SCC access: scc_access/scc_access.py@8d487e4e20ae (annotated)

scc_access/scc_access.py@8d487e4e20ae (annotated)

scc_access/scc_access.py

Tue, 09 Feb 2021 17:12:25 +0200

author: ioannis@ioannis-VirtualBox
date: Tue, 09 Feb 2021 17:12:25 +0200
changeset 57: 8d487e4e20ae
parent 55: c226bda2bb71
child 60: 2fe60db870df
permissions: -rw-r--r--

Temporary workaround for missing "has_finished" flag from the API.

 import sys
 import requests
 try:
     import urllib.parse as urlparse  # Python 3
 except ImportError:
     import urlparse  # Python 2
 import argparse
 import datetime
 import logging
 import os
 import re
 from io import BytesIO
 import time
 from zipfile import ZipFile
 import yaml
 import netCDF4 as netcdf
 requests.packages.urllib3.disable_warnings()
 logger = logging.getLogger(__name__)
 # The regex to find the measurement id from the measurement page
 # This should be read from the uploaded file, but would require an extra NetCDF module.
 regex = "<h3>Measurement (?P<measurement_id>.{12,15}) <small>"  # {12, 15} to handle both old- and new-style measurement ids.
 class SCC:
     """A simple class that will attempt to upload a file on the SCC server.
     The uploading is done by simulating a normal browser session. In the current
     version no check is performed, and no feedback is given if the upload
     was successful. If everything is setup correctly, it will work.
     """
     def __init__(self, auth, output_dir, base_url):
         self.auth = auth
         self.output_dir = output_dir
         self.base_url = base_url
         self.session = requests.Session()
         self.session.auth = auth
         self.session.verify = False
         self.login_url = urlparse.urljoin(self.base_url, 'accounts/login/')
         self.logout_url = urlparse.urljoin(self.base_url, 'accounts/logout/')
         self.list_measurements_url = urlparse.urljoin(self.base_url, 'data_processing/measurements/')
         self.upload_url = urlparse.urljoin(self.base_url, 'data_processing/measurements/quick/')
         self.measurement_page_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/')
         self.download_hirelpp_pattern = urlparse.urljoin(self.base_url,
                                                              'data_processing/measurements/{0}/download-hirelpp/')
         self.download_cloudmask_pattern = urlparse.urljoin(self.base_url,
                                                          'data_processing/measurements/{0}/download-cloudmask/')
         self.download_elpp_pattern = urlparse.urljoin(self.base_url,
                                                               'data_processing/measurements/{0}/download-preprocessed/')
         self.download_elda_pattern = urlparse.urljoin(self.base_url,
                                                          'data_processing/measurements/{0}/download-optical/')
         self.download_plots_pattern = urlparse.urljoin(self.base_url,
                                                        'data_processing/measurements/{0}/download-plots/')
         self.download_elic_pattern = urlparse.urljoin(self.base_url,
                                                        'data_processing/measurements/{0}/download-elic/')
         self.delete_measurement_pattern = urlparse.urljoin(self.base_url, 'admin/database/measurements/{0}/delete/')
         self.api_base_url = urlparse.urljoin(self.base_url, 'api/v1/')
         self.api_measurement_pattern = urlparse.urljoin(self.api_base_url, 'measurements/{0}/')
         self.api_measurements_url = urlparse.urljoin(self.api_base_url, 'measurements')
         self.api_sounding_search_pattern = urlparse.urljoin(self.api_base_url, 'sounding_files/?filename={0}')
         self.api_lidarratio_search_pattern = urlparse.urljoin(self.api_base_url, 'lidarratio_files/?filename={0}')
         self.api_overlap_search_pattern = urlparse.urljoin(self.api_base_url, 'overlap_files/?filename={0}')
     def login(self, credentials):
         """ Login to SCC. """
         logger.debug("Attempting to login to SCC, username %s." % credentials[0])
         login_credentials = {'username': credentials[0],
                              'password': credentials[1]}
         logger.debug("Accessing login page at %s." % self.login_url)
         # Get upload form
         login_page = self.session.get(self.login_url)
         if not login_page.ok:
             raise self.PageNotAccessibleError('Could not access login pages. Status code %s' % login_page.status_code)
         logger.debug("Submitting credentials.")
         # Submit the login data
         login_submit = self.session.post(self.login_url,
                                          data=login_credentials,
                                          headers={'X-CSRFToken': login_page.cookies['csrftoken'],
                                                   'referer': self.login_url})
         return login_submit
     def logout(self):
         """ Logout from SCC """
         return self.session.get(self.logout_url, stream=True)
     def upload_file(self, filename, system_id, force_upload, delete_related, delay=0, rs_filename=None, ov_filename=None, lr_filename=None):
         """ Upload a filename for processing with a specific system. If the
         upload is successful, it returns the measurement id. """
         measurement_id = self.measurement_id_from_file(filename)
         logger.debug('Checking if a measurement with the same id already exists on the SCC server.')
         existing_measurement, _ = self.get_measurement(measurement_id)
         if existing_measurement:
             if force_upload:
                 logger.info(
                     "Measurement with id {} already exists on the SCC. Trying to delete it...".format(measurement_id))
                 self.delete_measurement(measurement_id, delete_related)
             else:
                 logger.error(
                     "Measurement with id {} already exists on the SCC. Use --force_upload flag to overwrite it.".format(
                         measurement_id))
                 # TODO: Implement handling at the proper place. This does not allow the SCC class to be used by external programs.
                 sys.exit(1)
         # Get submit page
         upload_page = self.session.get(self.upload_url)
         # Submit the data
         upload_data = {'system': system_id,
                        'delay': delay}
         logger.debug("Submitted processing parameters - System: {}, Delay: {}".format(system_id, delay))
         files = {'data': open(filename, 'rb')}
         if rs_filename is not None:
             ancillary_file, _ = self.get_ancillary(rs_filename, 'sounding')
             if ancillary_file.already_on_scc:
                 logger.warning("Sounding file {0.filename} already on the SCC with id {0.id}. Ignoring it.".format(ancillary_file))
             else:
                 logger.debug('Adding sounding file %s' % rs_filename)
                 files['sounding_file'] = open(rs_filename, 'rb')
         if ov_filename is not None:
             ancillary_file, _ = self.get_ancillary(ov_filename, 'overlap')
             if ancillary_file.already_on_scc:
                 logger.warning("Overlap file {0.filename} already on the SCC with id {0.id}. Ignoring it.".format(ancillary_file))
             else:
                 logger.debug('Adding overlap file %s' % ov_filename)
                 files['overlap_file'] = open(ov_filename, 'rb')
         if lr_filename is not None:
             ancillary_file, _ = self.get_ancillary(lr_filename, 'lidarratio')
             if ancillary_file.already_on_scc:
                 logger.warning(
                     "Lidar ratio file {0.filename} already on the SCC with id {0.id}. Ignoring it.".format(ancillary_file))
             else:
                 logger.debug('Adding lidar ratio file %s' % lr_filename)
                 files['lidar_ratio_file'] = open(lr_filename, 'rb')
         logger.info("Uploading of file %s started." % filename)
         upload_submit = self.session.post(self.upload_url,
                                           data=upload_data,
                                           files=files,
                                           headers={'X-CSRFToken': upload_page.cookies['csrftoken'],
                                                    'referer': self.upload_url})
         if upload_submit.status_code != 200:
             logger.warning("Connection error. Status code: %s" % upload_submit.status_code)
             return False
         # Check if there was a redirect to a new page.
         if upload_submit.url == self.upload_url:
             measurement_id = False
             logger.error("Uploaded file(s) rejected! Try to upload manually to see the error.")
         else:
             measurement_id = re.findall(regex, upload_submit.text)[0]
             logger.info("Successfully uploaded measurement with id %s." % measurement_id)
             logger.info("You can monitor the processing progress online: {}".format(self.measurement_page_pattern.format(measurement_id)))
         return measurement_id
     @staticmethod
     def measurement_id_from_file(filename):
         """ Get the measurement id from the input file. """
         if not os.path.isfile(filename):
             logger.error("File {} does not exist.".format(filename))
             sys.exit(1)
         with netcdf.Dataset(filename) as f:
             try:
                 measurement_id = f.Measurement_ID
             except AttributeError:
                 logger.error(
                     "Input file {} does not contain a Measurement_ID global attribute. Wrong file format?".format(
                         filename))
                 sys.exit(1)
         return measurement_id
     def download_files(self, measurement_id, subdir, download_url):
         """ Downloads some files from the download_url to the specified
         subdir. This method is used to download preprocessed file, optical
         files etc.
         """
         # TODO: Make downloading more robust (e.g. in case that files do not exist on server).
         # Get the file
         request = self.session.get(download_url, stream=True)
         if not request.ok:
             raise Exception("Could not download files for measurement '%s'" % measurement_id)
         # Create the dir if it does not exist
         local_dir = os.path.join(self.output_dir, measurement_id, subdir)
         if not os.path.exists(local_dir):
             os.makedirs(local_dir)
         # Save the file by chunk, needed if the file is big.
         memory_file = BytesIO()
         for chunk in request.iter_content(chunk_size=1024):
             if chunk:  # filter out keep-alive new chunks
                 memory_file.write(chunk)
                 memory_file.flush()
         zip_file = ZipFile(memory_file)
         for ziped_name in zip_file.namelist():
             basename = os.path.basename(ziped_name)
             local_file = os.path.join(local_dir, basename)
             with open(local_file, 'wb') as f:
                 f.write(zip_file.read(ziped_name))
     def download_hirelpp(self, measurement_id):
         """ Download hirelpp files for the measurement id. """
         # Construct the download url
         download_url = self.download_hirelpp_pattern.format(measurement_id)
         try:
             self.download_files(measurement_id, 'hirelpp', download_url)
         except Exception as e:
             logger.error("Could not download HiRElPP files. Error message: {}".format(e))
             logger.debug('Download exception:', exc_info=True)
     def download_cloudmask(self, measurement_id):
         """ Download cloudmask files for the measurement id. """
         # Construct the download url
         download_url = self.download_cloudmask_pattern.format(measurement_id)
         try:
             self.download_files(measurement_id, 'cloudscreen', download_url)
         except Exception as e:
             logger.error("Could not download cloudscreen files. Error message: {}".format(e))
             logger.debug('Download exception:', exc_info=True)
     def download_elpp(self, measurement_id):
         """ Download preprocessed files for the measurement id. """
         # Construct the download url
         download_url = self.download_elpp_pattern.format(measurement_id)
         try:
             self.download_files(measurement_id, 'elpp', download_url)
         except Exception as e:
             logger.error("Could not download ElPP files. Error message: {}".format(e))
             logger.debug('Download exception:', exc_info=True)
     def download_elda(self, measurement_id):
         """ Download optical files for the measurement id. """
         # Construct the download url
         download_url = self.download_elda_pattern.format(measurement_id)
         try:
             self.download_files(measurement_id, 'elda', download_url)
         except Exception as e:
             logger.error("Could not download ELDA files. Error message: {}".format(e))
             logger.debug('Download exception:', exc_info=True)
     def download_plots(self, measurement_id):
         """ Download profile graphs for the measurement id. """
         # Construct the download url
         download_url = self.download_plots_pattern.format(measurement_id)
         try:
             self.download_files(measurement_id, 'elda_plots', download_url)
         except Exception as e:
             logger.error("Could not download ELDA plots. Error message: {}".format(e))
             logger.debug('Download exception:', exc_info=True)
     def download_elic(self, measurement_id):
         """ Download ELIC files for the measurement id. """
         # Construct the download url
         download_url = self.download_elic_pattern.format(measurement_id)
         try:
             self.download_files(measurement_id, 'elic', download_url)
         except Exception as e:
             logger.error("Could not download ELIC files. Error message: {}".format(e))
             logger.debug('Download exception:', exc_info=True)
     def download_eldec(self, measurement_id):
         """ Download ELDEC files for the measurement id. """
         # Construct the download url
         download_url = self.download_elda_pattern.format(measurement_id)  # ELDA patter is used for now
         try:
             self.download_files(measurement_id, 'eldec', download_url)
         except Exception as e:
             logger.error("Could not download EDELC files. Error message: {}".format(e))
             logger.debug('Download exception:', exc_info=True)
     def rerun_elpp(self, measurement_id, monitor=True):
         logger.debug("Started rerun_elpp procedure.")
         logger.debug("Getting measurement %s" % measurement_id)
         measurement, status = self.get_measurement(measurement_id)
         if measurement:
             logger.debug("Attempting to rerun ElPP through %s." % measurement.rerun_all_url)
             request = self.session.get(measurement.rerun_elpp_url, stream=True)
             if request.status_code != 200:
                 logger.error(
                     "Could not rerun processing for %s. Status code: %s" % (measurement_id, request.status_code))
             else:
                 logger.info("Rerun-elpp command submitted successfully for id {}.".format(measurement_id))
             if monitor:
                 self.monitor_processing(measurement_id)
     def rerun_all(self, measurement_id, monitor=True):
         logger.debug("Started rerun_all procedure.")
         logger.debug("Getting measurement %s" % measurement_id)
         measurement, status = self.get_measurement(measurement_id)
         if measurement:
             logger.debug("Attempting to rerun all processing through %s." % measurement.rerun_all_url)
             request = self.session.get(measurement.rerun_all_url, stream=True)
             if request.status_code != 200:
                 logger.error("Could not rerun pre processing for %s. Status code: %s" %
                              (measurement_id, request.status_code))
             else:
                 logger.info("Rerun-all command submitted successfully for id {}.".format(measurement_id))
             if monitor:
                 self.monitor_processing(measurement_id)
     def process(self, filename, system_id, monitor,  force_upload, delete_related, delay=0, rs_filename=None, lr_filename=None, ov_filename=None):
         """ Upload a file for processing and wait for the processing to finish.
         If the processing is successful, it will download all produced files.
         """
         logger.info("--- Processing started on %s. ---" % datetime.datetime.now())
         # Upload file
         logger.info("Uploading file.")
         measurement_id = self.upload_file(filename, system_id, force_upload, delete_related,
                                           delay=delay,
                                           rs_filename=rs_filename,
                                           lr_filename=lr_filename,
                                           ov_filename=ov_filename)
         if monitor and (delay > 0):
             logger.warning("Will not start monitoring, since a delay was specified: {} hours.".format(delay))
             return None
         if measurement_id and monitor:
             logger.info("Monitoring processing.")
             return self.monitor_processing(measurement_id)
         return None
     def monitor_processing(self, measurement_id):
         """ Monitor the processing progress of a measurement id"""
         # try to deal with error 404
         error_count = 0
         error_max = 3
         time_sleep = 3
         # try to wait for measurement to appear in API
         measurement = None
         logger.info("Looking for measurement %s on the SCC.", measurement_id)
         while error_count < error_max:
             time.sleep(time_sleep)
             measurement, status = self.get_measurement(measurement_id)
             if status != 200 and error_count < error_max:
                 logger.error("Measurement not found. waiting %ds", time_sleep)
                 error_count += 1
             else:
                 break
         if error_count == error_max:
             logger.critical("Measurement %s doesn't seem to exist", measurement_id)
             sys.exit(1)
         logger.info('Measurement %s found.', measurement_id)
         if measurement is not None:
             while not measurement.has_finished:
                 measurement.log_processing_status()
                 time.sleep(10)
                 measurement, status = self.get_measurement(measurement_id)
             logger.info("Measurement processing finished.")
             measurement.log_detailed_status()
             if measurement.hirelpp == 127:
                 logger.info("Downloading HiRElPP files.")
                 self.download_hirelpp(measurement_id)
             if measurement.cloudmask == 127:
                 logger.info("Downloading cloud screening files.")
                 self.download_cloudmask(measurement_id)
             if measurement.elpp == 127:
                 logger.info("Downloading ElPP files.")
                 self.download_elpp(measurement_id)
             if measurement.elda == 127:
                 logger.info("Downloading ELDA files.")
                 self.download_elda(measurement_id)
                 logger.info("Downloading ELDA plots.")
                 self.download_plots(measurement_id)
             if measurement.elic == 127:
                 logger.info("Downloading ELIC files.")
                 self.download_elic(measurement_id)
             if measurement.is_calibration and measurement.eldec==0:
                 logger.info("Downloading ELDEC files.")
                 self.download_eldec(measurement_id)
             logger.info("--- Processing finished. ---")
         return measurement
     def get_measurement(self, measurement_id):
         if measurement_id is None:  # Is this still required?
             return None
         measurement_url = self.api_measurement_pattern.format(measurement_id)
         logger.debug("Measurement API URL: %s" % measurement_url)
         response = self.session.get(measurement_url)
         response_dict = None
         if response.status_code == 200:
             response_dict = response.json()
         elif response.status_code == 404:
             logger.info("No measurement with id %s found on the SCC." % measurement_id)
         else:
             logger.error('Could not access API. Status code %s.' % response.status_code)
         # TODO: Implement better handling for status 401.
         if response_dict:
             measurement = Measurement(self.base_url, response_dict)
         else:
             measurement = None
         return measurement, response.status_code
     def delete_measurement(self, measurement_id, delete_related):
         """ Deletes a measurement with the provided measurement id. The user
         should have the appropriate permissions.
         The procedures is performed directly through the web interface and
         NOT through the API.
         """
         # Get the measurement object
         measurement, _ = self.get_measurement(measurement_id)
         # Check that it exists
         if measurement is None:
             logger.warning("Nothing to delete.")
             return None
         # Go the the page confirming the deletion
         delete_url = self.delete_measurement_pattern.format(measurement_id)
         confirm_page = self.session.get(delete_url)
         # Check that the page opened properly
         if confirm_page.status_code != 200:
             logger.warning("Could not open delete page. Status: {0}".format(confirm_page.status_code))
             return None
         # Get the delete related value
         if delete_related:
             delete_related_option = 'delete_related'
         else:
             delete_related_option = 'not_delete_related'
         # Delete the measurement
         delete_page = self.session.post(delete_url,
                                         data={'post': 'yes',
                                               'select_delete_related_measurements': delete_related_option},
                                         headers={'X-CSRFToken': confirm_page.cookies['csrftoken'],
                                                  'referer': delete_url}
                                         )
         if not delete_page.ok:
             logger.warning("Something went wrong. Delete page status: {0}".format(
                 delete_page.status_code))
             return None
         logger.info("Deleted measurement {0}".format(measurement_id))
         return True
     def available_measurements(self):
         """ Get a list of available measurement on the SCC. """
         response = self.session.get(self.api_measurements_url)
         response_dict = response.json()
         if response_dict:
             measurement_list = response_dict['objects']
             measurements = [Measurement(self.base_url, measurement_dict) for measurement_dict in measurement_list]
             logger.info("Found %s measurements on the SCC." % len(measurements))
         else:
             logger.warning("No response received from the SCC when asked for available measurements.")
             measurements = None
         return measurements
     def list_measurements(self, station=None, system=None, start=None, stop=None, upload_status=None,
                           processing_status=None, optical_processing=None):
         # TODO: Change this to work through the API
         # Need to set to empty string if not specified, we won't get any results
         params = {
             "station": station if station is not None else "",
             "system": system if system is not None else "",
             "stop": stop if stop is not None else "",
             "start": start if start is not None else "",
             "upload_status": upload_status if upload_status is not None else "",
             "preprocessing_status": processing_status if processing_status is not None else "",
             "optical_processing_status": optical_processing if optical_processing is not None else ""
         }
         response_txt = self.session.get(self.list_measurements_url, params=params).text
         tbl_rgx = re.compile(r'<table id="measurements">(.*?)</table>', re.DOTALL)
         entry_rgx = re.compile(r'<tr>(.*?)</tr>', re.DOTALL)
         measurement_rgx = re.compile(
             r'.*?<td><a[^>]*>(\w+)</a>.*?<td>.*?<td>([\w-]+ [\w:]+)</td>.*<td data-order="([-]?\d+),([-]?\d+),([-]?\d+)".*',
             re.DOTALL)
         matches = tbl_rgx.findall(response_txt)
         if len(matches) != 1:
             return []
         ret = []
         for entry in entry_rgx.finditer(matches[0]):
             m = measurement_rgx.match(entry.string[entry.start(0):entry.end(0)])
             if m:
                 name, date, upload, preproc, optical = m.groups()
                 ret.append(
                     Measurement(self.base_url, {"id": name, "upload": int(upload), "pre_processing": int(preproc),
                                                 "processing": int(optical)}))
         return ret
     def measurement_id_for_date(self, t1, call_sign, base_number=0):
         """ Give the first available measurement id on the SCC for the specific
         date.
         """
         date_str = t1.strftime('%Y%m%d')
         base_id = "%s%s" % (date_str, call_sign)
         search_url = urlparse.urljoin(self.api_base_url, 'measurements/?id__startswith=%s' % base_id)
         response = self.session.get(search_url)
         response_dict = response.json()
         measurement_id = None
         if response_dict:
             measurement_list = response_dict['objects']
             if len(measurement_list) == 100:
                 raise ValueError('No available measurement id found.')
             existing_ids = [measurement_dict['id'] for measurement_dict in measurement_list]
             measurement_number = base_number
             measurement_id = "%s%02i" % (base_id, measurement_number)
             while measurement_id in existing_ids:
                 measurement_number = measurement_number + 1
                 measurement_id = "%s%02i" % (base_id, measurement_number)
         return measurement_id
     def get_ancillary(self, file_path, file_type):
         """
         Try to get the ancillary file data from the SCC API.
         The result will always be an API object. If the file does not exist, the .exists property is set to False.
         Parameters
         ----------
         file_path : str
            Path  of the uploaded file.
         file_type : str
            Type of ancillary file. One of 'sounding', 'overlap', 'lidarratio'.
         Returns
         : AncillaryFile
            The api object.
         """
         assert file_type in ['sounding', 'overlap', 'lidarratio']
         filename = os.path.basename(file_path)
         if file_type == 'sounding':
             file_url = self.api_sounding_search_pattern.format(filename)
         elif file_type == 'overlap':
             file_url = self.api_overlap_search_pattern.format(filename)
         else:
             file_url = self.api_lidarratio_search_pattern.format(filename)
         response = self.session.get(file_url)
         if not response.ok:
             logger.error('Could not access API. Status code %s.' % response.status_code)
             return None, response.status_code
         response_dict = response.json()
         object_list = response_dict['objects']
         logger.debug("Ancillary file JSON: {0}".format(object_list))
         if object_list:
             ancillary_file = AncillaryFile(self.api_base_url, object_list[0])  # Assume only one file is returned
         else:
             ancillary_file = AncillaryFile(self.api_base_url, None)  # Create an empty object
         return ancillary_file, response.status_code
     def __enter__(self):
         return self
     def __exit__(self, *args):
         logger.debug("Closing SCC connection session.")
         self.session.close()
     class PageNotAccessibleError(RuntimeError):
         pass
 class ApiObject(object):
     """ A generic class object. """
     def __init__(self, base_url, dict_response):
         self.base_url = base_url
         if dict_response:
             # Add the dictionary key value pairs as object properties
             for key, value in dict_response.items():
                 # logger.debug('Setting key {0} to value {1}'.format(key, value))
                 try:
                     setattr(self, key, value)
                 except:
                     logger.warning('Could not set attribute {0} to value {1}'.format(key, value))
             self.exists = True
         else:
             self.exists = False
 class Measurement(ApiObject):
     """ This class represents the measurement object as returned in the SCC API.
     """
     def __init__(self, base_url, dict_response):
         # Define expected attributes to assist debugging
         self.hirelpp = None
         self.hirelpp_exit_code = None
         self.cloudmask = None
         self.cloudmask_exit_code = None
         self.elpp = None
         self.elpp_exit_code = None
         self.elda = None
         self.elda_exit_code = None
         self.elic = None
         self.elic_exit_code = None
         self.eldec = None
         self.eldec_exit_code = None
         self.elquick = None
         self.elquick_exit_code = None
         self.id = None
         self.is_calibration = None
         self.is_running = None
         self.resource_uri = None
         self.start = None
         self.stop = None
         self.system = None
         self.upload = None
         super().__init__(base_url, dict_response)
     @property
     def has_finished(self):
         """ Temporary implementation for SCC version 5.2.0, until the API returns a flag indicating if the
         processing measurement has finished. """
         if (self.is_running is False) and (self.hirelpp != 0 or self.elpp != 0):
             return True
         else:
             return False
     def log_processing_status(self):
         """ Log module status. """
         logger.info("Measurement is being processed. Status: {}, {}, {}, {}, {}, {}). Please wait.".format(
             self.upload,
             self.hirelpp,
             self.cloudmask,
             self.elpp,
             self.elda,
             self.elic))
     def log_detailed_status(self):
         """ Log module exit and status codes."""
         logger.info("Measurement exit status:".format(self.id))
         if self.is_calibration:
             self._log_module_status('ElPP', self.elpp, self.elpp_exit_code)
             self._log_module_status('ElDEC', self.eldec, self.eldec_exit_code)
         else:
             self._log_module_status('HiRElPP', self.hirelpp, self.hirelpp_exit_code)
             self._log_module_status('CloudScreen', self.cloudmask, self.cloudmask_exit_code)
             self._log_module_status('ElPP', self.elpp, self.elpp_exit_code)
             self._log_module_status('ELDA', self.elda, self.elda_exit_code)
             self._log_module_status('ELIC', self.elic, self.elic_exit_code)
             self._log_module_status('ELQuick', self.elquick, self.elquick_exit_code)
     def _log_module_status(self, name, status, exit_code):
         if exit_code:
             if exit_code['exit_code'] > 0:
                 logger.warning("{0} exit code: {2[exit_code]} - {2[description]}".format(name, status, exit_code))
             else:
                 logger.info("{0} exit code: {2[exit_code]} - {2[description]}".format(name, status, exit_code))
         else:
             logger.info("{0} exit code: {2}".format(name, status, exit_code))
     @property
     def rerun_elda_url(self):
         url_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/rerun-elda/')
         return url_pattern.format(self.id)
     @property
     def rerun_elpp_url(self):
         url_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/rerun-elpp/')
         return url_pattern.format(self.id)
     @property
     def rerun_all_url(self):
         ulr_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/rerun-all/')
         return ulr_pattern.format(self.id)
     def __str__(self):
         return "Measurement {}".format(self.id)
 class AncillaryFile(ApiObject):
     """ This class represents the ancilalry file object as returned in the SCC API.
     """
     @property
     def already_on_scc(self):
         if self.exists is False:
             return False
         return not self.status == 'missing'
     def __str__(self):
         return "%s: %s, %s" % (self.id,
                                self.filename,
                                self.status)
 def process_file(filename, system_id, settings, force_upload, delete_related,
                  delay=0, monitor=True, rs_filename=None, lr_filename=None, ov_filename=None):
     """ Shortcut function to process a file to the SCC. """
     logger.info("Processing file %s, using system %s" % (filename, system_id))
     with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc:
         scc.login(settings['website_credentials'])
         measurement = scc.process(filename, system_id,
                                   force_upload=force_upload,
                                   delete_related=delete_related,
                                   delay=delay,
                                   monitor=monitor,
                                   rs_filename=rs_filename,
                                   lr_filename=lr_filename,
                                   ov_filename=ov_filename)
         scc.logout()
     return measurement
 def delete_measurements(measurement_ids, delete_related, settings):
     """ Shortcut function to delete measurements from the SCC. """
     with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc:
         scc.login(settings['website_credentials'])
         for m_id in measurement_ids:
             logger.info("Deleting %s." % m_id)
             scc.delete_measurement(m_id, delete_related)
         scc.logout()
 def rerun_all(measurement_ids, monitor, settings):
     """ Shortcut function to rerun measurements from the SCC. """
     with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc:
         scc.login(settings['website_credentials'])
         for m_id in measurement_ids:
             logger.info("Rerunning all products for %s." % m_id)
             scc.rerun_all(m_id, monitor)
         scc.logout()
 def rerun_processing(measurement_ids, monitor, settings):
     """ Shortcut function to delete a measurement from the SCC. """
     with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc:
         scc.login(settings['website_credentials'])
         for m_id in measurement_ids:
             logger.info("Rerunning (optical) processing for %s" % m_id)
             scc.rerun_elpp(m_id, monitor)
         scc.logout()
 def list_measurements(settings, station=None, system=None, start=None, stop=None, upload_status=None,
                       preprocessing_status=None,
                       optical_processing=None):
     """List all available measurements"""
     with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc:
         scc.login(settings['website_credentials'])
         ret = scc.list_measurements(station=station, system=system, start=start, stop=stop, upload_status=upload_status,
                                     processing_status=preprocessing_status, optical_processing=optical_processing)
         for entry in ret:
             print("%s" % entry.id)
         scc.logout()
 def download_measurements(measurement_ids, download_preproc, download_optical, download_graph, settings):
     """Download all measurements for the specified IDs"""
     with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc:
         scc.login(settings['website_credentials'])
         for m_id in measurement_ids:
             if download_preproc:
                 logger.info("Downloading preprocessed files for '%s'" % m_id)
                 scc.download_elpp(m_id)
                 logger.info("Complete")
             if download_optical:
                 logger.info("Downloading optical files for '%s'" % m_id)
                 scc.download_elda(m_id)
                 logger.info("Complete")
             if download_graph:
                 logger.info("Downloading profile graph files for '%s'" % m_id)
                 scc.download_plots(m_id)
                 logger.info("Complete")
         scc.logout()
 def settings_from_path(config_file_path):
     """ Read the configuration file.
     The file should be in YAML syntax."""
     if not os.path.isfile(config_file_path):
         raise argparse.ArgumentTypeError("Wrong path for configuration file (%s)" % config_file_path)
     with open(config_file_path) as yaml_file:
         try:
             settings = yaml.safe_load(yaml_file)
             logger.debug("Read settings file(%s)" % config_file_path)
         except Exception:
             raise argparse.ArgumentTypeError("Could not parse YAML file (%s)" % config_file_path)
     # YAML limitation: does not read tuples
     settings['basic_credentials'] = tuple(settings['basic_credentials'])
     settings['website_credentials'] = tuple(settings['website_credentials'])
     return settings
 # Setup for command specific parsers
 def setup_delete(parser):
     def delete_from_args(parsed):
         delete_measurements(parsed.IDs,
                             delete_related=False,
                             settings=parsed.config)
     parser.add_argument("IDs", nargs="+", help="measurement IDs to delete.")
     parser.set_defaults(execute=delete_from_args)
 def setup_rerun_all(parser):
     def rerun_all_from_args(parsed):
         rerun_all(parsed.IDs, parsed.process, parsed.config)
     parser.add_argument("IDs", nargs="+", help="Measurement IDs to rerun.")
     parser.add_argument("-p", "--process", help="Wait for the results of the processing.",
                         action="store_true")
     parser.set_defaults(execute=rerun_all_from_args)
 def setup_rerun_elpp(parser):
     def rerun_processing_from_args(parsed):
         rerun_processing(parsed.IDs, parsed.process, parsed.config)
     parser.add_argument("IDs", nargs="+", help="Measurement IDs to rerun the processing on.")
     parser.add_argument("-p", "--process", help="Wait for the results of the processing.",
                         action="store_true")
     parser.set_defaults(execute=rerun_processing_from_args)
 def setup_upload_file(parser):
     """ Upload but do not monitor processing progress. """
     def upload_file_from_args(parsed):
         process_file(parsed.filename, parsed.system, parsed.config,
                      delay=parsed.delay,
                      monitor=parsed.process,
                      force_upload=parsed.force_upload,
                      delete_related=False,  # For now, use this as default
                      rs_filename=parsed.radiosounding,
                      ov_filename=parsed.overlap,
                      lr_filename=parsed.lidarratio)
     def delay(arg):
         try:
             int_arg = int(arg)
         except ValueError:
             raise argparse.ArgumentTypeError("Could not convert delay argument {} to integer.".format(arg))
         if 0 <= int_arg <= 96:
             return int_arg
         else:
             raise argparse.ArgumentTypeError("Delay should be an integer between 0 and 96.")
     parser.add_argument("filename", help="Measurement file name or path.")
     parser.add_argument("system", help="Processing system id.")
     parser.add_argument("--delay", help="Delay processing by the specified number of hours (0 to 96).",
                         default=0, type=delay)
     parser.add_argument("-p", "--process", help="Wait for the processing results.",
                         action="store_true")
     parser.add_argument("--force_upload", help="If measurement ID exists on SCC, delete before uploading.",
                         action="store_true")
     parser.add_argument("--radiosounding", default=None, help="Radiosounding file name or path")
     parser.add_argument("--overlap", default=None, help="Overlap file name or path")
     parser.add_argument("--lidarratio", default=None, help="Lidar ratio file name or path")
     parser.set_defaults(execute=upload_file_from_args)
 def setup_list_measurements(parser):
     def list_measurements_from_args(parsed):
         # TODO: Fix this
         logger.warning("This method needs to be updated. Cross-chceck any results.")
         list_measurements(parsed.config, station=parsed.station, system=parsed.system, start=parsed.start,
                           stop=parsed.stop,
                           upload_status=parsed.upload_status, preprocessing_status=parsed.preprocessing_status,
                           optical_processing=parsed.optical_processing_status)
     def status(arg):
         if -127 <= int(arg) <= 127:
             return arg
         else:
             raise argparse.ArgumentTypeError("Status must be between -127 and 127")
     def date(arg):
         if re.match(r'\d{4}-\d{2}-\d{2}', arg):
             return arg
         else:
             raise argparse.ArgumentTypeError("Date must be in format 'YYYY-MM-DD'")
     parser.add_argument("--station", help="Filter for only the selected station")
     parser.add_argument("--system", help="Filter for only the selected station")
     parser.add_argument("--start", help="Filter for only the selected station", type=date)
     parser.add_argument("--stop", help="Filter for only the selected station", type=date)
     parser.add_argument("--upload-status", help="Filter for only the selected station", type=status)
     parser.add_argument("--preprocessing-status", help="Filter for only the selected station", type=status)
     parser.add_argument("--optical-processing-status", help="Filter for only the selected station", type=status)
     parser.set_defaults(execute=list_measurements_from_args)
 def setup_download_measurements(parser):
     def download_measurements_from_args(parsed):
         # TODO: Fix this
         logger.warning("This method needs to be updated. Cross-chceck any results.")
         preproc = parsed.download_elpp
         optical = parsed.download_elda
         graphs = parsed.download_profile_graphs
         if not preproc and not graphs:
             optical = True
         download_measurements(parsed.IDs, preproc, optical, graphs, parsed.config)
     parser.add_argument("IDs", help="Measurement IDs that should be downloaded.", nargs="+")
     parser.add_argument("--download-preprocessed", action="store_true", help="Download preprocessed files.")
     parser.add_argument("--download-optical", action="store_true",
                         help="Download optical files (default if no other download is used).")
     parser.add_argument("--download-profile-graphs", action="store_true", help="Download profile graph files.")
     parser.set_defaults(execute=download_measurements_from_args)
 def main():
     # Define the command line arguments.
     parser = argparse.ArgumentParser()
     subparsers = parser.add_subparsers()
     delete_parser = subparsers.add_parser("delete", help="Deletes a measurement.")
     rerun_all_parser = subparsers.add_parser("rerun-all", help="Rerun all processing steps for the provided measurement IDs.")
     rerun_processing_parser = subparsers.add_parser("rerun-elpp",
                                                     help="Rerun low-resolution processing steps for the provided measurement ID.")
     upload_file_parser = subparsers.add_parser("upload-file", help="Submit a file and, optionally, download the output products.")
     list_parser = subparsers.add_parser("list", help="List measurements registered on the SCC.")
     download_parser = subparsers.add_parser("download", help="Download selected measurements.")
     setup_delete(delete_parser)
     setup_rerun_all(rerun_all_parser)
     setup_rerun_elpp(rerun_processing_parser)
     setup_upload_file(upload_file_parser)
     setup_list_measurements(list_parser)
     setup_download_measurements(download_parser)
     # Verbosity settings from http://stackoverflow.com/a/20663028
     parser.add_argument('-d', '--debug', help="Print debugging information.", action="store_const",
                         dest="loglevel", const=logging.DEBUG, default=logging.INFO,
                         )
     parser.add_argument('-s', '--silent', help="Show only warning and error messages.", action="store_const",
                         dest="loglevel", const=logging.WARNING
                         )
     # Setup default config location
     home = os.path.expanduser("~")
     default_config_location = os.path.abspath(os.path.join(home, ".scc_access.yaml"))
     parser.add_argument("-c", "--config", help="Path to the config file.", type=settings_from_path,
                         default=default_config_location)
     args = parser.parse_args()
     # Get the logger with the appropriate level
     logging.basicConfig(format='%(levelname)s: %(message)s', level=args.loglevel)
     # Dispatch to appropriate function
     args.execute(args)
 # When running through terminal
 if __name__ == '__main__':
     main()

Mercurial > public > scc_access / annotate

scc_access/scc_access.py@8d487e4e20ae (annotated)

scc_access/scc_access.py