Sat, 09 Jan 2021 17:26:30 +0200
Merged scc_access.py
ioannis@45 | 1 | import sys |
ioannis@45 | 2 | |
victor@7 | 3 | import requests |
moritz@29 | 4 | |
ioannis@17 | 5 | try: |
ioannis@17 | 6 | import urllib.parse as urlparse # Python 3 |
ioannis@17 | 7 | except ImportError: |
ioannis@17 | 8 | import urlparse # Python 2 |
victor@7 | 9 | |
victor@7 | 10 | import argparse |
madrouin@24 | 11 | import datetime |
madrouin@24 | 12 | import logging |
victor@7 | 13 | import os |
victor@7 | 14 | import re |
ioannis@32 | 15 | from io import BytesIO |
ioannis@45 | 16 | |
victor@7 | 17 | import time |
i@40 | 18 | |
victor@7 | 19 | from zipfile import ZipFile |
madrouin@24 | 20 | |
i@14 | 21 | import yaml |
victor@7 | 22 | |
ioannis@45 | 23 | import netCDF4 as netcdf |
ioannis@45 | 24 | |
madrouin@24 | 25 | requests.packages.urllib3.disable_warnings() |
i@14 | 26 | logger = logging.getLogger(__name__) |
victor@7 | 27 | |
victor@7 | 28 | # The regex to find the measurement id from the measurement page |
victor@7 | 29 | # This should be read from the uploaded file, but would require an extra NetCDF module. |
i@36 | 30 | regex = "<h3>Measurement (?P<measurement_id>.{12,15}) <small>" # {12, 15} to handle both old- and new-style measurement ids. |
victor@7 | 31 | |
victor@7 | 32 | |
victor@7 | 33 | class SCC: |
madrouin@24 | 34 | """A simple class that will attempt to upload a file on the SCC server. |
i@14 | 35 | |
victor@7 | 36 | The uploading is done by simulating a normal browser session. In the current |
madrouin@20 | 37 | version no check is performed, and no feedback is given if the upload |
madrouin@20 | 38 | was successful. If everything is setup correctly, it will work. |
victor@7 | 39 | """ |
victor@7 | 40 | |
i@14 | 41 | def __init__(self, auth, output_dir, base_url): |
moritz@29 | 42 | |
victor@7 | 43 | self.auth = auth |
victor@7 | 44 | self.output_dir = output_dir |
i@14 | 45 | self.base_url = base_url |
victor@7 | 46 | self.session = requests.Session() |
moritz@29 | 47 | self.session.auth = auth |
moritz@29 | 48 | self.session.verify = False |
i@31 | 49 | |
i@14 | 50 | self.login_url = urlparse.urljoin(self.base_url, 'accounts/login/') |
i@31 | 51 | self.logout_url = urlparse.urljoin(self.base_url, 'accounts/logout/') |
i@31 | 52 | self.list_measurements_url = urlparse.urljoin(self.base_url, 'data_processing/measurements/') |
i@31 | 53 | |
i@14 | 54 | self.upload_url = urlparse.urljoin(self.base_url, 'data_processing/measurements/quick/') |
ioannis@34 | 55 | self.download_hirelpp_pattern = urlparse.urljoin(self.base_url, |
ioannis@34 | 56 | 'data_processing/measurements/{0}/download-hirelpp/') |
ioannis@34 | 57 | self.download_cloudmask_pattern = urlparse.urljoin(self.base_url, |
ioannis@34 | 58 | 'data_processing/measurements/{0}/download-cloudmask/') |
ioannis@34 | 59 | |
ioannis@45 | 60 | self.download_elpp_pattern = urlparse.urljoin(self.base_url, |
moritz@29 | 61 | 'data_processing/measurements/{0}/download-preprocessed/') |
ioannis@45 | 62 | self.download_elda_pattern = urlparse.urljoin(self.base_url, |
moritz@29 | 63 | 'data_processing/measurements/{0}/download-optical/') |
ioannis@45 | 64 | self.download_plots_pattern = urlparse.urljoin(self.base_url, |
moritz@29 | 65 | 'data_processing/measurements/{0}/download-plots/') |
ioannis@34 | 66 | self.download_elic_pattern = urlparse.urljoin(self.base_url, |
ioannis@34 | 67 | 'data_processing/measurements/{0}/download-elic/') |
i@14 | 68 | self.delete_measurement_pattern = urlparse.urljoin(self.base_url, 'admin/database/measurements/{0}/delete/') |
i@31 | 69 | |
i@14 | 70 | self.api_base_url = urlparse.urljoin(self.base_url, 'api/v1/') |
i@31 | 71 | self.api_measurement_pattern = urlparse.urljoin(self.api_base_url, 'measurements/{0}/') |
i@31 | 72 | self.api_measurements_url = urlparse.urljoin(self.api_base_url, 'measurements') |
i@38 | 73 | self.api_sounding_search_pattern = urlparse.urljoin(self.api_base_url, 'sounding_files/?filename={0}') |
i@38 | 74 | self.api_lidarratio_search_pattern = urlparse.urljoin(self.api_base_url, 'lidarratio_files/?filename={0}') |
i@38 | 75 | self.api_overlap_search_pattern = urlparse.urljoin(self.api_base_url, 'overlap_files/?filename={0}') |
i@14 | 76 | |
i@14 | 77 | def login(self, credentials): |
i@31 | 78 | """ Login to SCC. """ |
victor@7 | 79 | logger.debug("Attempting to login to SCC, username %s." % credentials[0]) |
moritz@29 | 80 | login_credentials = {'username': credentials[0], |
moritz@29 | 81 | 'password': credentials[1]} |
victor@7 | 82 | |
i@14 | 83 | logger.debug("Accessing login page at %s." % self.login_url) |
victor@7 | 84 | |
victor@7 | 85 | # Get upload form |
moritz@29 | 86 | login_page = self.session.get(self.login_url) |
victor@7 | 87 | |
i@31 | 88 | if not login_page.ok: |
i@31 | 89 | raise self.PageNotAccessibleError('Could not access login pages. Status code %s' % login_page.status_code) |
victor@7 | 90 | |
i@31 | 91 | logger.debug("Submitting credentials.") |
victor@7 | 92 | # Submit the login data |
i@14 | 93 | login_submit = self.session.post(self.login_url, |
moritz@29 | 94 | data=login_credentials, |
victor@7 | 95 | headers={'X-CSRFToken': login_page.cookies['csrftoken'], |
moritz@29 | 96 | 'referer': self.login_url}) |
victor@7 | 97 | return login_submit |
victor@7 | 98 | |
victor@7 | 99 | def logout(self): |
i@31 | 100 | """ Logout from SCC """ |
i@31 | 101 | return self.session.get(self.logout_url, stream=True) |
victor@7 | 102 | |
ioannis@45 | 103 | def upload_file(self, filename, system_id, force_upload, delete_related, rs_filename=None, ov_filename=None, lr_filename=None): |
madrouin@20 | 104 | """ Upload a filename for processing with a specific system. If the |
victor@7 | 105 | upload is successful, it returns the measurement id. """ |
ioannis@45 | 106 | measurement_id = self.measurement_id_from_file(filename) |
ioannis@45 | 107 | |
ioannis@45 | 108 | logger.debug('Checking if a measurement with the same id already exists on the SCC server.') |
ioannis@45 | 109 | existing_measurement = self.get_measurement(measurement_id) |
ioannis@45 | 110 | |
ioannis@45 | 111 | if existing_measurement: |
ioannis@45 | 112 | if force_upload: |
ioannis@45 | 113 | logger.info( |
ioannis@45 | 114 | "Measurement with id {} already exists on the SCC. Trying to delete it...".format(measurement_id)) |
ioannis@45 | 115 | self.delete_measurement(measurement_id, delete_related) |
ioannis@45 | 116 | else: |
ioannis@45 | 117 | logger.error( |
ioannis@45 | 118 | "Measurement with id {} already exists on the SCC. Use --force_upload flag to overwrite it.".format( |
ioannis@45 | 119 | measurement_id)) |
ioannis@45 | 120 | sys.exit(1) |
ioannis@45 | 121 | |
victor@7 | 122 | # Get submit page |
moritz@29 | 123 | upload_page = self.session.get(self.upload_url) |
victor@7 | 124 | |
victor@7 | 125 | # Submit the data |
victor@7 | 126 | upload_data = {'system': system_id} |
victor@7 | 127 | files = {'data': open(filename, 'rb')} |
victor@7 | 128 | |
madrouin@20 | 129 | if rs_filename is not None: |
i@38 | 130 | ancillary_file, _ = self.get_ancillary(rs_filename, 'sounding') |
i@38 | 131 | |
i@38 | 132 | if ancillary_file.already_on_scc: |
i@38 | 133 | logger.warning("Sounding file {0.filename} already on the SCC with id {0.id}. Ignoring it.".format(ancillary_file)) |
i@38 | 134 | else: |
i@38 | 135 | logger.debug('Adding sounding file %s' % rs_filename) |
i@38 | 136 | files['sounding_file'] = open(rs_filename, 'rb') |
madrouin@20 | 137 | |
ioannis@32 | 138 | if ov_filename is not None: |
i@38 | 139 | ancillary_file, _ = self.get_ancillary(ov_filename, 'overlap') |
i@38 | 140 | |
i@38 | 141 | if ancillary_file.already_on_scc: |
i@38 | 142 | logger.warning("Overlap file {0.filename} already on the SCC with id {0.id}. Ignoring it.".format(ancillary_file)) |
i@38 | 143 | else: |
i@38 | 144 | logger.debug('Adding overlap file %s' % ov_filename) |
i@38 | 145 | files['overlap_file'] = open(ov_filename, 'rb') |
i@31 | 146 | |
i@31 | 147 | if lr_filename is not None: |
i@38 | 148 | ancillary_file, _ = self.get_ancillary(lr_filename, 'lidarratio') |
i@38 | 149 | |
i@38 | 150 | if ancillary_file.already_on_scc: |
i@38 | 151 | logger.warning( |
i@38 | 152 | "Lidar ratio file {0.filename} already on the SCC with id {0.id}. Ignoring it.".format(ancillary_file)) |
i@38 | 153 | else: |
i@38 | 154 | logger.debug('Adding lidar ratio file %s' % lr_filename) |
i@38 | 155 | files['lidar_ratio_file'] = open(lr_filename, 'rb') |
i@31 | 156 | |
ioannis@32 | 157 | logger.info("Uploading of file(s) %s started." % filename) |
victor@7 | 158 | |
i@14 | 159 | upload_submit = self.session.post(self.upload_url, |
victor@7 | 160 | data=upload_data, |
victor@7 | 161 | files=files, |
victor@7 | 162 | headers={'X-CSRFToken': upload_page.cookies['csrftoken'], |
moritz@29 | 163 | 'referer': self.upload_url}) |
victor@7 | 164 | |
victor@7 | 165 | if upload_submit.status_code != 200: |
i@14 | 166 | logger.warning("Connection error. Status code: %s" % upload_submit.status_code) |
victor@7 | 167 | return False |
victor@7 | 168 | |
victor@7 | 169 | # Check if there was a redirect to a new page. |
i@14 | 170 | if upload_submit.url == self.upload_url: |
victor@7 | 171 | measurement_id = False |
ioannis@32 | 172 | logger.error("Uploaded file(s) rejected! Try to upload manually to see the error.") |
victor@7 | 173 | else: |
victor@7 | 174 | measurement_id = re.findall(regex, upload_submit.text)[0] |
madrouin@23 | 175 | logger.info("Successfully uploaded measurement with id %s." % measurement_id) |
victor@7 | 176 | |
victor@7 | 177 | return measurement_id |
victor@7 | 178 | |
ioannis@45 | 179 | @staticmethod |
ioannis@45 | 180 | def measurement_id_from_file(filename): |
ioannis@45 | 181 | """ Get the measurement id from the input file. """ |
ioannis@45 | 182 | |
ioannis@45 | 183 | if not os.path.isfile(filename): |
ioannis@45 | 184 | logger.error("File {} does not exist.".format(filename)) |
ioannis@45 | 185 | sys.exit(1) |
ioannis@45 | 186 | |
ioannis@45 | 187 | with netcdf.Dataset(filename) as f: |
ioannis@45 | 188 | try: |
ioannis@45 | 189 | measurement_id = f.Measurement_ID |
ioannis@45 | 190 | except AttributeError: |
ioannis@45 | 191 | logger.error( |
ioannis@45 | 192 | "Input file {} does not contain a Measurement_ID global attribute. Wrong file format?".format( |
ioannis@45 | 193 | filename)) |
ioannis@45 | 194 | sys.exit(1) |
ioannis@45 | 195 | |
ioannis@45 | 196 | return measurement_id |
ioannis@45 | 197 | |
victor@7 | 198 | def download_files(self, measurement_id, subdir, download_url): |
victor@7 | 199 | """ Downloads some files from the download_url to the specified |
madrouin@20 | 200 | subdir. This method is used to download preprocessed file, optical |
victor@7 | 201 | files etc. |
victor@7 | 202 | """ |
ioannis@32 | 203 | # TODO: Make downloading more robust (e.g. in case that files do not exist on server). |
victor@7 | 204 | # Get the file |
moritz@29 | 205 | request = self.session.get(download_url, stream=True) |
moritz@29 | 206 | |
moritz@29 | 207 | if not request.ok: |
moritz@29 | 208 | raise Exception("Could not download files for measurement '%s'" % measurement_id) |
victor@7 | 209 | |
victor@7 | 210 | # Create the dir if it does not exist |
victor@7 | 211 | local_dir = os.path.join(self.output_dir, measurement_id, subdir) |
victor@7 | 212 | if not os.path.exists(local_dir): |
victor@7 | 213 | os.makedirs(local_dir) |
victor@7 | 214 | |
victor@7 | 215 | # Save the file by chunk, needed if the file is big. |
ioannis@32 | 216 | memory_file = BytesIO() |
victor@7 | 217 | |
victor@7 | 218 | for chunk in request.iter_content(chunk_size=1024): |
victor@7 | 219 | if chunk: # filter out keep-alive new chunks |
victor@7 | 220 | memory_file.write(chunk) |
victor@7 | 221 | memory_file.flush() |
victor@7 | 222 | |
victor@7 | 223 | zip_file = ZipFile(memory_file) |
victor@7 | 224 | |
victor@7 | 225 | for ziped_name in zip_file.namelist(): |
victor@7 | 226 | basename = os.path.basename(ziped_name) |
victor@7 | 227 | |
victor@7 | 228 | local_file = os.path.join(local_dir, basename) |
victor@7 | 229 | |
victor@7 | 230 | with open(local_file, 'wb') as f: |
victor@7 | 231 | f.write(zip_file.read(ziped_name)) |
victor@7 | 232 | |
ioannis@34 | 233 | def download_hirelpp(self, measurement_id): |
ioannis@45 | 234 | """ Download hirelpp files for the measurement id. """ |
ioannis@34 | 235 | # Construct the download url |
ioannis@34 | 236 | download_url = self.download_hirelpp_pattern.format(measurement_id) |
ioannis@45 | 237 | try: |
ioannis@45 | 238 | self.download_files(measurement_id, 'scc_hirelpp', download_url) |
ioannis@45 | 239 | except Exception as e: |
ioannis@45 | 240 | logger.error("Could not download HiRElPP files. Error message: {}".format(e)) |
ioannis@45 | 241 | logger.debug('Download exception:', exc_info=True) |
ioannis@34 | 242 | |
ioannis@34 | 243 | def download_cloudmask(self, measurement_id): |
ioannis@45 | 244 | """ Download cloudmask files for the measurement id. """ |
ioannis@34 | 245 | # Construct the download url |
ioannis@34 | 246 | download_url = self.download_cloudmask_pattern.format(measurement_id) |
ioannis@45 | 247 | try: |
ioannis@45 | 248 | self.download_files(measurement_id, 'scc_cloudscreen', download_url) |
ioannis@45 | 249 | except Exception as e: |
ioannis@45 | 250 | logger.error("Could not download cloudscreen files. Error message: {}".format(e)) |
ioannis@45 | 251 | logger.debug('Download exception:', exc_info=True) |
ioannis@34 | 252 | |
ioannis@45 | 253 | def download_elpp(self, measurement_id): |
victor@7 | 254 | """ Download preprocessed files for the measurement id. """ |
victor@7 | 255 | # Construct the download url |
ioannis@45 | 256 | download_url = self.download_elpp_pattern.format(measurement_id) |
ioannis@45 | 257 | try: |
ioannis@45 | 258 | self.download_files(measurement_id, 'scc_preprocessed', download_url) |
ioannis@45 | 259 | except Exception as e: |
ioannis@45 | 260 | logger.error("Could not download ElPP files. Error message: {}".format(e)) |
ioannis@45 | 261 | logger.debug('Download exception:', exc_info=True) |
victor@7 | 262 | |
ioannis@45 | 263 | def download_elda(self, measurement_id): |
victor@7 | 264 | """ Download optical files for the measurement id. """ |
victor@7 | 265 | # Construct the download url |
ioannis@45 | 266 | download_url = self.download_elda_pattern.format(measurement_id) |
ioannis@45 | 267 | try: |
ioannis@45 | 268 | self.download_files(measurement_id, 'scc_optical', download_url) |
ioannis@45 | 269 | except Exception as e: |
ioannis@45 | 270 | logger.error("Could not download ELDA files. Error message: {}".format(e)) |
ioannis@45 | 271 | logger.debug('Download exception:', exc_info=True) |
victor@7 | 272 | |
ioannis@45 | 273 | def download_plots(self, measurement_id): |
victor@7 | 274 | """ Download profile graphs for the measurement id. """ |
victor@7 | 275 | # Construct the download url |
ioannis@45 | 276 | download_url = self.download_plots_pattern.format(measurement_id) |
ioannis@45 | 277 | try: |
ioannis@45 | 278 | self.download_files(measurement_id, 'scc_plots', download_url) |
ioannis@45 | 279 | except Exception as e: |
ioannis@45 | 280 | logger.error("Could not download ELDA plots. Error message: {}".format(e)) |
ioannis@45 | 281 | logger.debug('Download exception:', exc_info=True) |
victor@7 | 282 | |
ioannis@34 | 283 | def download_elic(self, measurement_id): |
ioannis@45 | 284 | """ Download ELIC files for the measurement id. """ |
ioannis@34 | 285 | # Construct the download url |
ioannis@34 | 286 | download_url = self.download_elic_pattern.format(measurement_id) |
ioannis@45 | 287 | try: |
ioannis@45 | 288 | self.download_files(measurement_id, 'scc_elic', download_url) |
ioannis@45 | 289 | except Exception as e: |
ioannis@45 | 290 | logger.error("Could not download ELIC files. Error message: {}".format(e)) |
ioannis@45 | 291 | logger.debug('Download exception:', exc_info=True) |
ioannis@32 | 292 | |
ioannis@45 | 293 | def download_eldec(self, measurement_id): |
ioannis@45 | 294 | """ Download ELDEC files for the measurement id. """ |
ioannis@45 | 295 | # Construct the download url |
ioannis@45 | 296 | download_url = self.download_elda_pattern.format(measurement_id) # ELDA patter is used for now |
ioannis@45 | 297 | try: |
ioannis@45 | 298 | self.download_files(measurement_id, 'scc_eldec', download_url) |
ioannis@45 | 299 | except Exception as e: |
ioannis@45 | 300 | logger.error("Could not download EDELC files. Error message: {}".format(e)) |
ioannis@45 | 301 | logger.debug('Download exception:', exc_info=True) |
ioannis@45 | 302 | |
ioannis@45 | 303 | def rerun_elpp(self, measurement_id, monitor=True): |
ioannis@45 | 304 | logger.debug("Started rerun_elpp procedure.") |
ioannis@45 | 305 | |
ioannis@45 | 306 | logger.debug("Getting measurement %s" % measurement_id) |
madrouin@26 | 307 | measurement, status = self.get_measurement(measurement_id) |
victor@7 | 308 | |
victor@7 | 309 | if measurement: |
ioannis@45 | 310 | logger.debug("Attempting to rerun ElPP through %s." % measurement.rerun_all_url) |
ioannis@45 | 311 | request = self.session.get(measurement.rerun_elpp_url, stream=True) |
victor@7 | 312 | |
victor@7 | 313 | if request.status_code != 200: |
i@14 | 314 | logger.error( |
i@14 | 315 | "Could not rerun processing for %s. Status code: %s" % (measurement_id, request.status_code)) |
ioannis@45 | 316 | else: |
ioannis@45 | 317 | logger.info("Rerun-elpp command submitted successfully for id {}.".format(measurement_id)) |
victor@7 | 318 | |
victor@7 | 319 | if monitor: |
victor@7 | 320 | self.monitor_processing(measurement_id) |
victor@7 | 321 | |
victor@7 | 322 | def rerun_all(self, measurement_id, monitor=True): |
victor@7 | 323 | logger.debug("Started rerun_all procedure.") |
victor@7 | 324 | |
victor@7 | 325 | logger.debug("Getting measurement %s" % measurement_id) |
madrouin@26 | 326 | measurement, status = self.get_measurement(measurement_id) |
victor@7 | 327 | |
victor@7 | 328 | if measurement: |
victor@7 | 329 | logger.debug("Attempting to rerun all processing through %s." % measurement.rerun_all_url) |
victor@7 | 330 | |
moritz@29 | 331 | request = self.session.get(measurement.rerun_all_url, stream=True) |
victor@7 | 332 | |
victor@7 | 333 | if request.status_code != 200: |
victor@7 | 334 | logger.error("Could not rerun pre processing for %s. Status code: %s" % |
victor@7 | 335 | (measurement_id, request.status_code)) |
ioannis@45 | 336 | else: |
ioannis@45 | 337 | logger.info("Rerun-all command submitted successfully for id {}.".format(measurement_id)) |
victor@7 | 338 | |
victor@7 | 339 | if monitor: |
victor@7 | 340 | self.monitor_processing(measurement_id) |
victor@7 | 341 | |
ioannis@45 | 342 | def process(self, filename, system_id, monitor, force_upload, delete_related, rs_filename=None, lr_filename=None, ov_filename=None): |
victor@7 | 343 | """ Upload a file for processing and wait for the processing to finish. |
victor@7 | 344 | If the processing is successful, it will download all produced files. |
victor@7 | 345 | """ |
victor@7 | 346 | logger.info("--- Processing started on %s. ---" % datetime.datetime.now()) |
victor@7 | 347 | # Upload file |
madrouin@26 | 348 | logger.info("--- Uploading file") |
ioannis@45 | 349 | measurement_id = self.upload_file(filename, system_id, force_upload, delete_related, |
ioannis@32 | 350 | rs_filename=rs_filename, |
ioannis@32 | 351 | lr_filename=lr_filename, |
ioannis@32 | 352 | ov_filename=ov_filename) |
victor@7 | 353 | |
ioannis@32 | 354 | if measurement_id and monitor: |
ioannis@32 | 355 | logger.info("--- Monitoring processing") |
moritz@29 | 356 | return self.monitor_processing(measurement_id) |
ioannis@32 | 357 | |
moritz@29 | 358 | return None |
victor@7 | 359 | |
victor@7 | 360 | def monitor_processing(self, measurement_id): |
victor@7 | 361 | """ Monitor the processing progress of a measurement id""" |
victor@7 | 362 | |
madrouin@24 | 363 | # try to deal with error 404 |
madrouin@24 | 364 | error_count = 0 |
madrouin@24 | 365 | error_max = 6 |
madrouin@26 | 366 | time_sleep = 10 |
madrouin@24 | 367 | |
madrouin@25 | 368 | # try to wait for measurement to appear in API |
madrouin@24 | 369 | measurement = None |
ioannis@45 | 370 | logger.info("Looking for measurement %s on SCC", measurement_id) |
madrouin@26 | 371 | while error_count < error_max: |
madrouin@26 | 372 | time.sleep(time_sleep) |
madrouin@26 | 373 | measurement, status = self.get_measurement(measurement_id) |
madrouin@26 | 374 | if status != 200 and error_count < error_max: |
ioannis@32 | 375 | logger.error("Measurement not found. waiting %ds", time_sleep) |
madrouin@24 | 376 | error_count += 1 |
madrouin@26 | 377 | else: |
madrouin@26 | 378 | break |
madrouin@24 | 379 | |
madrouin@24 | 380 | if error_count == error_max: |
ioannis@32 | 381 | logger.critical("Measurement %s doesn't seem to exist", measurement_id) |
madrouin@26 | 382 | sys.exit(1) |
madrouin@26 | 383 | |
ioannis@45 | 384 | logger.info('Measurement %s found.', measurement_id) |
madrouin@24 | 385 | |
victor@7 | 386 | if measurement is not None: |
victor@7 | 387 | while measurement.is_running: |
ioannis@45 | 388 | logger.info("Measurement is being processed. status: {}, {}, {}, {}, {}, {}). Please wait.".format( |
ioannis@45 | 389 | measurement.upload, |
ioannis@45 | 390 | measurement.hirelpp, |
ioannis@45 | 391 | measurement.cloudmask, |
ioannis@45 | 392 | measurement.elpp, |
ioannis@45 | 393 | measurement.elda, |
ioannis@45 | 394 | measurement.elic)) |
victor@7 | 395 | time.sleep(10) |
madrouin@26 | 396 | measurement, status = self.get_measurement(measurement_id) |
madrouin@24 | 397 | |
ioannis@34 | 398 | logger.info("Measurement processing finished.") |
ioannis@34 | 399 | if measurement.hirelpp == 127: |
ioannis@45 | 400 | logger.info("Downloading HiRElPP files.") |
ioannis@34 | 401 | self.download_hirelpp(measurement_id) |
ioannis@34 | 402 | if measurement.cloudmask == 127: |
ioannis@45 | 403 | logger.info("Downloading cloud screening files.") |
ioannis@34 | 404 | self.download_cloudmask(measurement_id) |
ioannis@34 | 405 | if measurement.elpp == 127: |
ioannis@45 | 406 | logger.info("Downloading ElPP files.") |
ioannis@45 | 407 | self.download_elpp(measurement_id) |
ioannis@34 | 408 | if measurement.elda == 127: |
ioannis@45 | 409 | logger.info("Downloading ELDA files.") |
ioannis@45 | 410 | self.download_elda(measurement_id) |
victor@7 | 411 | logger.info("Downloading graphs.") |
ioannis@45 | 412 | self.download_plots(measurement_id) |
ioannis@34 | 413 | if measurement.elic == 127: |
ioannis@45 | 414 | logger.info("Downloading ELIC files.") |
ioannis@34 | 415 | self.download_elic(measurement_id) |
ioannis@45 | 416 | |
ioannis@45 | 417 | # TODO: Need to check ELDEC code (when it becomes available in the API) |
ioannis@45 | 418 | if measurement.is_calibration: |
ioannis@45 | 419 | logger.info("Downloading ELDEC files.") |
ioannis@45 | 420 | self.download_eldec(measurement_id) |
victor@7 | 421 | logger.info("--- Processing finished. ---") |
ioannis@45 | 422 | |
victor@7 | 423 | return measurement |
victor@7 | 424 | |
victor@7 | 425 | def get_measurement(self, measurement_id): |
ioannis@45 | 426 | |
ioannis@45 | 427 | if measurement_id is None: # Is this still required? |
ioannis@45 | 428 | return None |
ioannis@45 | 429 | |
i@31 | 430 | measurement_url = self.api_measurement_pattern.format(measurement_id) |
i@31 | 431 | logger.debug("Measurement API URL: %s" % measurement_url) |
victor@7 | 432 | |
moritz@29 | 433 | response = self.session.get(measurement_url) |
victor@7 | 434 | |
ioannis@45 | 435 | response_dict = None |
ioannis@45 | 436 | |
ioannis@45 | 437 | if response.status_code == 200: |
ioannis@45 | 438 | response_dict = response.json() |
ioannis@45 | 439 | elif response.status_code == 404: |
ioannis@45 | 440 | logger.info("No measurement with id %s found on the SCC." % measurement_id) |
ioannis@45 | 441 | else: |
i@14 | 442 | logger.error('Could not access API. Status code %s.' % response.status_code) |
victor@7 | 443 | |
victor@7 | 444 | if response_dict: |
moritz@29 | 445 | measurement = Measurement(self.base_url, response_dict) |
victor@7 | 446 | else: |
ioannis@45 | 447 | measurement = None |
victor@7 | 448 | |
ioannis@45 | 449 | return measurement, response.status_code |
ioannis@45 | 450 | |
ioannis@45 | 451 | def delete_measurement(self, measurement_id, delete_related): |
victor@7 | 452 | """ Deletes a measurement with the provided measurement id. The user |
madrouin@20 | 453 | should have the appropriate permissions. |
madrouin@20 | 454 | |
victor@7 | 455 | The procedures is performed directly through the web interface and |
victor@7 | 456 | NOT through the API. |
victor@7 | 457 | """ |
victor@7 | 458 | # Get the measurement object |
i@31 | 459 | measurement, _ = self.get_measurement(measurement_id) |
victor@7 | 460 | |
victor@7 | 461 | # Check that it exists |
victor@7 | 462 | if measurement is None: |
victor@7 | 463 | logger.warning("Nothing to delete.") |
victor@7 | 464 | return None |
victor@7 | 465 | |
victor@7 | 466 | # Go the the page confirming the deletion |
moritz@29 | 467 | delete_url = self.delete_measurement_pattern.format(measurement_id) |
victor@7 | 468 | |
moritz@29 | 469 | confirm_page = self.session.get(delete_url) |
victor@7 | 470 | |
victor@7 | 471 | # Check that the page opened properly |
victor@7 | 472 | if confirm_page.status_code != 200: |
victor@7 | 473 | logger.warning("Could not open delete page. Status: {0}".format(confirm_page.status_code)) |
victor@7 | 474 | return None |
victor@7 | 475 | |
ioannis@45 | 476 | # Get the delete related value |
ioannis@45 | 477 | if delete_related: |
ioannis@45 | 478 | delete_related_option = 'delete_related' |
ioannis@45 | 479 | else: |
ioannis@45 | 480 | delete_related_option = 'not_delete_related' |
ioannis@45 | 481 | |
victor@7 | 482 | # Delete the measurement |
victor@7 | 483 | delete_page = self.session.post(delete_url, |
ioannis@45 | 484 | data={'post': 'yes', |
ioannis@45 | 485 | 'select_delete_related_measurements': delete_related_option}, |
victor@7 | 486 | headers={'X-CSRFToken': confirm_page.cookies['csrftoken'], |
victor@7 | 487 | 'referer': delete_url} |
victor@7 | 488 | ) |
i@31 | 489 | if not delete_page.ok: |
victor@7 | 490 | logger.warning("Something went wrong. Delete page status: {0}".format( |
victor@7 | 491 | delete_page.status_code)) |
victor@7 | 492 | return None |
victor@7 | 493 | |
victor@7 | 494 | logger.info("Deleted measurement {0}".format(measurement_id)) |
victor@7 | 495 | return True |
victor@7 | 496 | |
victor@7 | 497 | def available_measurements(self): |
victor@7 | 498 | """ Get a list of available measurement on the SCC. """ |
i@31 | 499 | response = self.session.get(self.api_measurements_url) |
victor@7 | 500 | response_dict = response.json() |
victor@7 | 501 | |
victor@7 | 502 | if response_dict: |
victor@7 | 503 | measurement_list = response_dict['objects'] |
i@14 | 504 | measurements = [Measurement(self.base_url, measurement_dict) for measurement_dict in measurement_list] |
victor@7 | 505 | logger.info("Found %s measurements on the SCC." % len(measurements)) |
victor@7 | 506 | else: |
victor@7 | 507 | logger.warning("No response received from the SCC when asked for available measurements.") |
i@31 | 508 | measurements = None |
victor@7 | 509 | |
victor@7 | 510 | return measurements |
victor@7 | 511 | |
moritz@29 | 512 | def list_measurements(self, station=None, system=None, start=None, stop=None, upload_status=None, |
moritz@29 | 513 | processing_status=None, optical_processing=None): |
moritz@29 | 514 | |
i@31 | 515 | # TODO: Change this to work through the API |
i@31 | 516 | |
moritz@29 | 517 | # Need to set to empty string if not specified, we won't get any results |
moritz@29 | 518 | params = { |
moritz@29 | 519 | "station": station if station is not None else "", |
moritz@29 | 520 | "system": system if system is not None else "", |
moritz@29 | 521 | "stop": stop if stop is not None else "", |
moritz@29 | 522 | "start": start if start is not None else "", |
moritz@29 | 523 | "upload_status": upload_status if upload_status is not None else "", |
moritz@29 | 524 | "preprocessing_status": processing_status if processing_status is not None else "", |
moritz@29 | 525 | "optical_processing_status": optical_processing if optical_processing is not None else "" |
moritz@29 | 526 | } |
i@31 | 527 | |
i@31 | 528 | response_txt = self.session.get(self.list_measurements_url, params=params).text |
moritz@29 | 529 | tbl_rgx = re.compile(r'<table id="measurements">(.*?)</table>', re.DOTALL) |
moritz@29 | 530 | entry_rgx = re.compile(r'<tr>(.*?)</tr>', re.DOTALL) |
moritz@29 | 531 | measurement_rgx = re.compile( |
moritz@29 | 532 | r'.*?<td><a[^>]*>(\w+)</a>.*?<td>.*?<td>([\w-]+ [\w:]+)</td>.*<td data-order="([-]?\d+),([-]?\d+),([-]?\d+)".*', |
moritz@29 | 533 | re.DOTALL) |
i@31 | 534 | matches = tbl_rgx.findall(response_txt) |
moritz@29 | 535 | if len(matches) != 1: |
moritz@29 | 536 | return [] |
moritz@29 | 537 | |
moritz@29 | 538 | ret = [] |
moritz@29 | 539 | for entry in entry_rgx.finditer(matches[0]): |
moritz@29 | 540 | m = measurement_rgx.match(entry.string[entry.start(0):entry.end(0)]) |
moritz@29 | 541 | if m: |
moritz@29 | 542 | name, date, upload, preproc, optical = m.groups() |
moritz@29 | 543 | ret.append( |
moritz@29 | 544 | Measurement(self.base_url, {"id": name, "upload": int(upload), "pre_processing": int(preproc), |
moritz@29 | 545 | "processing": int(optical)})) |
moritz@29 | 546 | |
moritz@29 | 547 | return ret |
moritz@29 | 548 | |
i@31 | 549 | def measurement_id_for_date(self, t1, call_sign, base_number=0): |
victor@7 | 550 | """ Give the first available measurement id on the SCC for the specific |
madrouin@20 | 551 | date. |
victor@7 | 552 | """ |
victor@7 | 553 | date_str = t1.strftime('%Y%m%d') |
i@31 | 554 | base_id = "%s%s" % (date_str, call_sign) |
i@31 | 555 | search_url = urlparse.urljoin(self.api_base_url, 'measurements/?id__startswith=%s' % base_id) |
victor@7 | 556 | |
moritz@29 | 557 | response = self.session.get(search_url) |
victor@7 | 558 | |
victor@7 | 559 | response_dict = response.json() |
victor@7 | 560 | |
victor@7 | 561 | measurement_id = None |
victor@7 | 562 | |
victor@7 | 563 | if response_dict: |
victor@7 | 564 | measurement_list = response_dict['objects'] |
i@31 | 565 | |
i@31 | 566 | if len(measurement_list) == 100: |
i@31 | 567 | raise ValueError('No available measurement id found.') |
i@31 | 568 | |
victor@7 | 569 | existing_ids = [measurement_dict['id'] for measurement_dict in measurement_list] |
victor@7 | 570 | |
victor@7 | 571 | measurement_number = base_number |
i@31 | 572 | measurement_id = "%s%02i" % (base_id, measurement_number) |
victor@7 | 573 | |
victor@7 | 574 | while measurement_id in existing_ids: |
victor@7 | 575 | measurement_number = measurement_number + 1 |
i@31 | 576 | measurement_id = "%s%02i" % (base_id, measurement_number) |
victor@7 | 577 | |
victor@7 | 578 | return measurement_id |
victor@7 | 579 | |
i@40 | 580 | def get_ancillary(self, file_path, file_type): |
i@38 | 581 | """ |
i@38 | 582 | Try to get the ancillary file data from the SCC API. |
i@38 | 583 | |
i@38 | 584 | The result will always be an API object. If the file does not exist, the .exists property is set to False. |
i@38 | 585 | |
i@38 | 586 | Parameters |
i@38 | 587 | ---------- |
i@40 | 588 | file_path : str |
i@40 | 589 | Path of the uploaded file. |
i@38 | 590 | file_type : str |
i@38 | 591 | Type of ancillary file. One of 'sounding', 'overlap', 'lidarratio'. |
i@38 | 592 | |
i@38 | 593 | Returns |
i@38 | 594 | : AncillaryFile |
i@38 | 595 | The api object. |
i@38 | 596 | """ |
i@38 | 597 | assert file_type in ['sounding', 'overlap', 'lidarratio'] |
i@38 | 598 | |
i@40 | 599 | filename = os.path.basename(file_path) |
i@40 | 600 | |
i@38 | 601 | if file_type == 'sounding': |
i@38 | 602 | file_url = self.api_sounding_search_pattern.format(filename) |
i@38 | 603 | elif file_type == 'overlap': |
i@38 | 604 | file_url = self.api_overlap_search_pattern.format(filename) |
i@38 | 605 | else: |
i@38 | 606 | file_url = self.api_lidarratio_search_pattern.format(filename) |
i@38 | 607 | |
i@38 | 608 | response = self.session.get(file_url) |
i@38 | 609 | |
i@38 | 610 | if not response.ok: |
i@38 | 611 | logger.error('Could not access API. Status code %s.' % response.status_code) |
i@38 | 612 | return None, response.status_code |
i@38 | 613 | |
i@38 | 614 | response_dict = response.json() |
i@38 | 615 | object_list = response_dict['objects'] |
i@38 | 616 | |
i@38 | 617 | logger.debug("Ancillary file JSON: {0}".format(object_list)) |
i@38 | 618 | |
i@38 | 619 | if object_list: |
i@38 | 620 | ancillary_file = AncillaryFile(self.api_base_url, object_list[0]) # Assume only one file is returned |
i@38 | 621 | else: |
i@38 | 622 | ancillary_file = AncillaryFile(self.api_base_url, None) # Create an empty object |
i@38 | 623 | |
i@38 | 624 | return ancillary_file, response.status_code |
i@38 | 625 | |
ioannis@45 | 626 | def __enter__(self): |
ioannis@45 | 627 | return self |
ioannis@45 | 628 | |
ioannis@45 | 629 | def __exit__(self, *args): |
ioannis@45 | 630 | logger.debug("Closing SCC connection session.") |
ioannis@45 | 631 | self.session.close() |
ioannis@45 | 632 | |
i@31 | 633 | class PageNotAccessibleError(RuntimeError): |
i@31 | 634 | pass |
i@31 | 635 | |
victor@7 | 636 | |
ioannis@17 | 637 | class ApiObject(object): |
victor@7 | 638 | """ A generic class object. """ |
victor@7 | 639 | |
i@14 | 640 | def __init__(self, base_url, dict_response): |
i@14 | 641 | self.base_url = base_url |
victor@7 | 642 | |
victor@7 | 643 | if dict_response: |
victor@7 | 644 | # Add the dictionary key value pairs as object properties |
victor@7 | 645 | for key, value in dict_response.items(): |
ioannis@17 | 646 | # logger.debug('Setting key {0} to value {1}'.format(key, value)) |
ioannis@17 | 647 | try: |
ioannis@17 | 648 | setattr(self, key, value) |
ioannis@17 | 649 | except: |
ioannis@17 | 650 | logger.warning('Could not set attribute {0} to value {1}'.format(key, value)) |
victor@7 | 651 | self.exists = True |
victor@7 | 652 | else: |
victor@7 | 653 | self.exists = False |
victor@7 | 654 | |
victor@7 | 655 | |
victor@7 | 656 | class Measurement(ApiObject): |
victor@7 | 657 | """ This class represents the measurement object as returned in the SCC API. |
victor@7 | 658 | """ |
victor@7 | 659 | |
ioannis@45 | 660 | def __init__(self, base_url, dict_response): |
ioannis@45 | 661 | |
ioannis@45 | 662 | # Define expected attributes to assist debugging |
ioannis@45 | 663 | self.cloudmask = None |
ioannis@45 | 664 | self.elda = None |
ioannis@45 | 665 | self.elic = None |
ioannis@45 | 666 | self.elpp = None |
ioannis@45 | 667 | self.hirelpp = None |
ioannis@45 | 668 | self.id = None |
ioannis@45 | 669 | self.is_calibration = None |
ioannis@45 | 670 | self.is_running = None |
ioannis@45 | 671 | self.pre_processing_exit_code = None |
ioannis@45 | 672 | self.processing_exit_code = None |
ioannis@45 | 673 | self.resource_uri = None |
ioannis@45 | 674 | self.start = None |
ioannis@45 | 675 | self.stop = None |
ioannis@45 | 676 | self.system = None |
ioannis@45 | 677 | self.upload = None |
ioannis@45 | 678 | |
ioannis@45 | 679 | super().__init__(base_url, dict_response) |
ioannis@45 | 680 | |
victor@7 | 681 | @property |
ioannis@45 | 682 | def rerun_elda_url(self): |
ioannis@34 | 683 | url_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/rerun-elda/') |
i@14 | 684 | return url_pattern.format(self.id) |
victor@7 | 685 | |
victor@7 | 686 | @property |
ioannis@45 | 687 | def rerun_elpp_url(self): |
ioannis@45 | 688 | url_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/rerun-elpp/') |
ioannis@45 | 689 | return url_pattern.format(self.id) |
ioannis@45 | 690 | |
ioannis@45 | 691 | @property |
victor@7 | 692 | def rerun_all_url(self): |
i@14 | 693 | ulr_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/rerun-all/') |
i@14 | 694 | return ulr_pattern.format(self.id) |
victor@7 | 695 | |
victor@7 | 696 | def __str__(self): |
ioannis@45 | 697 | return "Measurement {}".format(self.id) |
victor@7 | 698 | |
victor@7 | 699 | |
i@38 | 700 | class AncillaryFile(ApiObject): |
i@38 | 701 | """ This class represents the ancilalry file object as returned in the SCC API. |
i@38 | 702 | """ |
i@38 | 703 | @property |
i@38 | 704 | def already_on_scc(self): |
i@38 | 705 | if self.exists is False: |
i@38 | 706 | return False |
i@38 | 707 | |
i@38 | 708 | return not self.status == 'missing' |
i@38 | 709 | |
i@38 | 710 | def __str__(self): |
i@38 | 711 | return "%s: %s, %s" % (self.id, |
i@38 | 712 | self.filename, |
i@38 | 713 | self.status) |
i@38 | 714 | |
i@38 | 715 | |
ioannis@45 | 716 | def process_file(filename, system_id, settings, force_upload, delete_related, |
ioannis@45 | 717 | monitor=True, rs_filename=None, lr_filename=None, ov_filename=None): |
ioannis@32 | 718 | """ Shortcut function to process a file to the SCC. """ |
ioannis@32 | 719 | logger.info("Processing file %s, using system %s" % (filename, system_id)) |
victor@7 | 720 | |
ioannis@45 | 721 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@45 | 722 | scc.login(settings['website_credentials']) |
ioannis@45 | 723 | measurement = scc.process(filename, system_id, |
ioannis@45 | 724 | force_upload=force_upload, |
ioannis@45 | 725 | delete_related=delete_related, |
ioannis@45 | 726 | monitor=monitor, |
ioannis@45 | 727 | rs_filename=rs_filename, |
ioannis@45 | 728 | lr_filename=lr_filename, |
ioannis@45 | 729 | ov_filename=ov_filename) |
ioannis@45 | 730 | scc.logout() |
victor@7 | 731 | return measurement |
victor@7 | 732 | |
victor@7 | 733 | |
ioannis@45 | 734 | def delete_measurements(measurement_ids, delete_related, settings): |
moritz@29 | 735 | """ Shortcut function to delete measurements from the SCC. """ |
ioannis@45 | 736 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@45 | 737 | scc.login(settings['website_credentials']) |
ioannis@45 | 738 | for m_id in measurement_ids: |
ioannis@45 | 739 | logger.info("Deleting %s" % m_id) |
ioannis@45 | 740 | scc.delete_measurement(m_id, delete_related) |
ioannis@45 | 741 | scc.logout() |
moritz@29 | 742 | |
moritz@29 | 743 | |
moritz@29 | 744 | def rerun_all(measurement_ids, monitor, settings): |
moritz@29 | 745 | """ Shortcut function to rerun measurements from the SCC. """ |
i@14 | 746 | |
ioannis@45 | 747 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@45 | 748 | scc.login(settings['website_credentials']) |
ioannis@45 | 749 | for m_id in measurement_ids: |
ioannis@45 | 750 | logger.info("Rerunning all products for %s" % m_id) |
ioannis@45 | 751 | scc.rerun_all(m_id, monitor) |
ioannis@45 | 752 | scc.logout() |
victor@7 | 753 | |
victor@7 | 754 | |
moritz@29 | 755 | def rerun_processing(measurement_ids, monitor, settings): |
victor@7 | 756 | """ Shortcut function to delete a measurement from the SCC. """ |
i@14 | 757 | |
ioannis@45 | 758 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@45 | 759 | scc.login(settings['website_credentials']) |
ioannis@45 | 760 | for m_id in measurement_ids: |
ioannis@45 | 761 | logger.info("Rerunning (optical) processing for %s" % m_id) |
ioannis@45 | 762 | scc.rerun_elpp(m_id, monitor) |
ioannis@45 | 763 | scc.logout() |
moritz@29 | 764 | |
moritz@29 | 765 | |
moritz@29 | 766 | def list_measurements(settings, station=None, system=None, start=None, stop=None, upload_status=None, |
moritz@29 | 767 | preprocessing_status=None, |
moritz@29 | 768 | optical_processing=None): |
moritz@29 | 769 | """List all available measurements""" |
ioannis@45 | 770 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@45 | 771 | scc.login(settings['website_credentials']) |
ioannis@45 | 772 | ret = scc.list_measurements(station=station, system=system, start=start, stop=stop, upload_status=upload_status, |
ioannis@45 | 773 | processing_status=preprocessing_status, optical_processing=optical_processing) |
ioannis@45 | 774 | for entry in ret: |
ioannis@45 | 775 | print("%s" % entry.id) |
ioannis@45 | 776 | scc.logout() |
victor@7 | 777 | |
victor@7 | 778 | |
moritz@29 | 779 | def download_measurements(measurement_ids, download_preproc, download_optical, download_graph, settings): |
moritz@29 | 780 | """Download all measurements for the specified IDs""" |
ioannis@45 | 781 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@45 | 782 | scc.login(settings['website_credentials']) |
ioannis@45 | 783 | for m_id in measurement_ids: |
ioannis@45 | 784 | if download_preproc: |
ioannis@45 | 785 | logger.info("Downloading preprocessed files for '%s'" % m_id) |
ioannis@45 | 786 | scc.download_elpp(m_id) |
ioannis@45 | 787 | logger.info("Complete") |
ioannis@45 | 788 | if download_optical: |
ioannis@45 | 789 | logger.info("Downloading optical files for '%s'" % m_id) |
ioannis@45 | 790 | scc.download_elda(m_id) |
ioannis@45 | 791 | logger.info("Complete") |
ioannis@45 | 792 | if download_graph: |
ioannis@45 | 793 | logger.info("Downloading profile graph files for '%s'" % m_id) |
ioannis@45 | 794 | scc.download_plots(m_id) |
ioannis@45 | 795 | logger.info("Complete") |
ioannis@45 | 796 | scc.logout() |
i@14 | 797 | |
i@14 | 798 | |
moritz@29 | 799 | def settings_from_path(config_file_path): |
i@14 | 800 | """ Read the configuration file. |
i@14 | 801 | |
i@14 | 802 | The file should be in YAML syntax.""" |
i@14 | 803 | |
i@14 | 804 | if not os.path.isfile(config_file_path): |
moritz@29 | 805 | raise argparse.ArgumentTypeError("Wrong path for configuration file (%s)" % config_file_path) |
i@14 | 806 | |
i@14 | 807 | with open(config_file_path) as yaml_file: |
i@14 | 808 | try: |
i@14 | 809 | settings = yaml.safe_load(yaml_file) |
i@14 | 810 | logger.debug("Read settings file(%s)" % config_file_path) |
moritz@29 | 811 | except Exception: |
moritz@29 | 812 | raise argparse.ArgumentTypeError("Could not parse YAML file (%s)" % config_file_path) |
i@14 | 813 | |
i@14 | 814 | # YAML limitation: does not read tuples |
i@14 | 815 | settings['basic_credentials'] = tuple(settings['basic_credentials']) |
i@14 | 816 | settings['website_credentials'] = tuple(settings['website_credentials']) |
i@14 | 817 | return settings |
i@14 | 818 | |
i@14 | 819 | |
moritz@29 | 820 | # Setup for command specific parsers |
moritz@29 | 821 | def setup_delete(parser): |
moritz@29 | 822 | def delete_from_args(parsed): |
ioannis@45 | 823 | delete_measurements(parsed.IDs, |
ioannis@45 | 824 | delete_related=False, |
ioannis@45 | 825 | settings=parsed.config) |
moritz@29 | 826 | |
moritz@29 | 827 | parser.add_argument("IDs", nargs="+", help="measurement IDs to delete.") |
moritz@29 | 828 | parser.set_defaults(execute=delete_from_args) |
moritz@29 | 829 | |
moritz@29 | 830 | |
moritz@29 | 831 | def setup_rerun_all(parser): |
moritz@29 | 832 | def rerun_all_from_args(parsed): |
moritz@29 | 833 | rerun_all(parsed.IDs, parsed.process, parsed.config) |
moritz@29 | 834 | |
moritz@29 | 835 | parser.add_argument("IDs", nargs="+", help="Measurement IDs to rerun.") |
moritz@29 | 836 | parser.add_argument("-p", "--process", help="Wait for the results of the processing.", |
moritz@29 | 837 | action="store_true") |
moritz@29 | 838 | parser.set_defaults(execute=rerun_all_from_args) |
moritz@29 | 839 | |
moritz@29 | 840 | |
ioannis@45 | 841 | def setup_rerun_elpp(parser): |
moritz@29 | 842 | def rerun_processing_from_args(parsed): |
moritz@29 | 843 | rerun_processing(parsed.IDs, parsed.process, parsed.config) |
moritz@29 | 844 | |
moritz@29 | 845 | parser.add_argument("IDs", nargs="+", help="Measurement IDs to rerun the processing on.") |
moritz@29 | 846 | parser.add_argument("-p", "--process", help="Wait for the results of the processing.", |
moritz@29 | 847 | action="store_true") |
moritz@29 | 848 | parser.set_defaults(execute=rerun_processing_from_args) |
moritz@29 | 849 | |
moritz@29 | 850 | |
ioannis@45 | 851 | def setup_upload_file(parser): |
ioannis@45 | 852 | """ Upload but do not monitor processing progress. """ |
ioannis@45 | 853 | def upload_file_from_args(parsed): |
ioannis@45 | 854 | process_file(parsed.filename, parsed.system, parsed.config, |
ioannis@45 | 855 | monitor=parsed.process, |
ioannis@45 | 856 | force_upload=parsed.force_upload, |
ioannis@45 | 857 | delete_related=False, # For now, use this as default |
ioannis@32 | 858 | rs_filename=parsed.radiosounding, |
ioannis@32 | 859 | ov_filename=parsed.overlap, |
ioannis@32 | 860 | lr_filename=parsed.lidarratio) |
moritz@29 | 861 | |
moritz@29 | 862 | parser.add_argument("filename", help="Measurement file name or path.") |
moritz@29 | 863 | parser.add_argument("system", help="Processing system id.") |
ioannis@45 | 864 | parser.add_argument("-p", "--process", help="Wait for the processing results.", |
ioannis@45 | 865 | action="store_true") |
ioannis@45 | 866 | parser.add_argument("--force_upload", help="If measurement ID exists on SCC, delete before uploading.", |
ioannis@45 | 867 | action="store_true") |
i@30 | 868 | parser.add_argument("--radiosounding", default=None, help="Radiosounding file name or path") |
ioannis@32 | 869 | parser.add_argument("--overlap", default=None, help="Overlap file name or path") |
ioannis@32 | 870 | parser.add_argument("--lidarratio", default=None, help="Lidar ratio file name or path") |
i@30 | 871 | |
moritz@29 | 872 | parser.set_defaults(execute=upload_file_from_args) |
moritz@29 | 873 | |
moritz@29 | 874 | |
moritz@29 | 875 | def setup_list_measurements(parser): |
moritz@29 | 876 | def list_measurements_from_args(parsed): |
ioannis@45 | 877 | # TODO: Fix this |
ioannis@45 | 878 | logger.warning("This method needs to be updated. Cross-chceck any results.") |
ioannis@45 | 879 | |
moritz@29 | 880 | list_measurements(parsed.config, station=parsed.station, system=parsed.system, start=parsed.start, |
moritz@29 | 881 | stop=parsed.stop, |
moritz@29 | 882 | upload_status=parsed.upload_status, preprocessing_status=parsed.preprocessing_status, |
moritz@29 | 883 | optical_processing=parsed.optical_processing_status) |
moritz@29 | 884 | |
moritz@29 | 885 | def status(arg): |
moritz@29 | 886 | if -127 <= int(arg) <= 127: |
moritz@29 | 887 | return arg |
moritz@29 | 888 | else: |
moritz@29 | 889 | raise argparse.ArgumentTypeError("Status must be between -127 and 127") |
moritz@29 | 890 | |
moritz@29 | 891 | def date(arg): |
moritz@29 | 892 | if re.match(r'\d{4}-\d{2}-\d{2}', arg): |
moritz@29 | 893 | return arg |
moritz@29 | 894 | else: |
moritz@29 | 895 | raise argparse.ArgumentTypeError("Date must be in format 'YYYY-MM-DD'") |
moritz@29 | 896 | |
moritz@29 | 897 | parser.add_argument("--station", help="Filter for only the selected station") |
moritz@29 | 898 | parser.add_argument("--system", help="Filter for only the selected station") |
moritz@29 | 899 | parser.add_argument("--start", help="Filter for only the selected station", type=date) |
moritz@29 | 900 | parser.add_argument("--stop", help="Filter for only the selected station", type=date) |
moritz@29 | 901 | parser.add_argument("--upload-status", help="Filter for only the selected station", type=status) |
moritz@29 | 902 | parser.add_argument("--preprocessing-status", help="Filter for only the selected station", type=status) |
moritz@29 | 903 | parser.add_argument("--optical-processing-status", help="Filter for only the selected station", type=status) |
moritz@29 | 904 | parser.set_defaults(execute=list_measurements_from_args) |
moritz@29 | 905 | |
moritz@29 | 906 | |
moritz@29 | 907 | def setup_download_measurements(parser): |
moritz@29 | 908 | def download_measurements_from_args(parsed): |
ioannis@45 | 909 | # TODO: Fix this |
ioannis@45 | 910 | logger.warning("This method needs to be updated. Cross-chceck any results.") |
ioannis@45 | 911 | |
ioannis@45 | 912 | preproc = parsed.download_elpp |
ioannis@45 | 913 | optical = parsed.download_elda |
moritz@29 | 914 | graphs = parsed.download_profile_graphs |
moritz@29 | 915 | if not preproc and not graphs: |
moritz@29 | 916 | optical = True |
moritz@29 | 917 | download_measurements(parsed.IDs, preproc, optical, graphs, parsed.config) |
moritz@29 | 918 | |
moritz@29 | 919 | parser.add_argument("IDs", help="Measurement IDs that should be downloaded.", nargs="+") |
moritz@29 | 920 | parser.add_argument("--download-preprocessed", action="store_true", help="Download preprocessed files.") |
moritz@29 | 921 | parser.add_argument("--download-optical", action="store_true", |
moritz@29 | 922 | help="Download optical files (default if no other download is used).") |
moritz@29 | 923 | parser.add_argument("--download-profile-graphs", action="store_true", help="Download profile graph files.") |
moritz@29 | 924 | parser.set_defaults(execute=download_measurements_from_args) |
moritz@29 | 925 | |
moritz@29 | 926 | |
victor@7 | 927 | def main(): |
victor@7 | 928 | # Define the command line arguments. |
victor@7 | 929 | parser = argparse.ArgumentParser() |
moritz@29 | 930 | subparsers = parser.add_subparsers() |
moritz@29 | 931 | |
moritz@29 | 932 | delete_parser = subparsers.add_parser("delete", help="Deletes a measurement.") |
ioannis@45 | 933 | rerun_all_parser = subparsers.add_parser("rerun-all", help="Rerun all processing steps for the provided measurement IDs.") |
ioannis@45 | 934 | rerun_processing_parser = subparsers.add_parser("rerun-elpp", |
ioannis@45 | 935 | help="Rerun low-resolution processing steps for the provided measurement ID.") |
ioannis@45 | 936 | upload_file_parser = subparsers.add_parser("upload-file", help="Submit a file and, optionally, download the output products.") |
ioannis@32 | 937 | list_parser = subparsers.add_parser("list", help="List measurements registered on the SCC.") |
moritz@29 | 938 | download_parser = subparsers.add_parser("download", help="Download selected measurements.") |
moritz@29 | 939 | |
moritz@29 | 940 | setup_delete(delete_parser) |
moritz@29 | 941 | setup_rerun_all(rerun_all_parser) |
ioannis@45 | 942 | setup_rerun_elpp(rerun_processing_parser) |
ioannis@45 | 943 | |
moritz@29 | 944 | setup_upload_file(upload_file_parser) |
moritz@29 | 945 | setup_list_measurements(list_parser) |
moritz@29 | 946 | setup_download_measurements(download_parser) |
victor@7 | 947 | |
victor@7 | 948 | # Verbosity settings from http://stackoverflow.com/a/20663028 |
victor@7 | 949 | parser.add_argument('-d', '--debug', help="Print debugging information.", action="store_const", |
victor@7 | 950 | dest="loglevel", const=logging.DEBUG, default=logging.INFO, |
victor@7 | 951 | ) |
victor@7 | 952 | parser.add_argument('-s', '--silent', help="Show only warning and error messages.", action="store_const", |
victor@7 | 953 | dest="loglevel", const=logging.WARNING |
victor@7 | 954 | ) |
victor@7 | 955 | |
ioannis@32 | 956 | # Setup default config location |
moritz@29 | 957 | home = os.path.expanduser("~") |
moritz@29 | 958 | default_config_location = os.path.abspath(os.path.join(home, ".scc_access.yaml")) |
moritz@29 | 959 | parser.add_argument("-c", "--config", help="Path to the config file.", type=settings_from_path, |
moritz@29 | 960 | default=default_config_location) |
moritz@29 | 961 | |
victor@7 | 962 | args = parser.parse_args() |
victor@7 | 963 | |
victor@7 | 964 | # Get the logger with the appropriate level |
victor@7 | 965 | logging.basicConfig(format='%(levelname)s: %(message)s', level=args.loglevel) |
victor@7 | 966 | |
moritz@29 | 967 | # Dispatch to appropriate function |
moritz@29 | 968 | args.execute(args) |
moritz@29 | 969 | |
i@14 | 970 | |
moritz@29 | 971 | # When running through terminal |
moritz@29 | 972 | if __name__ == '__main__': |
moritz@29 | 973 | main() |