From c77630a97116cfe48788a474eaf76b1887d1479f Mon Sep 17 00:00:00 2001
From: Anne Philipp <anne.philipp@univie.ac.at>
Date: Tue, 13 Aug 2019 14:32:22 +0200
Subject: [PATCH] BUGFIX: for python3-eccodes the file openings need to be in
binary mode! added binary marker in filemode
---
Source/Python/Classes/EcFlexpart.py | 26 +++++++++---------
Source/Python/Classes/GribUtil.py | 37 +++++++++-----------------
Source/Python/Classes/MarsRetrieval.py | 4 +--
Source/Python/Mods/tools.py | 2 +-
4 files changed, 29 insertions(+), 40 deletions(-)
diff --git a/Source/Python/Classes/EcFlexpart.py b/Source/Python/Classes/EcFlexpart.py
index a41442a..85c458c 100644
--- a/Source/Python/Classes/EcFlexpart.py
+++ b/Source/Python/Classes/EcFlexpart.py
@@ -1093,9 +1093,9 @@ class EcFlexpart(object):
t_dt.strftime('%Y%m%d%H') + numbersuffix)
print("outputfile = " + fnout)
- f_handle = open(fnout, 'w')
- h_handle = open(hnout, 'w')
- g_handle = open(gnout, 'w')
+ f_handle = open(fnout, 'wb')
+ h_handle = open(hnout, 'wb')
+ g_handle = open(gnout, 'wb')
# read message for message and store relevant data fields, where
# data keywords are stored in pars
@@ -1401,13 +1401,13 @@ class EcFlexpart(object):
# write original time step to flux file as usual
fluxfile = GribUtil(os.path.join(c.inputdir, fluxfilename))
- fluxfile.set_keys(tmpfile, filemode='a', strict=True,
+ fluxfile.set_keys(tmpfile, filemode='ab', strict=True,
wherekeynames=['paramId'], wherekeyvalues=[142],
keynames=['perturbationNumber','date','time','stepRange','values'],
keyvalues=[inumb, int(date.strftime('%Y%m%d')),
date.hour*100, 0, lsp_new_np[inumb,:,it]],
)
- fluxfile.set_keys(tmpfile, filemode='a', strict=True,
+ fluxfile.set_keys(tmpfile, filemode='ab', strict=True,
wherekeynames=['paramId'], wherekeyvalues=[143],
keynames=['perturbationNumber','date','time','stepRange','values'],
keyvalues=[inumb,int(date.strftime('%Y%m%d')),
@@ -1415,13 +1415,13 @@ class EcFlexpart(object):
)
# rr for first subgrid point is identified by step = 1
- fluxfile.set_keys(tmpfile, filemode='a', strict=True,
+ fluxfile.set_keys(tmpfile, filemode='ab', strict=True,
wherekeynames=['paramId'], wherekeyvalues=[142],
keynames=['perturbationNumber','date','time','stepRange','values'],
keyvalues=[inumb,int(date.strftime('%Y%m%d')),
date.hour*100, '1', lsp_new_np[inumb,:,it+1]]
)
- fluxfile.set_keys(tmpfile, filemode='a', strict=True,
+ fluxfile.set_keys(tmpfile, filemode='ab', strict=True,
wherekeynames=['paramId'], wherekeyvalues=[143],
keynames=['perturbationNumber','date','time','stepRange','values'],
keyvalues=[inumb,int(date.strftime('%Y%m%d')),
@@ -1429,13 +1429,13 @@ class EcFlexpart(object):
)
# rr for second subgrid point is identified by step = 2
- fluxfile.set_keys(tmpfile, filemode='a', strict=True,
+ fluxfile.set_keys(tmpfile, filemode='ab', strict=True,
wherekeynames=['paramId'], wherekeyvalues=[142],
keynames=['perturbationNumber','date','time','stepRange','values'],
keyvalues=[inumb,int(date.strftime('%Y%m%d')),
date.hour*100, '2', lsp_new_np[inumb,:,it+2]]
)
- fluxfile.set_keys(tmpfile, filemode='a', strict=True,
+ fluxfile.set_keys(tmpfile, filemode='ab', strict=True,
wherekeynames=['paramId'], wherekeyvalues=[143],
keynames=['perturbationNumber','date','time','stepRange','values'],
keyvalues=[inumb,int(date.strftime('%Y%m%d')),
@@ -1465,10 +1465,10 @@ class EcFlexpart(object):
gribfile = GribUtil(os.path.join(inputdir,'rr_grib_dummy.grb'))
gribfile.copy_dummy_msg(ifile, keynames=['paramId'],
- keyvalues=[142], filemode='w')
+ keyvalues=[142], filemode='wb')
gribfile.copy_dummy_msg(ifile, keynames=['paramId'],
- keyvalues=[143], filemode='a')
+ keyvalues=[143], filemode='ab')
return
@@ -1572,7 +1572,7 @@ class EcFlexpart(object):
for k, f in fdict.items():
fortfile = os.path.join(c.inputdir, 'fort.' + k)
silent_remove(fortfile)
- fdict[k] = open(fortfile, 'w')
+ fdict[k] = open(fortfile, 'wb')
#============================================================================================
# create correct timestamp from the three time informations
cdate = str(codes_get(gid, 'date'))
@@ -1607,7 +1607,7 @@ class EcFlexpart(object):
#if c.wrf:
# if 'olddate' not in locals() or cdate != olddate:
# fwrf = open(os.path.join(c.outputdir,
- # 'WRF' + cdate + '.' + ctime + '.000.grb2'), 'w')
+ # 'WRF' + cdate + '.' + ctime + '.000.grb2'), 'wb')
# olddate = cdate[:]
#============================================================================================
# savedfields remembers which fields were already used.
diff --git a/Source/Python/Classes/GribUtil.py b/Source/Python/Classes/GribUtil.py
index 68e8746..2a895d6 100644
--- a/Source/Python/Classes/GribUtil.py
+++ b/Source/Python/Classes/GribUtil.py
@@ -90,15 +90,11 @@ class GribUtil(object):
from eccodes import (codes_new_from_file, codes_is_defined, codes_get,
codes_release)
- fileid = open(self.filenames, 'r')
-
return_list = []
- while 1:
- gid = codes_new_from_file(fileid)
+ with open(self.filenames, 'rb') as fileid:
- if gid is None:
- break
+ gid = codes_new_from_file(fileid)
if len(wherekeynames) != len(wherekeyvalues):
raise Exception("Number of key values and key names must be \
@@ -122,13 +118,11 @@ class GribUtil(object):
codes_release(gid)
- fileid.close()
-
return return_list
def set_keys(self, fromfile, keynames, keyvalues, wherekeynames=[],
- wherekeyvalues=[], strict=False, filemode='w'):
+ wherekeyvalues=[], strict=False, filemode='wb'):
'''Opens the file to read the grib messages and then write
the selected messages (with wherekeys) to a new output file.
Also, the keyvalues of the passed list of keynames are set.
@@ -160,7 +154,7 @@ class GribUtil(object):
meeting the where statement (True). Default is False.
filemode : :obj:`string`, optional
- Sets the mode for the output file. Default is "w".
+ Sets the mode for the output file. Default is "wb".
Return
------
@@ -174,14 +168,10 @@ class GribUtil(object):
raise Exception("Give a value for each keyname!")
fout = open(self.filenames, filemode)
- fin = open(fromfile)
- while 1:
+ with open(fromfile, 'rb') as fin:
gid = codes_grib_new_from_file(fin)
- if gid is None:
- break
-
select = True
i = 0
for wherekey in wherekeynames:
@@ -205,13 +195,12 @@ class GribUtil(object):
codes_release(gid)
- fin.close()
fout.close()
return
def copy_dummy_msg(self, filename_in, selectWhere=True,
- keynames=[], keyvalues=[], filemode='w'):
+ keynames=[], keyvalues=[], filemode='wb'):
'''Add the content of another input grib file to the objects file but
only messages corresponding to keys/values passed to the function.
The selectWhere switch decides if to copy the keys equal to (True) or
@@ -234,7 +223,7 @@ class GribUtil(object):
List of keyvalues. Default is an empty list.
filemode : :obj:`string`, optional
- Sets the mode for the output file. Default is "w".
+ Sets the mode for the output file. Default is "wb".
Return
------
@@ -246,16 +235,17 @@ class GribUtil(object):
if len(keynames) != len(keyvalues):
raise Exception("Give a value for each keyname!")
- fin = open(filename_in, 'rb')
+
fout = open(self.filenames, filemode)
fields = 0
- while fields < 1:
- gid = codes_grib_new_from_file(fin)
+ with open(filename_in, 'rb') as fin:
+ if fields >= 1:
+ fout.close()
+ return
- if gid is None:
- break
+ gid = codes_grib_new_from_file(fin)
select = True
i = 0
@@ -277,7 +267,6 @@ class GribUtil(object):
codes_release(gid)
- fin.close()
fout.close()
return
diff --git a/Source/Python/Classes/MarsRetrieval.py b/Source/Python/Classes/MarsRetrieval.py
index 5fe2211..d68c183 100644
--- a/Source/Python/Classes/MarsRetrieval.py
+++ b/Source/Python/Classes/MarsRetrieval.py
@@ -487,7 +487,7 @@ class MarsRetrieval(object):
for key in empty_keys:
del attrs[key]
- attrs['ppengine'] = 'emos'
+# attrs['ppengine'] = 'emos'
# MARS request via Python script
if self.server:
@@ -519,7 +519,7 @@ class MarsRetrieval(object):
for key, value in attrs.items():
request_str = request_str + ',' + key + '=' + str(value)
request_str += ',target="' + target + '"'
- p = subprocess.Popen(['mars', '-e'],
+ p = subprocess.Popen(['mars'], #'-e'],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
diff --git a/Source/Python/Mods/tools.py b/Source/Python/Mods/tools.py
index 8a94f58..078c77e 100644
--- a/Source/Python/Mods/tools.py
+++ b/Source/Python/Mods/tools.py
@@ -762,7 +762,7 @@ def get_informations(filename):
# --- open file ---
print("Opening file for getting information data --- %s" % filename)
- with open(filename) as f:
+ with open(filename, 'rb') as f:
# load first message from file
gid = codes_grib_new_from_file(f)
--
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