Batch download data from OpenDAP using Python
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I am trying to download multiple .nc files from OpenDAP. When I download the files manually (without a script) the files work as expected. To try speed the process up, I have a script that batch downloads data. However, when I download data using xarray the files are 10x larger and the files seem to be corrupted.
My script looks like this:
import pandas as pd
import xarray as xr
import os
import numpy as np
dates = pd.date_range(start='2016-01-01',end='2016-01-05',freq='D')
my_url = "http://www.ifremer.fr/opendap/cerdap1/ghrsst/l4/saf/odyssea-nrt/data/"
print(" ")
print("Downloading data from OPeNDAP - sit back, relax, this will take a while...")
print("...")
print("...")
# Create a list of url's
data_url =
cnt = 0
for i in np.arange(1,5):
ii = i+1
data_url.append(my_url + str(dates[cnt].year)+"/"+ str('%03d'%+ii)+"/"
+str(dates[cnt+1].year)+str('%02d'%dates[cnt+1].month)+str('%02d'%dates[cnt+1].day)
+"-IFR-L4_GHRSST-SSTfnd-ODYSSEA-SAF_002-v2.0-fv1.0.nc?time[0:1:0],lat[0:1:1749],lon[0:1:2249],analysed_sst[0:1:0][0:1:1749][0:1:2249],analysis_error[0:1:0][0:1:1749][0:1:2249],mask[0:1:0][0:1:1749][0:1:2249],sea_ice_fraction[0:1:0][0:1:1749][0:1:2249]")
cnt = cnt+1
url_list = data_url
# Download data from the url's
count = 0
for data in url_list:
print('Downloading file:', str(count))
ds = xr.open_dataset(data,autoclose=True)
fname = 'SAFodyssea_sst'+str(dates[count+1].year)+str('%02d'%dates[count+1].month)+str('%02d'%dates[count+1].day)+'.nc'
ds.to_netcdf(fname)
count = count +1
del ds, fname
print('DONE !!!')
I have xarray version 0.10.8. I have tried running this using python 2.7 and python 3.5.6 as well as on windows 10 and Ubuntu 16.04 and I get the same result.
Your help is much appreciated.
python python-xarray opendap
asked Nov 15 '18 at 7:12
JetmanJetman
3081617
add a comment |
I am trying to download multiple .nc files from OpenDAP. When I download the files manually (without a script) the files work as expected. To try speed the process up, I have a script that batch downloads data. However, when I download data using xarray the files are 10x larger and the files seem to be corrupted.
My script looks like this:
import pandas as pd
import xarray as xr
import os
import numpy as np
dates = pd.date_range(start='2016-01-01',end='2016-01-05',freq='D')
my_url = "http://www.ifremer.fr/opendap/cerdap1/ghrsst/l4/saf/odyssea-nrt/data/"
print(" ")
print("Downloading data from OPeNDAP - sit back, relax, this will take a while...")
print("...")
print("...")
# Create a list of url's
data_url =
cnt = 0
for i in np.arange(1,5):
ii = i+1
data_url.append(my_url + str(dates[cnt].year)+"/"+ str('%03d'%+ii)+"/"
+str(dates[cnt+1].year)+str('%02d'%dates[cnt+1].month)+str('%02d'%dates[cnt+1].day)
+"-IFR-L4_GHRSST-SSTfnd-ODYSSEA-SAF_002-v2.0-fv1.0.nc?time[0:1:0],lat[0:1:1749],lon[0:1:2249],analysed_sst[0:1:0][0:1:1749][0:1:2249],analysis_error[0:1:0][0:1:1749][0:1:2249],mask[0:1:0][0:1:1749][0:1:2249],sea_ice_fraction[0:1:0][0:1:1749][0:1:2249]")
cnt = cnt+1
url_list = data_url
# Download data from the url's
count = 0
for data in url_list:
print('Downloading file:', str(count))
ds = xr.open_dataset(data,autoclose=True)
fname = 'SAFodyssea_sst'+str(dates[count+1].year)+str('%02d'%dates[count+1].month)+str('%02d'%dates[count+1].day)+'.nc'
ds.to_netcdf(fname)
count = count +1
del ds, fname
print('DONE !!!')
I have xarray version 0.10.8. I have tried running this using python 2.7 and python 3.5.6 as well as on windows 10 and Ubuntu 16.04 and I get the same result.
Your help is much appreciated.
python python-xarray opendap
asked Nov 15 '18 at 7:12
JetmanJetman
3081617
There’s no particular reason why you should use opendap to access this data. If you can access a server with netcdf files, you can download them using Python, e.g., with the requests library.
– shoyer
Nov 15 '18 at 7:57
@shoyer I'm not sure I completely understand. I only have access to the data through opendap
– Jetman
Nov 15 '18 at 8:05
How do you "download the files manually"?
– shoyer
Nov 15 '18 at 21:25
@shoyer I copy and paste the url into my web browser. If you have an alternative method toxarrayi'd be interested to see. This is my first attempt at using a script to batch download data and I'm not sure how else to do this?
– Jetman
Nov 16 '18 at 4:22
add a comment |
I am trying to download multiple .nc files from OpenDAP. When I download the files manually (without a script) the files work as expected. To try speed the process up, I have a script that batch downloads data. However, when I download data using xarray the files are 10x larger and the files seem to be corrupted.
My script looks like this:
import pandas as pd
import xarray as xr
import os
import numpy as np
dates = pd.date_range(start='2016-01-01',end='2016-01-05',freq='D')
my_url = "http://www.ifremer.fr/opendap/cerdap1/ghrsst/l4/saf/odyssea-nrt/data/"
print(" ")
print("Downloading data from OPeNDAP - sit back, relax, this will take a while...")
print("...")
print("...")
# Create a list of url's
data_url =
cnt = 0
for i in np.arange(1,5):
ii = i+1
data_url.append(my_url + str(dates[cnt].year)+"/"+ str('%03d'%+ii)+"/"
+str(dates[cnt+1].year)+str('%02d'%dates[cnt+1].month)+str('%02d'%dates[cnt+1].day)
+"-IFR-L4_GHRSST-SSTfnd-ODYSSEA-SAF_002-v2.0-fv1.0.nc?time[0:1:0],lat[0:1:1749],lon[0:1:2249],analysed_sst[0:1:0][0:1:1749][0:1:2249],analysis_error[0:1:0][0:1:1749][0:1:2249],mask[0:1:0][0:1:1749][0:1:2249],sea_ice_fraction[0:1:0][0:1:1749][0:1:2249]")
cnt = cnt+1
url_list = data_url
# Download data from the url's
count = 0
for data in url_list:
print('Downloading file:', str(count))
ds = xr.open_dataset(data,autoclose=True)
fname = 'SAFodyssea_sst'+str(dates[count+1].year)+str('%02d'%dates[count+1].month)+str('%02d'%dates[count+1].day)+'.nc'
ds.to_netcdf(fname)
count = count +1
del ds, fname
print('DONE !!!')
I have xarray version 0.10.8. I have tried running this using python 2.7 and python 3.5.6 as well as on windows 10 and Ubuntu 16.04 and I get the same result.
Your help is much appreciated.
python python-xarray opendap
asked Nov 15 '18 at 7:12
JetmanJetman
3081617
I am trying to download multiple .nc files from OpenDAP. When I download the files manually (without a script) the files work as expected. To try speed the process up, I have a script that batch downloads data. However, when I download data using xarray the files are 10x larger and the files seem to be corrupted.
My script looks like this:
import pandas as pd
import xarray as xr
import os
import numpy as np
dates = pd.date_range(start='2016-01-01',end='2016-01-05',freq='D')
my_url = "http://www.ifremer.fr/opendap/cerdap1/ghrsst/l4/saf/odyssea-nrt/data/"
print(" ")
print("Downloading data from OPeNDAP - sit back, relax, this will take a while...")
print("...")
print("...")
# Create a list of url's
data_url =
cnt = 0
for i in np.arange(1,5):
ii = i+1
data_url.append(my_url + str(dates[cnt].year)+"/"+ str('%03d'%+ii)+"/"
+str(dates[cnt+1].year)+str('%02d'%dates[cnt+1].month)+str('%02d'%dates[cnt+1].day)
+"-IFR-L4_GHRSST-SSTfnd-ODYSSEA-SAF_002-v2.0-fv1.0.nc?time[0:1:0],lat[0:1:1749],lon[0:1:2249],analysed_sst[0:1:0][0:1:1749][0:1:2249],analysis_error[0:1:0][0:1:1749][0:1:2249],mask[0:1:0][0:1:1749][0:1:2249],sea_ice_fraction[0:1:0][0:1:1749][0:1:2249]")
cnt = cnt+1
url_list = data_url
# Download data from the url's
count = 0
for data in url_list:
print('Downloading file:', str(count))
ds = xr.open_dataset(data,autoclose=True)
fname = 'SAFodyssea_sst'+str(dates[count+1].year)+str('%02d'%dates[count+1].month)+str('%02d'%dates[count+1].day)+'.nc'
ds.to_netcdf(fname)
count = count +1
del ds, fname
print('DONE !!!')
I have xarray version 0.10.8. I have tried running this using python 2.7 and python 3.5.6 as well as on windows 10 and Ubuntu 16.04 and I get the same result.
Your help is much appreciated.
python python-xarray opendap
python python-xarray opendap
asked Nov 15 '18 at 7:12
JetmanJetman
3081617
asked Nov 15 '18 at 7:12
JetmanJetman
3081617
edited Nov 15 '18 at 8:03
Jetman
asked Nov 15 '18 at 7:12
JetmanJetman
3081617
asked Nov 15 '18 at 7:12
JetmanJetman
3081617
asked Nov 15 '18 at 7:12
JetmanJetman
3081617
3081617
There’s no particular reason why you should use opendap to access this data. If you can access a server with netcdf files, you can download them using Python, e.g., with the requests library.
– shoyer
Nov 15 '18 at 7:57
@shoyer I'm not sure I completely understand. I only have access to the data through opendap
– Jetman
Nov 15 '18 at 8:05
How do you "download the files manually"?
– shoyer
Nov 15 '18 at 21:25
@shoyer I copy and paste the url into my web browser. If you have an alternative method toxarrayi'd be interested to see. This is my first attempt at using a script to batch download data and I'm not sure how else to do this?
– Jetman
Nov 16 '18 at 4:22
add a comment |
There’s no particular reason why you should use opendap to access this data. If you can access a server with netcdf files, you can download them using Python, e.g., with the requests library.
– shoyer
Nov 15 '18 at 7:57
@shoyer I'm not sure I completely understand. I only have access to the data through opendap
– Jetman
Nov 15 '18 at 8:05
How do you "download the files manually"?
– shoyer
Nov 15 '18 at 21:25
@shoyer I copy and paste the url into my web browser. If you have an alternative method toxarrayi'd be interested to see. This is my first attempt at using a script to batch download data and I'm not sure how else to do this?
– Jetman
Nov 16 '18 at 4:22
There’s no particular reason why you should use opendap to access this data. If you can access a server with netcdf files, you can download them using Python, e.g., with the requests library.
– shoyer
Nov 15 '18 at 7:57
There’s no particular reason why you should use opendap to access this data. If you can access a server with netcdf files, you can download them using Python, e.g., with the requests library.
– shoyer
Nov 15 '18 at 7:57
@shoyer I'm not sure I completely understand. I only have access to the data through opendap
– Jetman
Nov 15 '18 at 8:05
@shoyer I'm not sure I completely understand. I only have access to the data through opendap
– Jetman
Nov 15 '18 at 8:05
How do you "download the files manually"?
– shoyer
Nov 15 '18 at 21:25
How do you "download the files manually"?
– shoyer
Nov 15 '18 at 21:25
@shoyer I copy and paste the url into my web browser. If you have an alternative method to
xarray i'd be interested to see. This is my first attempt at using a script to batch download data and I'm not sure how else to do this?– Jetman
Nov 16 '18 at 4:22
@shoyer I copy and paste the url into my web browser. If you have an alternative method to
xarray i'd be interested to see. This is my first attempt at using a script to batch download data and I'm not sure how else to do this?– Jetman
Nov 16 '18 at 4:22
add a comment |
1 Answer
1
active
oldest
votes
Each of these files as an associated URL for the netCDF file, e.g.,
http://www.ifremer.fr/opendap/cerdap1/ghrsst/l4/saf/odyssea-nrt/data/2018/001/20180101-IFR-L4_GHRSST-SSTfnd-ODYSSEA-SAF_002-v2.0-fv1.0.nc
One simple way to solve this problem would be to use a library such as requests to download each file, e.g., as described here:
How to download large file in python with requests.py?
answered Nov 16 '18 at 23:45
shoyershoyer
5,1271534
Thanks very much. I ended up usingurllibto download the data. It was a lot easier than I initially though it would be.
– Jetman
Nov 17 '18 at 10:44
add a comment |
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1 Answer
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1 Answer
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active
oldest
votes
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votes
Each of these files as an associated URL for the netCDF file, e.g.,
http://www.ifremer.fr/opendap/cerdap1/ghrsst/l4/saf/odyssea-nrt/data/2018/001/20180101-IFR-L4_GHRSST-SSTfnd-ODYSSEA-SAF_002-v2.0-fv1.0.nc
One simple way to solve this problem would be to use a library such as requests to download each file, e.g., as described here:
How to download large file in python with requests.py?
answered Nov 16 '18 at 23:45
shoyershoyer
5,1271534
Thanks very much. I ended up usingurllibto download the data. It was a lot easier than I initially though it would be.
– Jetman
Nov 17 '18 at 10:44
add a comment |
Each of these files as an associated URL for the netCDF file, e.g.,
http://www.ifremer.fr/opendap/cerdap1/ghrsst/l4/saf/odyssea-nrt/data/2018/001/20180101-IFR-L4_GHRSST-SSTfnd-ODYSSEA-SAF_002-v2.0-fv1.0.nc
One simple way to solve this problem would be to use a library such as requests to download each file, e.g., as described here:
How to download large file in python with requests.py?
answered Nov 16 '18 at 23:45
shoyershoyer
5,1271534
Thanks very much. I ended up usingurllibto download the data. It was a lot easier than I initially though it would be.
– Jetman
Nov 17 '18 at 10:44
add a comment |
Each of these files as an associated URL for the netCDF file, e.g.,
http://www.ifremer.fr/opendap/cerdap1/ghrsst/l4/saf/odyssea-nrt/data/2018/001/20180101-IFR-L4_GHRSST-SSTfnd-ODYSSEA-SAF_002-v2.0-fv1.0.nc
One simple way to solve this problem would be to use a library such as requests to download each file, e.g., as described here:
How to download large file in python with requests.py?
answered Nov 16 '18 at 23:45
shoyershoyer
5,1271534
Each of these files as an associated URL for the netCDF file, e.g.,
http://www.ifremer.fr/opendap/cerdap1/ghrsst/l4/saf/odyssea-nrt/data/2018/001/20180101-IFR-L4_GHRSST-SSTfnd-ODYSSEA-SAF_002-v2.0-fv1.0.nc
One simple way to solve this problem would be to use a library such as requests to download each file, e.g., as described here:
How to download large file in python with requests.py?
answered Nov 16 '18 at 23:45
shoyershoyer
5,1271534
answered Nov 16 '18 at 23:45
shoyershoyer
5,1271534
answered Nov 16 '18 at 23:45
shoyershoyer
5,1271534
answered Nov 16 '18 at 23:45
shoyershoyer
5,1271534
5,1271534
Thanks very much. I ended up usingurllibto download the data. It was a lot easier than I initially though it would be.
– Jetman
Nov 17 '18 at 10:44
add a comment |
Thanks very much. I ended up usingurllibto download the data. It was a lot easier than I initially though it would be.
– Jetman
Nov 17 '18 at 10:44
Thanks very much. I ended up using
urllib to download the data. It was a lot easier than I initially though it would be.– Jetman
Nov 17 '18 at 10:44
Thanks very much. I ended up using
urllib to download the data. It was a lot easier than I initially though it would be.– Jetman
Nov 17 '18 at 10:44
add a comment |
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There’s no particular reason why you should use opendap to access this data. If you can access a server with netcdf files, you can download them using Python, e.g., with the requests library.
– shoyer
Nov 15 '18 at 7:57
@shoyer I'm not sure I completely understand. I only have access to the data through opendap
– Jetman
Nov 15 '18 at 8:05
How do you "download the files manually"?
– shoyer
Nov 15 '18 at 21:25
@shoyer I copy and paste the url into my web browser. If you have an alternative method to
xarrayi'd be interested to see. This is my first attempt at using a script to batch download data and I'm not sure how else to do this?– Jetman
Nov 16 '18 at 4:22