notebook.community

Edit and run 





In [3]:



    


import file_transfer.datamover as dm



    











In [5]:



    


import os
import h5py



    











In [6]:



    


s3handle = dm.S3EnramHandler(bucket_name="lw-enram", profile_name="lw-enram")



    











In [7]:



    


s3handle.bucket.objects.all()



    


















    
Out[7]:








s3.Bucket.objectsCollection(s3.Bucket(name='lw-enram'), s3.ObjectSummary)

Temp





In [11]:



    


from file_transfer.creds import URL, LOGIN, PASSWORD



    











In [12]:



    


btos = dm.BaltradToS3(URL, LOGIN, PASSWORD, "lw-enram", profile_name="lw-enram")



    











In [13]:



    


btos.transfer(name_match="_vp_", overwrite=True, 
              limit=5, verbose=True)



    


















    






czbrd_vp_20170912223000.h5 is succesfully transferred to S3 bucket
czbrd_vp_20170912224500.h5 is succesfully transferred to S3 bucket
czbrd_vp_20170912230000.h5 is succesfully transferred to S3 bucket
czbrd_vp_20170912233000.h5 is succesfully transferred to S3 bucket
czbrd_vp_20170912234500.h5 is succesfully transferred to S3 bucket

















In [15]:



    


btos.transferred



    


















    
Out[15]:








['czbrd_vp_20170912223000.h5',
 'czbrd_vp_20170912224500.h5',
 'czbrd_vp_20170912230000.h5',
 'czbrd_vp_20170912233000.h5',
 'czbrd_vp_20170912234500.h5']

















In [29]:



    


s3handle.create_zip_version(btos.transferred)



    


















    






---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/site-packages/botocore/vendored/requests/packages/urllib3/connectionpool.py in _make_request(self, conn, method, url, timeout, **httplib_request_kw)
    371             try:  # Python 2.7, use buffering of HTTP responses
--> 372                 httplib_response = conn.getresponse(buffering=True)
    373             except TypeError:  # Python 2.6 and older

TypeError: getresponse() got an unexpected keyword argument 'buffering'

During handling of the above exception, another exception occurred:

KeyboardInterrupt                         Traceback (most recent call last)
<ipython-input-29-e0aa4f0bc90a> in <module>()
----> 1 s3handle.create_zip_version(btos.transferred)

~/githubs/enram_infrastructure/file_transfer/datamover/s3enram.py in create_zip_version(self, keylisting)
    101             for key in self.list_files(
    102                     path="/".join([country, radar, year, month])):
--> 103                 self.download_file(key)
    104                 current_keys.append(key)
    105 

~/githubs/enram_infrastructure/file_transfer/datamover/connectors.py in download_file(self, file)
    166         """
    167         response = self.s3client.get_object(Bucket=self.bucket_name,
--> 168                                             Key=file)
    169         full_name = file
    170         os.makedirs(os.path.dirname(full_name), exist_ok=True)

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/site-packages/botocore/client.py in _api_call(self, *args, **kwargs)
    308                     "%s() only accepts keyword arguments." % py_operation_name)
    309             # The "self" in this scope is referring to the BaseClient.
--> 310             return self._make_api_call(operation_name, kwargs)
    311 
    312         _api_call.__name__ = str(py_operation_name)

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/site-packages/botocore/client.py in _make_api_call(self, operation_name, api_params)
    584         else:
    585             http, parsed_response = self._endpoint.make_request(
--> 586                 operation_model, request_dict)
    587 
    588         self.meta.events.emit(

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/site-packages/botocore/endpoint.py in make_request(self, operation_model, request_dict)
    139         logger.debug("Making request for %s (verify_ssl=%s) with params: %s",
    140                      operation_model, self.verify, request_dict)
--> 141         return self._send_request(request_dict, operation_model)
    142 
    143     def create_request(self, params, operation_model=None):

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/site-packages/botocore/endpoint.py in _send_request(self, request_dict, operation_model)
    166         request = self.create_request(request_dict, operation_model)
    167         success_response, exception = self._get_response(
--> 168             request, operation_model, attempts)
    169         while self._needs_retry(attempts, operation_model, request_dict,
    170                                 success_response, exception):

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/site-packages/botocore/endpoint.py in _get_response(self, request, operation_model, attempts)
    202                 request, verify=self.verify,
    203                 stream=operation_model.has_streaming_output,
--> 204                 proxies=self.proxies, timeout=self.timeout)
    205         except ConnectionError as e:
    206             # For a connection error, if it looks like it's a DNS

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/site-packages/botocore/vendored/requests/sessions.py in send(self, request, **kwargs)
    571 
    572         # Send the request
--> 573         r = adapter.send(request, **kwargs)
    574 
    575         # Total elapsed time of the request (approximately)

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/site-packages/botocore/vendored/requests/adapters.py in send(self, request, stream, timeout, verify, cert, proxies)
    368                     decode_content=False,
    369                     retries=self.max_retries,
--> 370                     timeout=timeout
    371                 )
    372 

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/site-packages/botocore/vendored/requests/packages/urllib3/connectionpool.py in urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, **response_kw)
    542             httplib_response = self._make_request(conn, method, url,
    543                                                   timeout=timeout_obj,
--> 544                                                   body=body, headers=headers)
    545 
    546             # If we're going to release the connection in ``finally:``, then

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/site-packages/botocore/vendored/requests/packages/urllib3/connectionpool.py in _make_request(self, conn, method, url, timeout, **httplib_request_kw)
    372                 httplib_response = conn.getresponse(buffering=True)
    373             except TypeError:  # Python 2.6 and older
--> 374                 httplib_response = conn.getresponse()
    375         except (SocketTimeout, BaseSSLError, SocketError) as e:
    376             self._raise_timeout(err=e, url=url, timeout_value=read_timeout)

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/http/client.py in getresponse(self)
   1196         try:
   1197             try:
-> 1198                 response.begin()
   1199             except ConnectionError:
   1200                 self.close()

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/http/client.py in begin(self)
    295         # read until we get a non-100 response
    296         while True:
--> 297             version, status, reason = self._read_status()
    298             if status != CONTINUE:
    299                 break

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/http/client.py in _read_status(self)
    256 
    257     def _read_status(self):
--> 258         line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
    259         if len(line) > _MAXLINE:
    260             raise LineTooLong("status line")

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/socket.py in readinto(self, b)
    574         while True:
    575             try:
--> 576                 return self._sock.recv_into(b)
    577             except timeout:
    578                 self._timeout_occurred = True

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/ssl.py in recv_into(self, buffer, nbytes, flags)
    935                   "non-zero flags not allowed in calls to recv_into() on %s" %
    936                   self.__class__)
--> 937             return self.read(nbytes, buffer)
    938         else:
    939             return socket.recv_into(self, buffer, nbytes, flags)

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/ssl.py in read(self, len, buffer)
    797             raise ValueError("Read on closed or unwrapped SSL socket.")
    798         try:
--> 799             return self._sslobj.read(len, buffer)
    800         except SSLError as x:
    801             if x.args[0] == SSL_ERROR_EOF and self.suppress_ragged_eofs:

~/.pyenv/versions/miniconda3-4.3.11/envs/inbobase/lib/python3.5/ssl.py in read(self, len, buffer)
    581         """
    582         if buffer is not None:
--> 583             v = self._sslobj.read(len, buffer)
    584         else:
    585             v = self._sslobj.read(len)

KeyboardInterrupt: 
















In [19]:



    


import shutil



    











In [30]:



    


shutil.rmtree(os.path.join(".", "cz"))



    











In [25]:



    


shutil.rmtree(os.path.join(".", "cz", "brd", "2017", "09"))



    











In [26]:



    


os.removedirs(os.path.join(".", "cz", "brd", "2017"))

Remove corrupted h5 files on the repo and remove all ZIP-files on the data repo





In [9]:



    


corrupted = []
country_exclude = ["be", "ch", "cz", "dk", "es"]
sat_exclude = ["boo", "drs", "eis", "emd", "ess", "fld", "hnr", "mem", "neu", "nhb", "anj", "ika", "kes"]
for j, file in enumerate(s3handle.bucket.objects.all()):
    if file.key.endswith(".h5") and not file.key.split("/")[0] in country_exclude and not file.key.split("/")[1] in sat_exclude:
        # download file
        s3handle.download_file(file.key)
        # check if it can be read
        try:
            h5py.File(file.key, mode="r")
        except:
            corrupted.append(file.key)
            file.delete()
        os.remove(file.key)
    elif file.key.endswith(".zip"):
        file.delete()



    











In [10]:



    


corrupted[-10:]



    


















    
Out[10]:








['sk/laz/2017/08/11/05/sklaz_vp_20170811050000.h5',
 'sk/laz/2017/08/11/05/sklaz_vp_20170811051500.h5',
 'sk/laz/2017/08/11/05/sklaz_vp_20170811053000.h5',
 'sk/laz/2017/08/11/05/sklaz_vp_20170811054500.h5',
 'sk/laz/2017/08/11/06/sklaz_vp_20170811060000.h5',
 'sk/laz/2017/08/11/06/sklaz_vp_20170811061500.h5',
 'sk/laz/2017/08/11/06/sklaz_vp_20170811063000.h5',
 'sk/laz/2017/08/11/06/sklaz_vp_20170811064500.h5',
 'sk/laz/2017/08/11/07/sklaz_vp_20170811070000.h5',
 'sk/laz/2017/08/11/07/sklaz_vp_20170811071500.h5']

Recreate all the ZIP folders

Load the existing h5 files and use this to create the zip files, we can use the coverage file information do to so as explained in the documentation of the datamover https://github.com/enram/data-repository/blob/master/file_transfer/tutorial_datamover.ipynb





In [5]:



    


s3enram = dm.S3EnramHandler("lw-enram", profile_name="lw-enram")



    











In [6]:



    


s3enram.create_zip_version(s3enram.count_enram_coverage(level="month"))



    


















    






Saved  plpoz201706.zip on S3 bucket.
Saved  depro201704.zip on S3 bucket.
Saved  fiuta201705.zip on S3 bucket.
Saved  frnim201704.zip on S3 bucket.
Saved  frniz201611.zip on S3 bucket.
Saved  depro201709.zip on S3 bucket.
Saved  selek201703.zip on S3 bucket.
Saved  frale201704.zip on S3 bucket.
Saved  deess201701.zip on S3 bucket.
Saved  dkste201708.zip on S3 bucket.
Saved  sevil201705.zip on S3 bucket.
Saved  fikuo201704.zip on S3 bucket.
Saved  czbrd201708.zip on S3 bucket.
Saved  sekir201709.zip on S3 bucket.
Saved  fikor201709.zip on S3 bucket.
Saved  defld201709.zip on S3 bucket.
Saved  sklaz201707.zip on S3 bucket.
Saved  sevax201701.zip on S3 bucket.
Saved  hrbil201707.zip on S3 bucket.
Saved  frcae201709.zip on S3 bucket.
Saved  fropo201705.zip on S3 bucket.
Saved  esval201611.zip on S3 bucket.
Saved  fiika201705.zip on S3 bucket.
Saved  frmom201707.zip on S3 bucket.
Saved  plram201703.zip on S3 bucket.
Saved  sklaz201705.zip on S3 bucket.
Saved  frabb201704.zip on S3 bucket.
Saved  dkbor201709.zip on S3 bucket.
Saved  plpoz201704.zip on S3 bucket.
Saved  frbla201708.zip on S3 bucket.
Saved  frbor201705.zip on S3 bucket.
Saved  deemd201702.zip on S3 bucket.
Saved  demem201705.zip on S3 bucket.
Saved  frtro201708.zip on S3 bucket.
Saved  selek201706.zip on S3 bucket.
Saved  dkste201707.zip on S3 bucket.
Saved  czbrd201611.zip on S3 bucket.
Saved  desna201708.zip on S3 bucket.
Saved  dkrom201702.zip on S3 bucket.
Saved  selul201704.zip on S3 bucket.
Saved  dkbor201705.zip on S3 bucket.
Saved  plswi201705.zip on S3 bucket.
Saved  dksin201702.zip on S3 bucket.
Saved  plpas201707.zip on S3 bucket.
Saved  plgda201705.zip on S3 bucket.
Saved  hrosi201611.zip on S3 bucket.
Saved  fiuta201706.zip on S3 bucket.
Saved  selul201703.zip on S3 bucket.
Saved  frtre201701.zip on S3 bucket.
Saved  filuo201707.zip on S3 bucket.
Saved  deumd201705.zip on S3 bucket.
Saved  frmom201708.zip on S3 bucket.
Saved  skkoj201705.zip on S3 bucket.
Saved  frbor201706.zip on S3 bucket.
Saved  depro201701.zip on S3 bucket.
Saved  deros201707.zip on S3 bucket.
Saved  sevil201701.zip on S3 bucket.
Saved  sekir201705.zip on S3 bucket.
Saved  frgre201704.zip on S3 bucket.
Saved  dkste201704.zip on S3 bucket.
Saved  fikes201611.zip on S3 bucket.
Saved  hrbil201701.zip on S3 bucket.
Saved  fikes201701.zip on S3 bucket.
Saved  frtou201611.zip on S3 bucket.
Saved  frcol201706.zip on S3 bucket.
Saved  fikuo201706.zip on S3 bucket.
Saved  sklaz201709.zip on S3 bucket.
Saved  seosd201705.zip on S3 bucket.
Saved  fipet201704.zip on S3 bucket.
Saved  dehnr201701.zip on S3 bucket.
Saved  skjav201709.zip on S3 bucket.
Saved  dkste201706.zip on S3 bucket.
Saved  plleg201703.zip on S3 bucket.
Saved  dkvir201611.zip on S3 bucket.
Saved  fikor201708.zip on S3 bucket.
Saved  frave201703.zip on S3 bucket.
Saved  dkrom201708.zip on S3 bucket.
Saved  dkste201703.zip on S3 bucket.
Saved  czbrd201702.zip on S3 bucket.
Saved  fropo201611.zip on S3 bucket.
Saved  dksin201704.zip on S3 bucket.
Saved  nldhl201704.zip on S3 bucket.
Saved  frtou201707.zip on S3 bucket.
Saved  esbad201611.zip on S3 bucket.
Saved  frtou201708.zip on S3 bucket.
Saved  frmtc201707.zip on S3 bucket.
Saved  dkvir201704.zip on S3 bucket.
Saved  czbrd201709.zip on S3 bucket.
Saved  frbol201707.zip on S3 bucket.
Saved  defld201707.zip on S3 bucket.
Saved  deemd201709.zip on S3 bucket.
Saved  frabb201709.zip on S3 bucket.
Saved  fropo201708.zip on S3 bucket.
Saved  essan201611.zip on S3 bucket.
Saved  frmtc201611.zip on S3 bucket.
Saved  czbrd201706.zip on S3 bucket.
Saved  skkub201704.zip on S3 bucket.
Saved  deros201706.zip on S3 bucket.
Saved  frbla201701.zip on S3 bucket.
Saved  detur201704.zip on S3 bucket.
Saved  desna201706.zip on S3 bucket.
Saved  frtra201708.zip on S3 bucket.
Saved  sevil201708.zip on S3 bucket.
Saved  frmcl201708.zip on S3 bucket.
Saved  deoft201707.zip on S3 bucket.
Saved  hrbil201705.zip on S3 bucket.
Saved  plbrz201704.zip on S3 bucket.
Saved  frcae201705.zip on S3 bucket.
Saved  denhb201707.zip on S3 bucket.
Saved  deess201704.zip on S3 bucket.
Saved  sekkr201708.zip on S3 bucket.
Saved  seang201709.zip on S3 bucket.
Saved  hrosi201705.zip on S3 bucket.
Saved  nldhl201706.zip on S3 bucket.
Saved  defld201706.zip on S3 bucket.
Saved  dedrs201702.zip on S3 bucket.
Saved  dehnr201708.zip on S3 bucket.
Saved  nldbl201701.zip on S3 bucket.
Saved  plswi201707.zip on S3 bucket.
Saved  desna201701.zip on S3 bucket.
Saved  silis201704.zip on S3 bucket.
Saved  frave201707.zip on S3 bucket.
Saved  fikes201704.zip on S3 bucket.
Saved  fianj201705.zip on S3 bucket.
Saved  dksin201709.zip on S3 bucket.
Saved  deemd201705.zip on S3 bucket.
Saved  dedrs201706.zip on S3 bucket.
Saved  fropo201707.zip on S3 bucket.
Saved  fiuta201704.zip on S3 bucket.
Saved  frabb201611.zip on S3 bucket.
Saved  deeis201701.zip on S3 bucket.
Saved  frcol201611.zip on S3 bucket.
Saved  detur201709.zip on S3 bucket.
Saved  frtra201703.zip on S3 bucket.
Saved  fikor201703.zip on S3 bucket.
Saved  plswi201706.zip on S3 bucket.
Saved  deeis201707.zip on S3 bucket.
Saved  frmcl201709.zip on S3 bucket.
Saved  frtra201706.zip on S3 bucket.
Saved  fivan201709.zip on S3 bucket.
Saved  plgda201701.zip on S3 bucket.
Saved  frlep201709.zip on S3 bucket.
Saved  fikuo201705.zip on S3 bucket.
Saved  dedrs201705.zip on S3 bucket.
Saved  searl201701.zip on S3 bucket.
Saved  fipet201705.zip on S3 bucket.
Saved  frbla201705.zip on S3 bucket.
Saved  sease201705.zip on S3 bucket.
Saved  deeis201611.zip on S3 bucket.
Saved  plswi201708.zip on S3 bucket.
Saved  seovi201701.zip on S3 bucket.
Saved  frcae201704.zip on S3 bucket.
Saved  deumd201709.zip on S3 bucket.
Saved  esmad201611.zip on S3 bucket.
Saved  frcol201705.zip on S3 bucket.
Saved  frtre201611.zip on S3 bucket.
Saved  esalm201611.zip on S3 bucket.
Saved  frbor201708.zip on S3 bucket.
Saved  fivim201703.zip on S3 bucket.
Saved  plrze201701.zip on S3 bucket.
Saved  frmtc201701.zip on S3 bucket.
Saved  sipas201709.zip on S3 bucket.
Saved  frale201707.zip on S3 bucket.
Saved  searl201707.zip on S3 bucket.
Saved  seang201707.zip on S3 bucket.
Saved  frave201611.zip on S3 bucket.
Saved  frnan201611.zip on S3 bucket.
Saved  plpas201704.zip on S3 bucket.
Saved  defld201611.zip on S3 bucket.
Saved  fropo201704.zip on S3 bucket.
Saved  dkbor201701.zip on S3 bucket.
Saved  frtra201707.zip on S3 bucket.
Saved  fikor201701.zip on S3 bucket.
Saved  skkub201706.zip on S3 bucket.
Saved  frmcl201705.zip on S3 bucket.
Saved  fiika201701.zip on S3 bucket.
Saved  depro201707.zip on S3 bucket.
Saved  plpas201708.zip on S3 bucket.
Saved  dkbor201707.zip on S3 bucket.
Saved  sevil201709.zip on S3 bucket.
Saved  frnim201708.zip on S3 bucket.
Saved  fipet201706.zip on S3 bucket.
Saved  selek201704.zip on S3 bucket.
Saved  frtro201703.zip on S3 bucket.
Saved  deemd201701.zip on S3 bucket.
Saved  dkvir201708.zip on S3 bucket.
Saved  deboo201701.zip on S3 bucket.
Saved  hrosi201701.zip on S3 bucket.
Saved  frche201701.zip on S3 bucket.
Saved  fipet201709.zip on S3 bucket.
Saved  skjav201704.zip on S3 bucket.
Saved  plgda201706.zip on S3 bucket.
Saved  deboo201706.zip on S3 bucket.
Saved  fivim201701.zip on S3 bucket.
Saved  frtre201705.zip on S3 bucket.
Saved  frbou201706.zip on S3 bucket.
Saved  deess201707.zip on S3 bucket.
Saved  dkste201611.zip on S3 bucket.
Saved  frnim201701.zip on S3 bucket.
Saved  frale201706.zip on S3 bucket.
Saved  plswi201704.zip on S3 bucket.
Saved  fivan201705.zip on S3 bucket.
Saved  silis201705.zip on S3 bucket.
Saved  plleg201707.zip on S3 bucket.
Saved  frlep201705.zip on S3 bucket.
Saved  plleg201701.zip on S3 bucket.
Saved  czska201709.zip on S3 bucket.
Saved  deess201706.zip on S3 bucket.
Saved  fiika201704.zip on S3 bucket.
Saved  frpla201707.zip on S3 bucket.
Saved  deros201708.zip on S3 bucket.
Saved  frtro201705.zip on S3 bucket.
Saved  espma201611.zip on S3 bucket.
Saved  hrosi201707.zip on S3 bucket.
Saved  plpoz201708.zip on S3 bucket.
Saved  fikes201707.zip on S3 bucket.
Saved  sevax201707.zip on S3 bucket.
Saved  plrze201709.zip on S3 bucket.
Saved  nober201611.zip on S3 bucket.
Saved  sekkr201706.zip on S3 bucket.
Saved  hrosi201709.zip on S3 bucket.
Saved  czska201706.zip on S3 bucket.
Saved  sekkr201705.zip on S3 bucket.
Saved  depro201706.zip on S3 bucket.
Saved  nldhl201708.zip on S3 bucket.
Saved  deess201708.zip on S3 bucket.
Saved  frniz201701.zip on S3 bucket.
Saved  frcol201701.zip on S3 bucket.
Saved  fropo201703.zip on S3 bucket.
Saved  sekir201704.zip on S3 bucket.
Saved  plpoz201703.zip on S3 bucket.
Saved  fivan201703.zip on S3 bucket.
Saved  fiuta201611.zip on S3 bucket.
Saved  detur201708.zip on S3 bucket.
Saved  deumd201708.zip on S3 bucket.
Saved  selek201709.zip on S3 bucket.
Saved  silis201707.zip on S3 bucket.
Saved  frtro201611.zip on S3 bucket.
Saved  hrosi201708.zip on S3 bucket.
Saved  denhb201611.zip on S3 bucket.
Saved  deoft201709.zip on S3 bucket.
Saved  frnan201701.zip on S3 bucket.
Saved  frnim201706.zip on S3 bucket.
Saved  sipas201701.zip on S3 bucket.
Saved  eslpa201611.zip on S3 bucket.
Saved  frmtc201706.zip on S3 bucket.
Saved  hrbil201704.zip on S3 bucket.
Saved  fikuo201703.zip on S3 bucket.
Saved  sekir201707.zip on S3 bucket.
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Content source: enram/data-repository

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