Batch download data from OpenDAP using Python
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
183417
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
183417
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
183417
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
183417
asked Nov 15 '18 at 7:12
JetmanJetman
183417
edited Nov 15 '18 at 8:03
Jetman
asked Nov 15 '18 at 7:12
JetmanJetman
183417
asked Nov 15 '18 at 7:12
JetmanJetman
183417
asked Nov 15 '18 at 7:12
JetmanJetman
183417
183417
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
4,9891533
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 |
Your Answer
StackExchange.ifUsing("editor", function () {
StackExchange.using("externalEditor", function () {
StackExchange.using("snippets", function () {
StackExchange.snippets.init();
});
});
}, "code-snippets");
StackExchange.ready(function() {
var channelOptions = {
tags: "".split(" "),
id: "1"
};
initTagRenderer("".split(" "), "".split(" "), channelOptions);
StackExchange.using("externalEditor", function() {
// Have to fire editor after snippets, if snippets enabled
if (StackExchange.settings.snippets.snippetsEnabled) {
StackExchange.using("snippets", function() {
createEditor();
});
}
else {
createEditor();
}
});
function createEditor() {
StackExchange.prepareEditor({
heartbeatType: 'answer',
autoActivateHeartbeat: false,
convertImagesToLinks: true,
noModals: true,
showLowRepImageUploadWarning: true,
reputationToPostImages: 10,
bindNavPrevention: true,
postfix: "",
imageUploader: {
brandingHtml: "Powered by u003ca class="icon-imgur-white" href="https://imgur.com/"u003eu003c/au003e",
contentPolicyHtml: "User contributions licensed under u003ca href="https://creativecommons.org/licenses/by-sa/3.0/"u003ecc by-sa 3.0 with attribution requiredu003c/au003e u003ca href="https://stackoverflow.com/legal/content-policy"u003e(content policy)u003c/au003e",
allowUrls: true
},
onDemand: true,
discardSelector: ".discard-answer"
,immediatelyShowMarkdownHelp:true
});
}
});
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
StackExchange.ready(
function () {
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fstackoverflow.com%2fquestions%2f53314156%2fbatch-download-data-from-opendap-using-python%23new-answer', 'question_page');
}
);
Post as a guest
Required, but never shown
1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
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
4,9891533
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
4,9891533
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
4,9891533
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
4,9891533
answered Nov 16 '18 at 23:45
shoyershoyer
4,9891533
answered Nov 16 '18 at 23:45
shoyershoyer
4,9891533
answered Nov 16 '18 at 23:45
shoyershoyer
4,9891533
4,9891533
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 |
Thanks for contributing an answer to Stack Overflow!
- Please be sure to answer the question. Provide details and share your research!
But avoid …
- Asking for help, clarification, or responding to other answers.
- Making statements based on opinion; back them up with references or personal experience.
To learn more, see our tips on writing great answers.
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
StackExchange.ready(
function () {
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fstackoverflow.com%2fquestions%2f53314156%2fbatch-download-data-from-opendap-using-python%23new-answer', 'question_page');
}
);
Post as a guest
Required, but never shown
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
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