source: CCCC/trunk/README.txt @ 147

Subversion URL: http://proj.badc.rl.ac.uk/svn/exarch/CCCC/trunk/README.txt@147
Revision 147, 6.1 KB checked in by mjuckes, 7 years ago (diff)

Support for netCDF4 added. File metadata module move to new file_utils.py file

Line 
1USAGE
2-----
3
4From the command line:
5----------------------
6
7Required arguments:
8
9python c4.py -p <project> -D <directory>  ## check all files in directory tree, for project in SPECS, CORDEX, CCMI.
10python c4.py -p <project> -d <directory>  ## check all files in directory
11python c4.py -p <project> -f <file>       ## check a single file.
12
13Optional arguments:
14
15  --ld <log file directory>  ## directory to take log files;
16  -R <record file name> ## file name for file to take one record per file checked;
17  --cae                 ## "catch all errors": will trap exceptions and record
18                             in  log files, and then continue. Default is to
19                            stop after unrecognised exceptions.
20  --log <single|multi>  ## Set log file management option -- see "Single log" and "Multi-log" below.
21  --blfmode <mode>      # set mode for batch log file -- see log file modes
22  --flfmode <mode>      # set mode for file-level log file -- see log file modes
23  --aMap                # Read in some attribute mappings and run tests with virtual substitutions, see also map2nco.py
24
25
26Called from python:
27------------------
28The code can also be called from a python script:
29
30import c4
31m = c4.main( args=argList )     # argList is a python list of command line arguments
32if not m.ok:
33  print 'check failed'
34else:
35  print 'success'
36  print 'DRS dictionary:', m.cc.drs    # print drs of last file checked -- not useful in multiple file mode.
37
38e.g.
39m = c4.main( args=[ '-p', 'CORDEX', '-f', dataFilePath, '--ld', logFileDirectory] )
40## run checks on a single file located at dataFilePath, and write logs to logFileDirectory
41
42DEPENDENCIES
43------------
44
45The library can uses the cdms2 module or the netCDF4 module to read NetCDF files.
46By default, it will use the cdms2 module if available. Support for the netCDF4 module has been added recently.
47
48OUTPUT
49------
50
51Single log (default for single file): 
52  -- log of errors found and checks passed
53  -- "Rec.txt" -- single record summarising results. If no errors are found, the archive directory path for the file will be in this record.
54
55Multi-log (default for multiple files):
56  -- separate log of errors for each file;
57  -- summary log, 3 records per file;
58  -- "Rec.txt" -- single record for each file, as above
59
60Log file modes.
61Valid modes are: 'a': append
62                 'n', 'np': new file, 'np': protect after closing (mode = 444)
63                 'w', 'wo': write (overwrite if present), 'wo': protect after closing (mode = 444)
64
65Note that the log files generated in multi-log mode will re-use file names. If running with --flfmode set to 'n','np' or 'wo' it will be necessary to change or clear the target directory. The names of batch log files include the time, to the nearest second, when the process is started, so will not generally suffer from re-use.
66
67Vocabulary lists GCMModelName.txt and RCMModelName.txt are held on the DMI CORDEX site:
68
69  http://cordex.dmi.dk/joomla/images/CORDEX/GCMModelName.txt
70  http://cordex.dmi.dk/joomla/images/CORDEX/RCMModelName.txt
71
72To update the CMOR tables use:
73"git clone git://uv-cdat.llnl.gov/gitweb/cordex-cmor-tables.git"
74
75VIRTUAL MODE
76------------
77
78The virtual mode can be used to validate substituions before adjusting systems which have been used to generate data, or as the first step of a procedure for repairing some classes of errors.
79
80To use this mode, a mapping file is needed. This can be generated by an initial run of the checker with no virtual substitutions. A file named "amapDraft.txt" will be generated. This file should be inspected to ensure that suggested changes make sense.
81
82A typical directive will be of the form:
83@var=rlus;standard_name=surface_upward_longwave_flux_in_air|standard_name=surface_upwelling_longwave_flux_in_air
84
85The meaning is: for variable "rlus", set the attribute "standard_name" to "surface_upwelling_longwave_flux_in_air" where the input file has "surface_upward_longwave_flux_in_air".
86
87"amapDraft.txt" should be copied to a new location before running in virtual mode. This draft will only contain directives for errors if the corect value is unique. The suggested corrections to variable attributes will make these consistent with the variable name. If the inconsistency has arisen because a variable has been given the wrong name this will exaggerate the problem rather than solving it. All changes should be checked.
88
89Additional directives can be added. e.g.
90@;institute_id=mohc|institute_id=MOHC
91will instruct the code to replace "mohc" with "MOHC" in the global attribute "institute_id".
92
93If run with the --aMap flag, the checker will test attributes after making virtual substituions. I.e. there are no changes made to the files at this stage, but results of the tests apply as if changes have been made.
94
95After running in virtual mode, c4.py will generate a file named "attributeMappingsLog.txt" which contains a record for every change to every file. If the results of running in virtual mode are positive, this file can be used to create a script to modify the files, by running "amap2nco.py":
96
97python amap2nco.py attributeMappingsLog.txt /tmp/batch1 /tmp/batch1_corrected
98## this will generate a list of NCO commands in "ncoscript.sh", which will apply the changes and create new files in "/tmp/batch1_corrected".
99
100It is recommended that the data values in the corrected files should be checked after running this script.
101
102By default, the amap2nco.py program will generate commands to modify the tracking_id and creation_date global attributes at the same time as making other changed. The "history" attribute is modified by the NCO library.
103
104EXCEPTIONS
105----------
106The exception handling is designed to ensure that problems analysing one file do not prevent testing of other files.
107Traceback information is written to log file.
108
109BUGS
110----
111The cmds2 library generates a data array for dimensions if there is none present in the file. Tests applied to this library generated array will generate mis-leading error messages. Within cmds2 there is no clear method of distinguishing between library generates arrays and those which exist in the data file. The solution may be to move to using the NetCDF4 module instead.
112
113----------
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