from .bgcvaltools.pftnames import getLongName
@@ -4167,6 +4169,7 @@ def load_comparison_yml(master_compare_yml_fn):
         exit(0)       
 
     details['do_analysis_timeseries'] = dictionary.get('do_analysis_timeseries', False) 
+    details['do_mass_download'] = dictionary.get('do_mass_download', False)
 
     details['master_suites'] = dictionary.get('master_suites', [])
 
@@ -4220,6 +4223,7 @@ def main():
     jobs = details['jobs']
     analysis_name = details['name']    
     do_analysis_timeseries = details['do_analysis_timeseries']
+    do_mass_download = details['do_mass_download']
     master_suites = details['master_suites']  
 
     colours = details['colours']
@@ -4239,9 +4243,12 @@ def main():
         print(jobID, 'Shift time by', shifttimes[jobID])
         print(jobID, 'suite:', suites[jobID])
 
-    # if do_mass_download:
-    # Not yet implemented.
-
+    for jobID in jobs:
+        # even if you don't want to download, it's good to run this
+        # as it clears up the path and ensures recently downloed data is 
+        # correctly symlinked.
+        download_from_mass(jobID, doMoo=do_mass_download)
+    
     if do_analysis_timeseries:
         for jobID in jobs:
             analysis_timeseries(