Sat, 09 Jan 2021 15:11:15 +0200
Multiple changes, based on wrong initial state.
ioannis@43 | 1 | import sys |
ioannis@43 | 2 | |
victor@7 | 3 | import requests |
victor@7 | 4 | |
ioannis@43 | 5 | # Python 2 and 3 support |
ioannis@43 | 6 | try: |
ioannis@43 | 7 | import urllib.parse as urlparse # Python 3 |
ioannis@43 | 8 | except ImportError: |
ioannis@43 | 9 | from urlparse import urlparse # Python 2 |
ioannis@43 | 10 | |
victor@7 | 11 | import argparse |
victor@7 | 12 | import os |
victor@7 | 13 | import re |
victor@7 | 14 | import time |
ioannis@43 | 15 | from io import BytesIO |
victor@7 | 16 | from zipfile import ZipFile |
victor@7 | 17 | import datetime |
victor@7 | 18 | import logging |
i@14 | 19 | import yaml |
victor@7 | 20 | |
ioannis@43 | 21 | import netCDF4 as netcdf |
ioannis@43 | 22 | |
ioannis@43 | 23 | requests.packages.urllib3.disable_warnings() |
victor@7 | 24 | |
i@14 | 25 | logger = logging.getLogger(__name__) |
victor@7 | 26 | |
victor@7 | 27 | # The regex to find the measurement id from the measurement page |
victor@7 | 28 | # This should be read from the uploaded file, but would require an extra NetCDF module. |
victor@7 | 29 | regex = "<h3>Measurement (?P<measurement_id>.{12}) <small>" |
victor@7 | 30 | |
victor@7 | 31 | |
victor@7 | 32 | class SCC: |
victor@7 | 33 | """ A simple class that will attempt to upload a file on the SCC server. |
i@14 | 34 | |
victor@7 | 35 | The uploading is done by simulating a normal browser session. In the current |
victor@7 | 36 | version no check is performed, and no feedback is given if the upload |
victor@7 | 37 | was successful. If everything is setup correctly, it will work. |
victor@7 | 38 | """ |
victor@7 | 39 | |
i@14 | 40 | def __init__(self, auth, output_dir, base_url): |
victor@7 | 41 | self.auth = auth |
victor@7 | 42 | self.output_dir = output_dir |
i@14 | 43 | self.base_url = base_url |
victor@7 | 44 | self.session = requests.Session() |
victor@7 | 45 | |
i@14 | 46 | # Construct the absolute URLs |
i@14 | 47 | self.login_url = urlparse.urljoin(self.base_url, 'accounts/login/') |
i@14 | 48 | self.upload_url = urlparse.urljoin(self.base_url, 'data_processing/measurements/quick/') |
ioannis@43 | 49 | self.download_hirelpp_pattern = urlparse.urljoin(self.base_url, |
ioannis@43 | 50 | 'data_processing/measurements/{0}/download-hirelpp/') |
ioannis@43 | 51 | self.download_cloudmask_pattern = urlparse.urljoin(self.base_url, |
ioannis@43 | 52 | 'data_processing/measurements/{0}/download-cloudmask/') |
ioannis@43 | 53 | self.download_elpp_pattern = urlparse.urljoin(self.base_url, |
ioannis@43 | 54 | 'data_processing/measurements/{0}/download-preprocessed/') |
ioannis@43 | 55 | self.download_elda_pattern = urlparse.urljoin(self.base_url, |
ioannis@43 | 56 | 'data_processing/measurements/{0}/download-optical/') |
ioannis@43 | 57 | self.download_plot_pattern = urlparse.urljoin(self.base_url, |
ioannis@43 | 58 | 'data_processing/measurements/{0}/download-plots/') |
ioannis@43 | 59 | self.download_elic_pattern = urlparse.urljoin(self.base_url, |
ioannis@43 | 60 | 'data_processing/measurements/{0}/download-elic/') |
i@14 | 61 | self.delete_measurement_pattern = urlparse.urljoin(self.base_url, 'admin/database/measurements/{0}/delete/') |
i@14 | 62 | self.api_base_url = urlparse.urljoin(self.base_url, 'api/v1/') |
i@14 | 63 | |
ioannis@43 | 64 | self.login_credentials = None |
ioannis@43 | 65 | |
i@14 | 66 | def login(self, credentials): |
victor@7 | 67 | """ Login the the website. """ |
victor@7 | 68 | logger.debug("Attempting to login to SCC, username %s." % credentials[0]) |
victor@7 | 69 | self.login_credentials = {'username': credentials[0], |
victor@7 | 70 | 'password': credentials[1]} |
victor@7 | 71 | |
i@14 | 72 | logger.debug("Accessing login page at %s." % self.login_url) |
victor@7 | 73 | |
victor@7 | 74 | # Get upload form |
i@14 | 75 | login_page = self.session.get(self.login_url, auth=self.auth, verify=False) |
i@14 | 76 | |
i@14 | 77 | if login_page.status_code != 200: |
i@14 | 78 | logger.error('Could not access login pages. Status code %s' % login_page.status_code) |
i@14 | 79 | sys.exit(1) |
victor@7 | 80 | |
victor@7 | 81 | logger.debug("Submiting credentials.") |
ioannis@43 | 82 | |
victor@7 | 83 | # Submit the login data |
i@14 | 84 | login_submit = self.session.post(self.login_url, |
victor@7 | 85 | data=self.login_credentials, |
victor@7 | 86 | headers={'X-CSRFToken': login_page.cookies['csrftoken'], |
i@14 | 87 | 'referer': self.login_url}, |
victor@7 | 88 | verify=False, |
victor@7 | 89 | auth=self.auth) |
victor@7 | 90 | return login_submit |
victor@7 | 91 | |
victor@7 | 92 | def logout(self): |
victor@7 | 93 | pass |
victor@7 | 94 | |
ioannis@43 | 95 | def upload_file(self, filename, system_id, force_upload, delete_related): |
victor@7 | 96 | """ Upload a filename for processing with a specific system. If the |
victor@7 | 97 | upload is successful, it returns the measurement id. """ |
ioannis@43 | 98 | |
ioannis@43 | 99 | measurement_id = self.measurement_id_from_file(filename) |
ioannis@43 | 100 | |
ioannis@43 | 101 | logger.debug('Checking if a measurement with the same id already exists on the SCC server.') |
ioannis@43 | 102 | existing_measurement = self.get_measurement(measurement_id) |
ioannis@43 | 103 | |
ioannis@43 | 104 | if existing_measurement: |
ioannis@43 | 105 | if force_upload: |
ioannis@43 | 106 | logger.info( |
ioannis@43 | 107 | "Measurement with id {} already exists on the SCC. Trying to delete it...".format(measurement_id)) |
ioannis@43 | 108 | self.delete_measurement(measurement_id, delete_related) |
ioannis@43 | 109 | else: |
ioannis@43 | 110 | logger.error( |
ioannis@43 | 111 | "Measurement with id {} already exists on the SCC. Use --force_upload flag to overwrite it.".format( |
ioannis@43 | 112 | measurement_id)) |
ioannis@43 | 113 | sys.exit(1) |
ioannis@43 | 114 | |
victor@7 | 115 | # Get submit page |
i@14 | 116 | upload_page = self.session.get(self.upload_url, |
victor@7 | 117 | auth=self.auth, |
victor@7 | 118 | verify=False) |
victor@7 | 119 | |
victor@7 | 120 | # Submit the data |
victor@7 | 121 | upload_data = {'system': system_id} |
victor@7 | 122 | files = {'data': open(filename, 'rb')} |
victor@7 | 123 | |
i@14 | 124 | logger.info("Uploading of file %s started." % filename) |
ioannis@43 | 125 | logger.debug("URL: {0}, data: {1}, 'X-CSRFToken': {2}".format(self.upload_url, |
ioannis@43 | 126 | upload_data, |
ioannis@43 | 127 | upload_page.cookies['csrftoken'])) |
i@14 | 128 | upload_submit = self.session.post(self.upload_url, |
victor@7 | 129 | data=upload_data, |
victor@7 | 130 | files=files, |
victor@7 | 131 | headers={'X-CSRFToken': upload_page.cookies['csrftoken'], |
ioannis@43 | 132 | 'referer': self.upload_url, }, |
victor@7 | 133 | verify=False, |
victor@7 | 134 | auth=self.auth) |
victor@7 | 135 | |
victor@7 | 136 | if upload_submit.status_code != 200: |
i@14 | 137 | logger.warning("Connection error. Status code: %s" % upload_submit.status_code) |
victor@7 | 138 | return False |
victor@7 | 139 | |
victor@7 | 140 | # Check if there was a redirect to a new page. |
i@14 | 141 | if upload_submit.url == self.upload_url: |
victor@7 | 142 | measurement_id = False |
i@14 | 143 | logger.error("Uploaded file rejected! Try to upload manually to see the error.") |
victor@7 | 144 | else: |
victor@7 | 145 | measurement_id = re.findall(regex, upload_submit.text)[0] |
ioannis@43 | 146 | logger.info("Successfully uploaded measurement with id %s." % measurement_id) |
ioannis@43 | 147 | |
ioannis@43 | 148 | return measurement_id |
ioannis@43 | 149 | |
ioannis@43 | 150 | @staticmethod |
ioannis@43 | 151 | def measurement_id_from_file(filename): |
ioannis@43 | 152 | """ Get the measurement id from the input file. """ |
ioannis@43 | 153 | |
ioannis@43 | 154 | if not os.path.isfile(filename): |
ioannis@43 | 155 | logger.error("File {} does not exist.".format(filename)) |
ioannis@43 | 156 | sys.exit(1) |
ioannis@43 | 157 | |
ioannis@43 | 158 | with netcdf.Dataset(filename) as f: |
ioannis@43 | 159 | try: |
ioannis@43 | 160 | measurement_id = f.Measurement_ID |
ioannis@43 | 161 | except AttributeError: |
ioannis@43 | 162 | logger.error( |
ioannis@43 | 163 | "Input file {} does not contain a Measurement_ID global attribute. Wrong file format?".format( |
ioannis@43 | 164 | filename)) |
ioannis@43 | 165 | sys.exit(1) |
victor@7 | 166 | |
victor@7 | 167 | return measurement_id |
victor@7 | 168 | |
victor@7 | 169 | def download_files(self, measurement_id, subdir, download_url): |
victor@7 | 170 | """ Downloads some files from the download_url to the specified |
victor@7 | 171 | subdir. This method is used to download preprocessed file, optical |
victor@7 | 172 | files etc. |
victor@7 | 173 | """ |
victor@7 | 174 | # Get the file |
victor@7 | 175 | request = self.session.get(download_url, auth=self.auth, |
victor@7 | 176 | verify=False, |
victor@7 | 177 | stream=True) |
victor@7 | 178 | |
victor@7 | 179 | # Create the dir if it does not exist |
victor@7 | 180 | local_dir = os.path.join(self.output_dir, measurement_id, subdir) |
victor@7 | 181 | if not os.path.exists(local_dir): |
victor@7 | 182 | os.makedirs(local_dir) |
victor@7 | 183 | |
victor@7 | 184 | # Save the file by chunk, needed if the file is big. |
ioannis@43 | 185 | memory_file = BytesIO() |
victor@7 | 186 | |
victor@7 | 187 | for chunk in request.iter_content(chunk_size=1024): |
victor@7 | 188 | if chunk: # filter out keep-alive new chunks |
victor@7 | 189 | memory_file.write(chunk) |
victor@7 | 190 | memory_file.flush() |
victor@7 | 191 | |
victor@7 | 192 | zip_file = ZipFile(memory_file) |
victor@7 | 193 | |
victor@7 | 194 | for ziped_name in zip_file.namelist(): |
victor@7 | 195 | basename = os.path.basename(ziped_name) |
victor@7 | 196 | |
victor@7 | 197 | local_file = os.path.join(local_dir, basename) |
victor@7 | 198 | |
victor@7 | 199 | with open(local_file, 'wb') as f: |
victor@7 | 200 | f.write(zip_file.read(ziped_name)) |
victor@7 | 201 | |
ioannis@43 | 202 | def download_hirelpp(self, measurement_id): |
ioannis@43 | 203 | """ Download hirelpp files for the measurement id. """ |
ioannis@43 | 204 | # Construct the download url |
ioannis@43 | 205 | download_url = self.download_hirelpp_pattern.format(measurement_id) |
ioannis@43 | 206 | try: |
ioannis@43 | 207 | self.download_files(measurement_id, 'scc_hirelpp', download_url) |
ioannis@43 | 208 | except Exception as e: |
ioannis@43 | 209 | logger.error("Could not download HiRElPP files. Error message: {}".format(e)) |
ioannis@43 | 210 | logger.debug('Download exception:', exc_info=True) |
ioannis@43 | 211 | |
ioannis@43 | 212 | def download_cloudmask(self, measurement_id): |
ioannis@43 | 213 | """ Download cloudmask files for the measurement id. """ |
ioannis@43 | 214 | # Construct the download url |
ioannis@43 | 215 | download_url = self.download_cloudmask_pattern.format(measurement_id) |
ioannis@43 | 216 | try: |
ioannis@43 | 217 | self.download_files(measurement_id, 'scc_cloudscreen', download_url) |
ioannis@43 | 218 | except Exception as e: |
ioannis@43 | 219 | logger.error("Could not download cloudscreen files. Error message: {}".format(e)) |
ioannis@43 | 220 | logger.debug('Download exception:', exc_info=True) |
ioannis@43 | 221 | |
ioannis@43 | 222 | def download_elpp(self, measurement_id): |
victor@7 | 223 | """ Download preprocessed files for the measurement id. """ |
victor@7 | 224 | # Construct the download url |
ioannis@43 | 225 | download_url = self.download_elpp_pattern.format(measurement_id) |
ioannis@43 | 226 | try: |
ioannis@43 | 227 | self.download_files(measurement_id, 'scc_preprocessed', download_url) |
ioannis@43 | 228 | except Exception as e: |
ioannis@43 | 229 | logger.error("Could not download ElPP files. Error message: {}".format(e)) |
ioannis@43 | 230 | logger.debug('Download exception:', exc_info=True) |
victor@7 | 231 | |
ioannis@43 | 232 | def download_elda(self, measurement_id): |
victor@7 | 233 | """ Download optical files for the measurement id. """ |
victor@7 | 234 | # Construct the download url |
ioannis@43 | 235 | download_url = self.download_elda_pattern.format(measurement_id) |
ioannis@43 | 236 | try: |
ioannis@43 | 237 | self.download_files(measurement_id, 'scc_optical', download_url) |
ioannis@43 | 238 | except Exception as e: |
ioannis@43 | 239 | logger.error("Could not download ELDA files. Error message: {}".format(e)) |
ioannis@43 | 240 | logger.debug('Download exception:', exc_info=True) |
victor@7 | 241 | |
ioannis@43 | 242 | def download_plots(self, measurement_id): |
victor@7 | 243 | """ Download profile graphs for the measurement id. """ |
victor@7 | 244 | # Construct the download url |
ioannis@43 | 245 | download_url = self.download_plot_pattern.format(measurement_id) |
ioannis@43 | 246 | try: |
ioannis@43 | 247 | self.download_files(measurement_id, 'scc_plots', download_url) |
ioannis@43 | 248 | except Exception as e: |
ioannis@43 | 249 | logger.error("Could not download ELDA plots. Error message: {}".format(e)) |
ioannis@43 | 250 | logger.debug('Download exception:', exc_info=True) |
victor@7 | 251 | |
ioannis@43 | 252 | def download_elic(self, measurement_id): |
ioannis@43 | 253 | """ Download ELIC files for the measurement id. """ |
ioannis@43 | 254 | # Construct the download url |
ioannis@43 | 255 | download_url = self.download_elic_pattern.format(measurement_id) |
ioannis@43 | 256 | try: |
ioannis@43 | 257 | self.download_files(measurement_id, 'scc_elic', download_url) |
ioannis@43 | 258 | except Exception as e: |
ioannis@43 | 259 | logger.error("Could not download ELIC files. Error message: {}".format(e)) |
ioannis@43 | 260 | logger.debug('Download exception:', exc_info=True) |
ioannis@43 | 261 | |
ioannis@43 | 262 | def download_eldec(self, measurement_id): |
ioannis@43 | 263 | """ Download ELDEC files for the measurement id. """ |
ioannis@43 | 264 | # Construct the download url |
ioannis@43 | 265 | download_url = self.download_elda_pattern.format(measurement_id) # ELDA patter is used for now |
ioannis@43 | 266 | try: |
ioannis@43 | 267 | self.download_files(measurement_id, 'scc_eldec', download_url) |
ioannis@43 | 268 | except Exception as e: |
ioannis@43 | 269 | logger.error("Could not download EDELC files. Error message: {}".format(e)) |
ioannis@43 | 270 | logger.debug('Download exception:', exc_info=True) |
ioannis@43 | 271 | |
ioannis@43 | 272 | def rerun_elpp(self, measurement_id, monitor=True): |
victor@7 | 273 | measurement = self.get_measurement(measurement_id) |
victor@7 | 274 | |
victor@7 | 275 | if measurement: |
ioannis@43 | 276 | request = self.session.get(measurement.rerun_elpp_url, auth=self.auth, |
victor@7 | 277 | verify=False, |
victor@7 | 278 | stream=True) |
victor@7 | 279 | |
victor@7 | 280 | if request.status_code != 200: |
i@14 | 281 | logger.error( |
ioannis@43 | 282 | "Could not rerun ELPP for %s. Status code: %s" % (measurement_id, request.status_code)) |
victor@7 | 283 | return |
victor@7 | 284 | |
victor@7 | 285 | if monitor: |
victor@7 | 286 | self.monitor_processing(measurement_id) |
victor@7 | 287 | |
victor@7 | 288 | def rerun_all(self, measurement_id, monitor=True): |
victor@7 | 289 | logger.debug("Started rerun_all procedure.") |
victor@7 | 290 | |
victor@7 | 291 | logger.debug("Getting measurement %s" % measurement_id) |
victor@7 | 292 | measurement = self.get_measurement(measurement_id) |
victor@7 | 293 | |
victor@7 | 294 | if measurement: |
victor@7 | 295 | logger.debug("Attempting to rerun all processing through %s." % measurement.rerun_all_url) |
victor@7 | 296 | |
victor@7 | 297 | request = self.session.get(measurement.rerun_all_url, auth=self.auth, |
victor@7 | 298 | verify=False, |
victor@7 | 299 | stream=True) |
victor@7 | 300 | |
victor@7 | 301 | if request.status_code != 200: |
victor@7 | 302 | logger.error("Could not rerun pre processing for %s. Status code: %s" % |
victor@7 | 303 | (measurement_id, request.status_code)) |
victor@7 | 304 | return |
victor@7 | 305 | |
victor@7 | 306 | if monitor: |
victor@7 | 307 | self.monitor_processing(measurement_id) |
victor@7 | 308 | |
ioannis@43 | 309 | def process(self, filename, system_id, force_upload, delete_related): |
victor@7 | 310 | """ Upload a file for processing and wait for the processing to finish. |
victor@7 | 311 | If the processing is successful, it will download all produced files. |
victor@7 | 312 | """ |
victor@7 | 313 | logger.info("--- Processing started on %s. ---" % datetime.datetime.now()) |
ioannis@43 | 314 | |
victor@7 | 315 | # Upload file |
ioannis@43 | 316 | measurement_id = self.upload_file(filename, system_id, force_upload, delete_related) |
victor@7 | 317 | |
victor@7 | 318 | measurement = self.monitor_processing(measurement_id) |
victor@7 | 319 | return measurement |
victor@7 | 320 | |
victor@7 | 321 | def monitor_processing(self, measurement_id): |
victor@7 | 322 | """ Monitor the processing progress of a measurement id""" |
victor@7 | 323 | |
victor@7 | 324 | measurement = self.get_measurement(measurement_id) |
victor@7 | 325 | if measurement is not None: |
victor@7 | 326 | while measurement.is_running: |
ioannis@43 | 327 | logger.info("Measurement is being processed (status: {}, {}, {}, {}, {}, {}). Please wait.".format( |
ioannis@43 | 328 | measurement.upload, |
ioannis@43 | 329 | measurement.hirelpp, |
ioannis@43 | 330 | measurement.cloudmask, |
ioannis@43 | 331 | measurement.elpp, |
ioannis@43 | 332 | measurement.elda, |
ioannis@43 | 333 | measurement.elic)) |
victor@7 | 334 | time.sleep(10) |
victor@7 | 335 | measurement = self.get_measurement(measurement_id) |
ioannis@43 | 336 | logger.info("Measurement processing finished (status: {}, {}, {}, {}, {}, {}). Please wait.".format( |
ioannis@43 | 337 | measurement.upload, |
ioannis@43 | 338 | measurement.hirelpp, |
ioannis@43 | 339 | measurement.cloudmask, |
ioannis@43 | 340 | measurement.elpp, |
ioannis@43 | 341 | measurement.elda, |
ioannis@43 | 342 | measurement.elic)) |
ioannis@43 | 343 | if measurement.hirelpp == 127: |
ioannis@43 | 344 | logger.info("Downloading HiRElPP files.") |
ioannis@43 | 345 | self.download_hirelpp(measurement_id) |
ioannis@43 | 346 | if measurement.cloudmask == 127: |
ioannis@43 | 347 | logger.info("Downloading cloud screening files.") |
ioannis@43 | 348 | self.download_cloudmask(measurement_id) |
ioannis@43 | 349 | if measurement.elpp == 127: |
ioannis@43 | 350 | logger.info("Downloading ELPP files.") |
ioannis@43 | 351 | self.download_elpp(measurement_id) |
ioannis@43 | 352 | if measurement.elda == 127: |
ioannis@43 | 353 | logger.info("Downloading ELDA files.") |
ioannis@43 | 354 | self.download_elda(measurement_id) |
victor@7 | 355 | logger.info("Downloading graphs.") |
ioannis@43 | 356 | self.download_plots(measurement_id) |
ioannis@43 | 357 | if measurement.elic == 127: |
ioannis@43 | 358 | logger.info("Downloading ELIC files.") |
ioannis@43 | 359 | self.download_elic(measurement_id) |
ioannis@43 | 360 | |
ioannis@43 | 361 | # TODO: Need to check ELDEC code (when it becomes available in the API) |
ioannis@43 | 362 | if measurement.is_calibration: |
ioannis@43 | 363 | logger.info("Downloading ELDEC files.") |
ioannis@43 | 364 | self.download_eldec(measurement_id) |
ioannis@43 | 365 | |
victor@7 | 366 | logger.info("--- Processing finished. ---") |
victor@7 | 367 | return measurement |
victor@7 | 368 | |
ioannis@43 | 369 | def get_measurement(self, measurement_id): |
victor@7 | 370 | |
ioannis@43 | 371 | if measurement_id is None: |
victor@7 | 372 | return None |
victor@7 | 373 | |
i@14 | 374 | measurement_url = urlparse.urljoin(self.api_base_url, 'measurements/%s/' % measurement_id) |
victor@7 | 375 | |
victor@7 | 376 | response = self.session.get(measurement_url, |
victor@7 | 377 | auth=self.auth, |
victor@7 | 378 | verify=False) |
victor@7 | 379 | |
ioannis@43 | 380 | response_dict = None |
ioannis@43 | 381 | if response.status_code == 200: |
ioannis@43 | 382 | response_dict = response.json() |
ioannis@43 | 383 | if response.status_code == 404: |
ioannis@43 | 384 | logger.info("No measurement with id %s found on the SCC." % measurement_id) |
ioannis@43 | 385 | elif response.status_code != 200: |
i@14 | 386 | logger.error('Could not access API. Status code %s.' % response.status_code) |
i@14 | 387 | sys.exit(1) |
i@14 | 388 | |
ioannis@43 | 389 | logger.debug("Response dictionary: {}".format(response_dict)) |
victor@7 | 390 | |
victor@7 | 391 | if response_dict: |
ioannis@43 | 392 | measurement = Measurement(self.base_url, response_dict) |
victor@7 | 393 | return measurement |
victor@7 | 394 | else: |
victor@7 | 395 | return None |
victor@7 | 396 | |
ioannis@43 | 397 | def delete_measurement(self, measurement_id, delete_related=False): |
victor@7 | 398 | """ Deletes a measurement with the provided measurement id. The user |
victor@7 | 399 | should have the appropriate permissions. |
victor@7 | 400 | |
victor@7 | 401 | The procedures is performed directly through the web interface and |
victor@7 | 402 | NOT through the API. |
victor@7 | 403 | """ |
victor@7 | 404 | # Get the measurement object |
victor@7 | 405 | measurement = self.get_measurement(measurement_id) |
victor@7 | 406 | |
victor@7 | 407 | # Check that it exists |
victor@7 | 408 | if measurement is None: |
victor@7 | 409 | logger.warning("Nothing to delete.") |
victor@7 | 410 | return None |
victor@7 | 411 | |
victor@7 | 412 | # Go the the page confirming the deletion |
i@14 | 413 | delete_url = self.delete_measurement_pattern.format(measurement.id) |
victor@7 | 414 | |
ioannis@43 | 415 | logger.debug("Delete url: {}".format(delete_url)) |
ioannis@43 | 416 | |
victor@7 | 417 | confirm_page = self.session.get(delete_url, |
victor@7 | 418 | auth=self.auth, |
victor@7 | 419 | verify=False) |
victor@7 | 420 | |
victor@7 | 421 | # Check that the page opened properly |
victor@7 | 422 | if confirm_page.status_code != 200: |
victor@7 | 423 | logger.warning("Could not open delete page. Status: {0}".format(confirm_page.status_code)) |
victor@7 | 424 | return None |
victor@7 | 425 | |
ioannis@43 | 426 | # Get the delete related value |
ioannis@43 | 427 | if delete_related: |
ioannis@43 | 428 | delete_related_option = 'delete_related' |
ioannis@43 | 429 | else: |
ioannis@43 | 430 | delete_related_option = 'not_delete_related' |
ioannis@43 | 431 | |
victor@7 | 432 | # Delete the measurement |
victor@7 | 433 | delete_page = self.session.post(delete_url, |
victor@7 | 434 | auth=self.auth, |
victor@7 | 435 | verify=False, |
ioannis@43 | 436 | data={'post': 'yes', |
ioannis@43 | 437 | 'select_delete_related_measurements': delete_related_option}, |
victor@7 | 438 | headers={'X-CSRFToken': confirm_page.cookies['csrftoken'], |
victor@7 | 439 | 'referer': delete_url} |
victor@7 | 440 | ) |
victor@7 | 441 | if delete_page.status_code != 200: |
victor@7 | 442 | logger.warning("Something went wrong. Delete page status: {0}".format( |
victor@7 | 443 | delete_page.status_code)) |
victor@7 | 444 | return None |
victor@7 | 445 | |
ioannis@43 | 446 | logger.info("Deleted measurement {0}.".format(measurement_id)) |
victor@7 | 447 | return True |
victor@7 | 448 | |
victor@7 | 449 | def available_measurements(self): |
victor@7 | 450 | """ Get a list of available measurement on the SCC. """ |
i@14 | 451 | measurement_url = urlparse.urljoin(self.api_base_url, 'measurements') |
victor@7 | 452 | response = self.session.get(measurement_url, |
victor@7 | 453 | auth=self.auth, |
victor@7 | 454 | verify=False) |
victor@7 | 455 | response_dict = response.json() |
victor@7 | 456 | |
victor@7 | 457 | if response_dict: |
victor@7 | 458 | measurement_list = response_dict['objects'] |
i@14 | 459 | measurements = [Measurement(self.base_url, measurement_dict) for measurement_dict in measurement_list] |
victor@7 | 460 | logger.info("Found %s measurements on the SCC." % len(measurements)) |
victor@7 | 461 | else: |
ioannis@43 | 462 | measurements = None |
victor@7 | 463 | logger.warning("No response received from the SCC when asked for available measurements.") |
victor@7 | 464 | |
victor@7 | 465 | return measurements |
victor@7 | 466 | |
ioannis@43 | 467 | def measurement_id_for_date(self, t1, call_sign, base_number=0): |
victor@7 | 468 | """ Give the first available measurement id on the SCC for the specific |
victor@7 | 469 | date. |
victor@7 | 470 | """ |
victor@7 | 471 | date_str = t1.strftime('%Y%m%d') |
i@14 | 472 | search_url = urlparse.urljoin(self.api_base_url, 'measurements/?id__startswith=%s' % date_str) |
victor@7 | 473 | |
victor@7 | 474 | response = self.session.get(search_url, |
victor@7 | 475 | auth=self.auth, |
victor@7 | 476 | verify=False) |
victor@7 | 477 | |
victor@7 | 478 | response_dict = response.json() |
victor@7 | 479 | |
victor@7 | 480 | measurement_id = None |
victor@7 | 481 | |
victor@7 | 482 | if response_dict: |
victor@7 | 483 | measurement_list = response_dict['objects'] |
victor@7 | 484 | existing_ids = [measurement_dict['id'] for measurement_dict in measurement_list] |
victor@7 | 485 | |
victor@7 | 486 | measurement_number = base_number |
ioannis@43 | 487 | measurement_id = "%s%s%04i" % (date_str, call_sign, measurement_number) |
victor@7 | 488 | |
victor@7 | 489 | while measurement_id in existing_ids: |
victor@7 | 490 | measurement_number = measurement_number + 1 |
ioannis@43 | 491 | measurement_id = "%s%s%04i" % (date_str, call_sign, measurement_number) |
ioannis@43 | 492 | if measurement_number == 1000: |
victor@7 | 493 | raise ValueError('No available measurement id found.') |
victor@7 | 494 | |
victor@7 | 495 | return measurement_id |
victor@7 | 496 | |
ioannis@43 | 497 | def __enter__(self): |
ioannis@43 | 498 | return self |
victor@7 | 499 | |
ioannis@43 | 500 | def __exit__(self, *args): |
ioannis@43 | 501 | logger.debug("Closing SCC connection session.") |
ioannis@43 | 502 | self.session.close() |
ioannis@43 | 503 | |
ioannis@43 | 504 | |
ioannis@43 | 505 | class Measurement: |
ioannis@43 | 506 | """ This class represents the measurement object as returned in the SCC API. |
ioannis@43 | 507 | """ |
victor@7 | 508 | |
i@14 | 509 | def __init__(self, base_url, dict_response): |
i@14 | 510 | self.base_url = base_url |
victor@7 | 511 | |
ioannis@43 | 512 | # Define expected attributes to assist debuggin |
ioannis@43 | 513 | self.cloudmask = None |
ioannis@43 | 514 | self.elda = None |
ioannis@43 | 515 | self.elic = None |
ioannis@43 | 516 | self.elpp = None |
ioannis@43 | 517 | self.hirelpp = None |
ioannis@43 | 518 | self.id = None |
ioannis@43 | 519 | self.is_calibration = None |
ioannis@43 | 520 | self.is_running = None |
ioannis@43 | 521 | self.pre_processing_exit_code = None |
ioannis@43 | 522 | self.processing_exit_code = None |
ioannis@43 | 523 | self.resource_uri = None |
ioannis@43 | 524 | self.start = None |
ioannis@43 | 525 | self.stop = None |
ioannis@43 | 526 | self.system = None |
ioannis@43 | 527 | self.upload = None |
ioannis@43 | 528 | |
victor@7 | 529 | if dict_response: |
victor@7 | 530 | # Add the dictionary key value pairs as object properties |
victor@7 | 531 | for key, value in dict_response.items(): |
victor@7 | 532 | setattr(self, key, value) |
victor@7 | 533 | self.exists = True |
victor@7 | 534 | else: |
victor@7 | 535 | self.exists = False |
victor@7 | 536 | |
ioannis@43 | 537 | @property |
ioannis@43 | 538 | def rerun_elda_url(self): |
ioannis@43 | 539 | url_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/rerun-elda/') |
ioannis@43 | 540 | return url_pattern.format(self.id) |
victor@7 | 541 | |
victor@7 | 542 | @property |
ioannis@43 | 543 | def rerun_elpp_url(self): |
ioannis@43 | 544 | url_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/rerun-elpp/') |
i@14 | 545 | return url_pattern.format(self.id) |
victor@7 | 546 | |
victor@7 | 547 | @property |
victor@7 | 548 | def rerun_all_url(self): |
i@14 | 549 | ulr_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/rerun-all/') |
i@14 | 550 | return ulr_pattern.format(self.id) |
victor@7 | 551 | |
victor@7 | 552 | def __str__(self): |
ioannis@43 | 553 | return "Measurement {}".format(self.id) |
victor@7 | 554 | |
victor@7 | 555 | |
ioannis@43 | 556 | def upload_file(filename, system_id, force_upload, delete_related, settings): |
victor@7 | 557 | """ Shortcut function to upload a file to the SCC. """ |
ioannis@43 | 558 | logger.info("Uploading file %s, using system %s." % (filename, system_id)) |
victor@7 | 559 | |
ioannis@43 | 560 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@43 | 561 | scc.login(settings['website_credentials']) |
ioannis@43 | 562 | measurement_id = scc.upload_file(filename, system_id, force_upload, delete_related) |
ioannis@43 | 563 | scc.logout() |
ioannis@43 | 564 | |
victor@7 | 565 | return measurement_id |
victor@7 | 566 | |
victor@7 | 567 | |
ioannis@43 | 568 | def process_file(filename, system_id, force_upload, delete_related, settings): |
victor@7 | 569 | """ Shortcut function to process a file to the SCC. """ |
ioannis@43 | 570 | logger.info("Processing file %s, using system %s." % (filename, system_id)) |
victor@7 | 571 | |
ioannis@43 | 572 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@43 | 573 | scc.login(settings['website_credentials']) |
ioannis@43 | 574 | measurement = scc.process(filename, system_id, force_upload, delete_related) |
ioannis@43 | 575 | scc.logout() |
ioannis@43 | 576 | |
victor@7 | 577 | return measurement |
victor@7 | 578 | |
victor@7 | 579 | |
ioannis@43 | 580 | def delete_measurement(measurement_id, settings, delete_related): |
victor@7 | 581 | """ Shortcut function to delete a measurement from the SCC. """ |
ioannis@43 | 582 | logger.info("Deleting %s." % measurement_id) |
i@14 | 583 | |
ioannis@43 | 584 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@43 | 585 | scc.login(settings['website_credentials']) |
ioannis@43 | 586 | scc.delete_measurement(measurement_id, delete_related) |
ioannis@43 | 587 | scc.logout() |
victor@7 | 588 | |
victor@7 | 589 | |
i@14 | 590 | def rerun_all(measurement_id, monitor, settings): |
victor@7 | 591 | """ Shortcut function to delete a measurement from the SCC. """ |
victor@7 | 592 | logger.info("Rerunning all products for %s" % measurement_id) |
i@14 | 593 | |
ioannis@43 | 594 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@43 | 595 | scc.login(settings['website_credentials']) |
ioannis@43 | 596 | scc.rerun_all(measurement_id, monitor) |
ioannis@43 | 597 | scc.logout() |
victor@7 | 598 | |
victor@7 | 599 | |
ioannis@43 | 600 | def rerun_elpp(measurement_id, monitor, settings): |
victor@7 | 601 | """ Shortcut function to delete a measurement from the SCC. """ |
victor@7 | 602 | logger.info("Rerunning (optical) processing for %s" % measurement_id) |
i@14 | 603 | |
ioannis@43 | 604 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@43 | 605 | scc.login(settings['website_credentials']) |
ioannis@43 | 606 | scc.rerun_elpp(measurement_id, monitor) |
ioannis@43 | 607 | scc.logout() |
i@14 | 608 | |
i@14 | 609 | |
i@14 | 610 | def import_settings(config_file_path): |
i@14 | 611 | """ Read the configuration file. |
i@14 | 612 | |
i@14 | 613 | The file should be in YAML syntax.""" |
i@14 | 614 | |
i@14 | 615 | if not os.path.isfile(config_file_path): |
i@14 | 616 | logger.error("Wrong path for configuration file (%s)" % config_file_path) |
i@14 | 617 | sys.exit(1) |
i@14 | 618 | |
i@14 | 619 | with open(config_file_path) as yaml_file: |
i@14 | 620 | try: |
i@14 | 621 | settings = yaml.safe_load(yaml_file) |
i@14 | 622 | logger.debug("Read settings file(%s)" % config_file_path) |
ioannis@43 | 623 | except Exception as e: |
i@14 | 624 | logger.error("Could not parse YAML file (%s)" % config_file_path) |
ioannis@43 | 625 | logger.debug("Error message: {}".format(e)) |
i@14 | 626 | sys.exit(1) |
i@14 | 627 | |
i@14 | 628 | # YAML limitation: does not read tuples |
i@14 | 629 | settings['basic_credentials'] = tuple(settings['basic_credentials']) |
i@14 | 630 | settings['website_credentials'] = tuple(settings['website_credentials']) |
i@14 | 631 | return settings |
i@14 | 632 | |
i@14 | 633 | |
victor@7 | 634 | def main(): |
victor@7 | 635 | # Define the command line arguments. |
victor@7 | 636 | parser = argparse.ArgumentParser() |
i@16 | 637 | parser.add_argument("config", help="Path to configuration file") |
victor@7 | 638 | parser.add_argument("filename", nargs='?', help="Measurement file name or path.", default='') |
victor@7 | 639 | parser.add_argument("system", nargs='?', help="Processing system id.", default=0) |
victor@7 | 640 | parser.add_argument("-p", "--process", help="Wait for the results of the processing.", |
victor@7 | 641 | action="store_true") |
victor@7 | 642 | parser.add_argument("--delete", help="Measurement ID to delete.") |
ioannis@43 | 643 | # parser.add_argument("--delete_related", help= |
ioannis@43 | 644 | # "Delete all related measurements. Use only if you know what you are doing!", |
ioannis@43 | 645 | # action="store_true") |
ioannis@43 | 646 | parser.add_argument("--force_upload", help="If measurement ID exists on SCC, delete before uploading.", |
ioannis@43 | 647 | action="store_true") |
ioannis@43 | 648 | parser.add_argument("--rerun-all", help="Rerun all processing steps for the provided measurement ID.") |
ioannis@43 | 649 | parser.add_argument("--rerun-elpp", help="Rerun low-resolution processing steps for the provided measurement ID.") |
victor@7 | 650 | |
victor@7 | 651 | # Verbosity settings from http://stackoverflow.com/a/20663028 |
victor@7 | 652 | parser.add_argument('-d', '--debug', help="Print debugging information.", action="store_const", |
victor@7 | 653 | dest="loglevel", const=logging.DEBUG, default=logging.INFO, |
victor@7 | 654 | ) |
victor@7 | 655 | parser.add_argument('-s', '--silent', help="Show only warning and error messages.", action="store_const", |
victor@7 | 656 | dest="loglevel", const=logging.WARNING |
victor@7 | 657 | ) |
victor@7 | 658 | |
victor@7 | 659 | args = parser.parse_args() |
victor@7 | 660 | |
ioannis@43 | 661 | # For now, don to allow to delete related measurements |
ioannis@43 | 662 | delete_related = False |
ioannis@43 | 663 | |
victor@7 | 664 | # Get the logger with the appropriate level |
victor@7 | 665 | logging.basicConfig(format='%(levelname)s: %(message)s', level=args.loglevel) |
victor@7 | 666 | |
i@14 | 667 | settings = import_settings(args.config) |
i@14 | 668 | |
i@14 | 669 | # If the arguments are OK, try to log-in to SCC and upload. |
victor@7 | 670 | if args.delete: |
victor@7 | 671 | # If the delete is provided, do nothing else |
ioannis@43 | 672 | delete_measurement(args.delete, settings, delete_related) |
victor@7 | 673 | elif args.rerun_all: |
i@14 | 674 | rerun_all(args.rerun_all, args.process, settings) |
ioannis@43 | 675 | elif args.rerun_elpp: |
ioannis@43 | 676 | rerun_elpp(args.rerun_elpp, args.process, settings) |
victor@7 | 677 | else: |
victor@7 | 678 | if (args.filename == '') or (args.system == 0): |
victor@7 | 679 | parser.error('Provide a valid filename and system parameters.\nRun with -h for help.\n') |
victor@7 | 680 | |
victor@7 | 681 | if args.process: |
ioannis@43 | 682 | process_file(args.filename, args.system, args.force_upload, delete_related, settings) |
victor@7 | 683 | else: |
ioannis@43 | 684 | upload_file(args.filename, args.system, args.force_upload, delete_related, settings) |