source: CCCC/tags/0.1/README.txt @ 151

Subversion URL: http://proj.badc.rl.ac.uk/svn/exarch/CCCC/tags/0.1/README.txt@283
Revision 151, 7.1 KB checked in by astephen, 6 years ago (diff)

Updates to run smoothly on CMIP5: taking type from mip tables; cleaned up error messages

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, CMIP5.
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
25After running:
26
27The log file directory may contain hundreds of files with reports of errors. To get a summary, run:
28
29python summary.py <log file directory>
30
31This will produce a listing of errors, the number of times they occur and up to two of the files which contain the error. It is hoped that inspection of one or 2 files will provide enough information to trace the problems which lead to the error reports.
32
33Called from python:
34------------------
35The code can also be called from a python script:
36
37import c4
38m = c4.main( args=argList )     # argList is a python list of command line arguments
39if not m.ok:
40  print 'check failed'
41else:
42  print 'success'
43  print 'DRS dictionary:', m.cc.drs    # print drs of last file checked -- not useful in multiple file mode.
44
45e.g.
46m = c4.main( args=[ '-p', 'CORDEX', '-f', dataFilePath, '--ld', logFileDirectory] )
47## run checks on a single file located at dataFilePath, and write logs to logFileDirectory
48
49DEPENDENCIES
50------------
51
52The library can uses the cdms2, python-netCDF4 or Scientific module to read NetCDF files.
53By default, it will use the cdms2 module if available. Support for the netCDF4 and Scientific modules has been added recently.
54To change the default, change the order in which modules are listed in the "supportedNetcdf" list in file_utils.py
55
56Is available as part of the cdat-lite package (http://proj.badc.rl.ac.uk/cedaservices/wiki/CdatLite ).
57For python-netCDF4, see http://code.google.com/p/netcdf4-python/.
58For Scientific see http://dirac.cnrs-orleans.fr/plone/software/scientificpython/  . Note that search engines confuse "ScientificPython" with "SciPy". The SciPy package also contains a netcdf API, but when tested in April 2014 this could not read data from NetCDF 4 files, and so is not supported here.
59
60OUTPUT
61------
62
63Single log (default for single file): 
64  -- log of errors found and checks passed
65  -- "Rec.txt" -- single record summarising results. If no errors are found, the archive directory path for the file will be in this record.
66
67Multi-log (default for multiple files):
68  -- separate log of errors for each file;
69  -- summary log, 3 records per file;
70  -- "Rec.txt" -- single record for each file, as above
71
72Log file modes.
73Valid modes are: 'a': append
74                 'n', 'np': new file, 'np': protect after closing (mode = 444)
75                 'w', 'wo': write (overwrite if present), 'wo': protect after closing (mode = 444)
76
77Note 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.
78
79Vocabulary lists GCMModelName.txt and RCMModelName.txt are held on the DMI CORDEX site:
80
81  http://cordex.dmi.dk/joomla/images/CORDEX/GCMModelName.txt
82  http://cordex.dmi.dk/joomla/images/CORDEX/RCMModelName.txt
83
84To update the CMOR tables use:
85"git clone git://uv-cdat.llnl.gov/gitweb/cordex-cmor-tables.git"
86
87VIRTUAL MODE
88------------
89
90The 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.
91
92To 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.
93
94A typical directive will be of the form:
95@var=rlus;standard_name=surface_upward_longwave_flux_in_air|standard_name=surface_upwelling_longwave_flux_in_air
96
97The 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".
98
99"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.
100
101Additional directives can be added. e.g.
102@;institute_id=mohc|institute_id=MOHC
103will instruct the code to replace "mohc" with "MOHC" in the global attribute "institute_id".
104
105If 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.
106
107After 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":
108
109python amap2nco.py attributeMappingsLog.txt /tmp/batch1 /tmp/batch1_corrected
110## this will generate a list of NCO commands in "ncoscript.sh", which will apply the changes and create new files in "/tmp/batch1_corrected".
111
112It is recommended that the data values in the corrected files should be checked after running this script.
113
114By 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.
115
116EXCEPTIONS
117----------
118The exception handling is designed to ensure that problems analysing one file do not prevent testing of other files.
119Traceback information is written to log file.
120
121BUGS
122----
123The 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.
124
125----------
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