Thu, 04 Feb 2021 10:22:30 +0200
Note for future improvements.
ioannis@43 | 1 | import sys |
ioannis@43 | 2 | |
victor@7 | 3 | import requests |
victor@7 | 4 | |
ioannis@43 | 5 | try: |
ioannis@43 | 6 | import urllib.parse as urlparse # Python 3 |
ioannis@43 | 7 | except ImportError: |
ioannis@17 | 8 | import urlparse # Python 2 |
ioannis@43 | 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@43 | 23 | import netCDF4 as netcdf |
ioannis@43 | 24 | |
ioannis@43 | 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 |
victor@7 | 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@54 | 55 | self.measurement_page_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/') |
ioannis@43 | 56 | self.download_hirelpp_pattern = urlparse.urljoin(self.base_url, |
ioannis@34 | 57 | 'data_processing/measurements/{0}/download-hirelpp/') |
ioannis@43 | 58 | self.download_cloudmask_pattern = urlparse.urljoin(self.base_url, |
ioannis@34 | 59 | 'data_processing/measurements/{0}/download-cloudmask/') |
ioannis@34 | 60 | |
ioannis@43 | 61 | self.download_elpp_pattern = urlparse.urljoin(self.base_url, |
moritz@29 | 62 | 'data_processing/measurements/{0}/download-preprocessed/') |
ioannis@43 | 63 | self.download_elda_pattern = urlparse.urljoin(self.base_url, |
moritz@29 | 64 | 'data_processing/measurements/{0}/download-optical/') |
ioannis@45 | 65 | self.download_plots_pattern = urlparse.urljoin(self.base_url, |
moritz@29 | 66 | 'data_processing/measurements/{0}/download-plots/') |
ioannis@43 | 67 | self.download_elic_pattern = urlparse.urljoin(self.base_url, |
ioannis@34 | 68 | 'data_processing/measurements/{0}/download-elic/') |
i@14 | 69 | self.delete_measurement_pattern = urlparse.urljoin(self.base_url, 'admin/database/measurements/{0}/delete/') |
i@31 | 70 | |
i@14 | 71 | self.api_base_url = urlparse.urljoin(self.base_url, 'api/v1/') |
i@31 | 72 | self.api_measurement_pattern = urlparse.urljoin(self.api_base_url, 'measurements/{0}/') |
i@31 | 73 | self.api_measurements_url = urlparse.urljoin(self.api_base_url, 'measurements') |
i@38 | 74 | self.api_sounding_search_pattern = urlparse.urljoin(self.api_base_url, 'sounding_files/?filename={0}') |
i@38 | 75 | self.api_lidarratio_search_pattern = urlparse.urljoin(self.api_base_url, 'lidarratio_files/?filename={0}') |
i@38 | 76 | self.api_overlap_search_pattern = urlparse.urljoin(self.api_base_url, 'overlap_files/?filename={0}') |
ioannis@43 | 77 | |
i@14 | 78 | def login(self, credentials): |
i@31 | 79 | """ Login to SCC. """ |
victor@7 | 80 | logger.debug("Attempting to login to SCC, username %s." % credentials[0]) |
moritz@29 | 81 | login_credentials = {'username': credentials[0], |
moritz@29 | 82 | 'password': credentials[1]} |
victor@7 | 83 | |
i@14 | 84 | logger.debug("Accessing login page at %s." % self.login_url) |
victor@7 | 85 | |
victor@7 | 86 | # Get upload form |
moritz@29 | 87 | login_page = self.session.get(self.login_url) |
i@14 | 88 | |
i@31 | 89 | if not login_page.ok: |
i@31 | 90 | raise self.PageNotAccessibleError('Could not access login pages. Status code %s' % login_page.status_code) |
victor@7 | 91 | |
i@31 | 92 | logger.debug("Submitting credentials.") |
victor@7 | 93 | # Submit the login data |
i@14 | 94 | login_submit = self.session.post(self.login_url, |
moritz@29 | 95 | data=login_credentials, |
victor@7 | 96 | headers={'X-CSRFToken': login_page.cookies['csrftoken'], |
moritz@29 | 97 | 'referer': self.login_url}) |
victor@7 | 98 | return login_submit |
victor@7 | 99 | |
victor@7 | 100 | def logout(self): |
i@31 | 101 | """ Logout from SCC """ |
i@31 | 102 | return self.session.get(self.logout_url, stream=True) |
victor@7 | 103 | |
ioannis@54 | 104 | def upload_file(self, filename, system_id, force_upload, delete_related, delay=0, rs_filename=None, ov_filename=None, lr_filename=None): |
madrouin@20 | 105 | """ Upload a filename for processing with a specific system. If the |
victor@7 | 106 | upload is successful, it returns the measurement id. """ |
ioannis@43 | 107 | measurement_id = self.measurement_id_from_file(filename) |
ioannis@43 | 108 | |
ioannis@43 | 109 | logger.debug('Checking if a measurement with the same id already exists on the SCC server.') |
ioannis@50 | 110 | existing_measurement, _ = self.get_measurement(measurement_id) |
ioannis@43 | 111 | |
ioannis@43 | 112 | if existing_measurement: |
ioannis@43 | 113 | if force_upload: |
ioannis@43 | 114 | logger.info( |
ioannis@43 | 115 | "Measurement with id {} already exists on the SCC. Trying to delete it...".format(measurement_id)) |
ioannis@43 | 116 | self.delete_measurement(measurement_id, delete_related) |
ioannis@43 | 117 | else: |
ioannis@43 | 118 | logger.error( |
ioannis@43 | 119 | "Measurement with id {} already exists on the SCC. Use --force_upload flag to overwrite it.".format( |
ioannis@43 | 120 | measurement_id)) |
ioannis@55 | 121 | # TODO: Implement handling at the proper place. This does not allow the SCC class to be used by external programs. |
ioannis@43 | 122 | sys.exit(1) |
ioannis@43 | 123 | |
victor@7 | 124 | # Get submit page |
moritz@29 | 125 | upload_page = self.session.get(self.upload_url) |
victor@7 | 126 | |
victor@7 | 127 | # Submit the data |
ioannis@54 | 128 | upload_data = {'system': system_id, |
ioannis@54 | 129 | 'delay': delay} |
ioannis@54 | 130 | |
ioannis@54 | 131 | logger.debug("Submitted processing parameters - System: {}, Delay: {}".format(system_id, delay)) |
ioannis@54 | 132 | |
victor@7 | 133 | files = {'data': open(filename, 'rb')} |
victor@7 | 134 | |
madrouin@20 | 135 | if rs_filename is not None: |
i@38 | 136 | ancillary_file, _ = self.get_ancillary(rs_filename, 'sounding') |
i@38 | 137 | |
i@38 | 138 | if ancillary_file.already_on_scc: |
i@38 | 139 | logger.warning("Sounding file {0.filename} already on the SCC with id {0.id}. Ignoring it.".format(ancillary_file)) |
i@38 | 140 | else: |
i@38 | 141 | logger.debug('Adding sounding file %s' % rs_filename) |
i@38 | 142 | files['sounding_file'] = open(rs_filename, 'rb') |
madrouin@20 | 143 | |
ioannis@32 | 144 | if ov_filename is not None: |
i@38 | 145 | ancillary_file, _ = self.get_ancillary(ov_filename, 'overlap') |
i@38 | 146 | |
i@38 | 147 | if ancillary_file.already_on_scc: |
i@38 | 148 | logger.warning("Overlap file {0.filename} already on the SCC with id {0.id}. Ignoring it.".format(ancillary_file)) |
i@38 | 149 | else: |
i@38 | 150 | logger.debug('Adding overlap file %s' % ov_filename) |
i@38 | 151 | files['overlap_file'] = open(ov_filename, 'rb') |
i@31 | 152 | |
i@31 | 153 | if lr_filename is not None: |
i@38 | 154 | ancillary_file, _ = self.get_ancillary(lr_filename, 'lidarratio') |
i@38 | 155 | |
i@38 | 156 | if ancillary_file.already_on_scc: |
i@38 | 157 | logger.warning( |
i@38 | 158 | "Lidar ratio file {0.filename} already on the SCC with id {0.id}. Ignoring it.".format(ancillary_file)) |
i@38 | 159 | else: |
i@38 | 160 | logger.debug('Adding lidar ratio file %s' % lr_filename) |
i@38 | 161 | files['lidar_ratio_file'] = open(lr_filename, 'rb') |
i@31 | 162 | |
i@14 | 163 | logger.info("Uploading of file %s started." % filename) |
victor@7 | 164 | |
i@14 | 165 | upload_submit = self.session.post(self.upload_url, |
victor@7 | 166 | data=upload_data, |
victor@7 | 167 | files=files, |
victor@7 | 168 | headers={'X-CSRFToken': upload_page.cookies['csrftoken'], |
moritz@29 | 169 | 'referer': self.upload_url}) |
victor@7 | 170 | |
victor@7 | 171 | if upload_submit.status_code != 200: |
i@14 | 172 | logger.warning("Connection error. Status code: %s" % upload_submit.status_code) |
victor@7 | 173 | return False |
victor@7 | 174 | |
victor@7 | 175 | # Check if there was a redirect to a new page. |
i@14 | 176 | if upload_submit.url == self.upload_url: |
victor@7 | 177 | measurement_id = False |
ioannis@32 | 178 | logger.error("Uploaded file(s) rejected! Try to upload manually to see the error.") |
victor@7 | 179 | else: |
victor@7 | 180 | measurement_id = re.findall(regex, upload_submit.text)[0] |
ioannis@43 | 181 | logger.info("Successfully uploaded measurement with id %s." % measurement_id) |
ioannis@54 | 182 | logger.info("You can monitor the processing progress online: {}".format(self.measurement_page_pattern.format(measurement_id))) |
ioannis@43 | 183 | return measurement_id |
ioannis@43 | 184 | |
ioannis@43 | 185 | @staticmethod |
ioannis@43 | 186 | def measurement_id_from_file(filename): |
ioannis@43 | 187 | """ Get the measurement id from the input file. """ |
ioannis@43 | 188 | |
ioannis@43 | 189 | if not os.path.isfile(filename): |
ioannis@43 | 190 | logger.error("File {} does not exist.".format(filename)) |
ioannis@43 | 191 | sys.exit(1) |
ioannis@43 | 192 | |
ioannis@43 | 193 | with netcdf.Dataset(filename) as f: |
ioannis@43 | 194 | try: |
ioannis@43 | 195 | measurement_id = f.Measurement_ID |
ioannis@43 | 196 | except AttributeError: |
ioannis@43 | 197 | logger.error( |
ioannis@43 | 198 | "Input file {} does not contain a Measurement_ID global attribute. Wrong file format?".format( |
ioannis@43 | 199 | filename)) |
ioannis@43 | 200 | sys.exit(1) |
victor@7 | 201 | |
victor@7 | 202 | return measurement_id |
victor@7 | 203 | |
victor@7 | 204 | def download_files(self, measurement_id, subdir, download_url): |
victor@7 | 205 | """ Downloads some files from the download_url to the specified |
madrouin@20 | 206 | subdir. This method is used to download preprocessed file, optical |
victor@7 | 207 | files etc. |
victor@7 | 208 | """ |
ioannis@32 | 209 | # TODO: Make downloading more robust (e.g. in case that files do not exist on server). |
victor@7 | 210 | # Get the file |
moritz@29 | 211 | request = self.session.get(download_url, stream=True) |
moritz@29 | 212 | |
moritz@29 | 213 | if not request.ok: |
moritz@29 | 214 | raise Exception("Could not download files for measurement '%s'" % measurement_id) |
victor@7 | 215 | |
victor@7 | 216 | # Create the dir if it does not exist |
victor@7 | 217 | local_dir = os.path.join(self.output_dir, measurement_id, subdir) |
victor@7 | 218 | if not os.path.exists(local_dir): |
victor@7 | 219 | os.makedirs(local_dir) |
victor@7 | 220 | |
victor@7 | 221 | # Save the file by chunk, needed if the file is big. |
ioannis@43 | 222 | memory_file = BytesIO() |
victor@7 | 223 | |
victor@7 | 224 | for chunk in request.iter_content(chunk_size=1024): |
victor@7 | 225 | if chunk: # filter out keep-alive new chunks |
victor@7 | 226 | memory_file.write(chunk) |
victor@7 | 227 | memory_file.flush() |
victor@7 | 228 | |
victor@7 | 229 | zip_file = ZipFile(memory_file) |
victor@7 | 230 | |
victor@7 | 231 | for ziped_name in zip_file.namelist(): |
victor@7 | 232 | basename = os.path.basename(ziped_name) |
victor@7 | 233 | |
victor@7 | 234 | local_file = os.path.join(local_dir, basename) |
victor@7 | 235 | |
victor@7 | 236 | with open(local_file, 'wb') as f: |
victor@7 | 237 | f.write(zip_file.read(ziped_name)) |
victor@7 | 238 | |
ioannis@43 | 239 | def download_hirelpp(self, measurement_id): |
ioannis@43 | 240 | """ Download hirelpp files for the measurement id. """ |
ioannis@43 | 241 | # Construct the download url |
ioannis@43 | 242 | download_url = self.download_hirelpp_pattern.format(measurement_id) |
ioannis@43 | 243 | try: |
ioannis@50 | 244 | self.download_files(measurement_id, 'hirelpp', download_url) |
ioannis@43 | 245 | except Exception as e: |
ioannis@43 | 246 | logger.error("Could not download HiRElPP files. Error message: {}".format(e)) |
ioannis@43 | 247 | logger.debug('Download exception:', exc_info=True) |
ioannis@43 | 248 | |
ioannis@43 | 249 | def download_cloudmask(self, measurement_id): |
ioannis@43 | 250 | """ Download cloudmask files for the measurement id. """ |
ioannis@43 | 251 | # Construct the download url |
ioannis@43 | 252 | download_url = self.download_cloudmask_pattern.format(measurement_id) |
ioannis@43 | 253 | try: |
ioannis@50 | 254 | self.download_files(measurement_id, 'cloudscreen', download_url) |
ioannis@43 | 255 | except Exception as e: |
ioannis@43 | 256 | logger.error("Could not download cloudscreen files. Error message: {}".format(e)) |
ioannis@43 | 257 | logger.debug('Download exception:', exc_info=True) |
ioannis@43 | 258 | |
ioannis@43 | 259 | def download_elpp(self, measurement_id): |
victor@7 | 260 | """ Download preprocessed files for the measurement id. """ |
victor@7 | 261 | # Construct the download url |
ioannis@43 | 262 | download_url = self.download_elpp_pattern.format(measurement_id) |
ioannis@43 | 263 | try: |
ioannis@50 | 264 | self.download_files(measurement_id, 'elpp', download_url) |
ioannis@43 | 265 | except Exception as e: |
ioannis@43 | 266 | logger.error("Could not download ElPP files. Error message: {}".format(e)) |
ioannis@43 | 267 | logger.debug('Download exception:', exc_info=True) |
victor@7 | 268 | |
ioannis@43 | 269 | def download_elda(self, measurement_id): |
victor@7 | 270 | """ Download optical files for the measurement id. """ |
victor@7 | 271 | # Construct the download url |
ioannis@43 | 272 | download_url = self.download_elda_pattern.format(measurement_id) |
ioannis@43 | 273 | try: |
ioannis@50 | 274 | self.download_files(measurement_id, 'elda', download_url) |
ioannis@43 | 275 | except Exception as e: |
ioannis@43 | 276 | logger.error("Could not download ELDA files. Error message: {}".format(e)) |
ioannis@43 | 277 | logger.debug('Download exception:', exc_info=True) |
victor@7 | 278 | |
ioannis@43 | 279 | def download_plots(self, measurement_id): |
victor@7 | 280 | """ Download profile graphs for the measurement id. """ |
victor@7 | 281 | # Construct the download url |
ioannis@45 | 282 | download_url = self.download_plots_pattern.format(measurement_id) |
ioannis@43 | 283 | try: |
ioannis@50 | 284 | self.download_files(measurement_id, 'elda_plots', download_url) |
ioannis@43 | 285 | except Exception as e: |
ioannis@43 | 286 | logger.error("Could not download ELDA plots. Error message: {}".format(e)) |
ioannis@43 | 287 | logger.debug('Download exception:', exc_info=True) |
victor@7 | 288 | |
ioannis@43 | 289 | def download_elic(self, measurement_id): |
ioannis@43 | 290 | """ Download ELIC files for the measurement id. """ |
ioannis@43 | 291 | # Construct the download url |
ioannis@43 | 292 | download_url = self.download_elic_pattern.format(measurement_id) |
ioannis@43 | 293 | try: |
ioannis@50 | 294 | self.download_files(measurement_id, 'elic', download_url) |
ioannis@43 | 295 | except Exception as e: |
ioannis@43 | 296 | logger.error("Could not download ELIC files. Error message: {}".format(e)) |
ioannis@43 | 297 | logger.debug('Download exception:', exc_info=True) |
ioannis@43 | 298 | |
ioannis@43 | 299 | def download_eldec(self, measurement_id): |
ioannis@43 | 300 | """ Download ELDEC files for the measurement id. """ |
ioannis@43 | 301 | # Construct the download url |
ioannis@43 | 302 | download_url = self.download_elda_pattern.format(measurement_id) # ELDA patter is used for now |
ioannis@43 | 303 | try: |
ioannis@50 | 304 | self.download_files(measurement_id, 'eldec', download_url) |
ioannis@43 | 305 | except Exception as e: |
ioannis@43 | 306 | logger.error("Could not download EDELC files. Error message: {}".format(e)) |
ioannis@43 | 307 | logger.debug('Download exception:', exc_info=True) |
ioannis@43 | 308 | |
ioannis@43 | 309 | def rerun_elpp(self, measurement_id, monitor=True): |
ioannis@45 | 310 | logger.debug("Started rerun_elpp procedure.") |
ioannis@45 | 311 | |
ioannis@45 | 312 | logger.debug("Getting measurement %s" % measurement_id) |
madrouin@26 | 313 | measurement, status = self.get_measurement(measurement_id) |
victor@7 | 314 | |
victor@7 | 315 | if measurement: |
ioannis@45 | 316 | logger.debug("Attempting to rerun ElPP through %s." % measurement.rerun_all_url) |
ioannis@45 | 317 | request = self.session.get(measurement.rerun_elpp_url, stream=True) |
victor@7 | 318 | |
victor@7 | 319 | if request.status_code != 200: |
i@14 | 320 | logger.error( |
i@14 | 321 | "Could not rerun processing for %s. Status code: %s" % (measurement_id, request.status_code)) |
ioannis@45 | 322 | else: |
ioannis@45 | 323 | logger.info("Rerun-elpp command submitted successfully for id {}.".format(measurement_id)) |
victor@7 | 324 | |
victor@7 | 325 | if monitor: |
victor@7 | 326 | self.monitor_processing(measurement_id) |
victor@7 | 327 | |
victor@7 | 328 | def rerun_all(self, measurement_id, monitor=True): |
victor@7 | 329 | logger.debug("Started rerun_all procedure.") |
victor@7 | 330 | |
victor@7 | 331 | logger.debug("Getting measurement %s" % measurement_id) |
madrouin@26 | 332 | measurement, status = self.get_measurement(measurement_id) |
victor@7 | 333 | |
victor@7 | 334 | if measurement: |
victor@7 | 335 | logger.debug("Attempting to rerun all processing through %s." % measurement.rerun_all_url) |
victor@7 | 336 | |
moritz@29 | 337 | request = self.session.get(measurement.rerun_all_url, stream=True) |
victor@7 | 338 | |
victor@7 | 339 | if request.status_code != 200: |
victor@7 | 340 | logger.error("Could not rerun pre processing for %s. Status code: %s" % |
victor@7 | 341 | (measurement_id, request.status_code)) |
ioannis@45 | 342 | else: |
ioannis@45 | 343 | logger.info("Rerun-all command submitted successfully for id {}.".format(measurement_id)) |
victor@7 | 344 | |
victor@7 | 345 | if monitor: |
victor@7 | 346 | self.monitor_processing(measurement_id) |
victor@7 | 347 | |
ioannis@54 | 348 | def process(self, filename, system_id, monitor, force_upload, delete_related, delay=0, rs_filename=None, lr_filename=None, ov_filename=None): |
victor@7 | 349 | """ Upload a file for processing and wait for the processing to finish. |
victor@7 | 350 | If the processing is successful, it will download all produced files. |
victor@7 | 351 | """ |
victor@7 | 352 | logger.info("--- Processing started on %s. ---" % datetime.datetime.now()) |
victor@7 | 353 | # Upload file |
ioannis@50 | 354 | logger.info("Uploading file.") |
ioannis@45 | 355 | measurement_id = self.upload_file(filename, system_id, force_upload, delete_related, |
ioannis@54 | 356 | delay=delay, |
ioannis@32 | 357 | rs_filename=rs_filename, |
ioannis@32 | 358 | lr_filename=lr_filename, |
ioannis@32 | 359 | ov_filename=ov_filename) |
ioannis@43 | 360 | |
ioannis@54 | 361 | if monitor and (delay > 0): |
ioannis@54 | 362 | logger.warning("Will not start monitoring, since a delay was specified: {} hours.".format(delay)) |
ioannis@54 | 363 | return None |
ioannis@54 | 364 | |
ioannis@32 | 365 | if measurement_id and monitor: |
ioannis@54 | 366 | logger.info("Monitoring processing.") |
moritz@29 | 367 | return self.monitor_processing(measurement_id) |
victor@7 | 368 | |
moritz@29 | 369 | return None |
victor@7 | 370 | |
victor@7 | 371 | def monitor_processing(self, measurement_id): |
victor@7 | 372 | """ Monitor the processing progress of a measurement id""" |
victor@7 | 373 | |
madrouin@24 | 374 | # try to deal with error 404 |
madrouin@24 | 375 | error_count = 0 |
ioannis@53 | 376 | error_max = 3 |
ioannis@53 | 377 | time_sleep = 3 |
madrouin@24 | 378 | |
madrouin@25 | 379 | # try to wait for measurement to appear in API |
madrouin@24 | 380 | measurement = None |
ioannis@50 | 381 | logger.info("Looking for measurement %s on the SCC.", measurement_id) |
madrouin@26 | 382 | while error_count < error_max: |
madrouin@26 | 383 | time.sleep(time_sleep) |
madrouin@26 | 384 | measurement, status = self.get_measurement(measurement_id) |
madrouin@26 | 385 | if status != 200 and error_count < error_max: |
ioannis@32 | 386 | logger.error("Measurement not found. waiting %ds", time_sleep) |
madrouin@24 | 387 | error_count += 1 |
madrouin@26 | 388 | else: |
madrouin@26 | 389 | break |
madrouin@24 | 390 | |
madrouin@24 | 391 | if error_count == error_max: |
ioannis@32 | 392 | logger.critical("Measurement %s doesn't seem to exist", measurement_id) |
madrouin@26 | 393 | sys.exit(1) |
madrouin@26 | 394 | |
ioannis@45 | 395 | logger.info('Measurement %s found.', measurement_id) |
madrouin@24 | 396 | |
victor@7 | 397 | if measurement is not None: |
victor@7 | 398 | while measurement.is_running: |
ioannis@53 | 399 | measurement.log_processing_status() |
victor@7 | 400 | time.sleep(10) |
madrouin@26 | 401 | measurement, status = self.get_measurement(measurement_id) |
madrouin@24 | 402 | |
ioannis@34 | 403 | logger.info("Measurement processing finished.") |
ioannis@53 | 404 | measurement.log_detailed_status() |
ioannis@53 | 405 | |
ioannis@43 | 406 | if measurement.hirelpp == 127: |
ioannis@43 | 407 | logger.info("Downloading HiRElPP files.") |
ioannis@43 | 408 | self.download_hirelpp(measurement_id) |
ioannis@43 | 409 | if measurement.cloudmask == 127: |
ioannis@43 | 410 | logger.info("Downloading cloud screening files.") |
ioannis@43 | 411 | self.download_cloudmask(measurement_id) |
ioannis@43 | 412 | if measurement.elpp == 127: |
ioannis@45 | 413 | logger.info("Downloading ElPP files.") |
ioannis@43 | 414 | self.download_elpp(measurement_id) |
ioannis@43 | 415 | if measurement.elda == 127: |
ioannis@43 | 416 | logger.info("Downloading ELDA files.") |
ioannis@43 | 417 | self.download_elda(measurement_id) |
ioannis@50 | 418 | logger.info("Downloading ELDA plots.") |
ioannis@43 | 419 | self.download_plots(measurement_id) |
ioannis@43 | 420 | if measurement.elic == 127: |
ioannis@43 | 421 | logger.info("Downloading ELIC files.") |
ioannis@43 | 422 | self.download_elic(measurement_id) |
ioannis@53 | 423 | if measurement.is_calibration and measurement.eldec==0: |
ioannis@43 | 424 | logger.info("Downloading ELDEC files.") |
ioannis@43 | 425 | self.download_eldec(measurement_id) |
victor@7 | 426 | logger.info("--- Processing finished. ---") |
ioannis@43 | 427 | |
victor@7 | 428 | return measurement |
victor@7 | 429 | |
ioannis@43 | 430 | def get_measurement(self, measurement_id): |
victor@7 | 431 | |
ioannis@45 | 432 | if measurement_id is None: # Is this still required? |
victor@7 | 433 | return None |
victor@7 | 434 | |
i@31 | 435 | measurement_url = self.api_measurement_pattern.format(measurement_id) |
i@31 | 436 | logger.debug("Measurement API URL: %s" % measurement_url) |
victor@7 | 437 | |
moritz@29 | 438 | response = self.session.get(measurement_url) |
victor@7 | 439 | |
ioannis@43 | 440 | response_dict = None |
ioannis@45 | 441 | |
ioannis@43 | 442 | if response.status_code == 200: |
ioannis@43 | 443 | response_dict = response.json() |
ioannis@45 | 444 | elif response.status_code == 404: |
ioannis@43 | 445 | logger.info("No measurement with id %s found on the SCC." % measurement_id) |
ioannis@45 | 446 | else: |
i@14 | 447 | logger.error('Could not access API. Status code %s.' % response.status_code) |
victor@7 | 448 | |
ioannis@55 | 449 | # TODO: Implement better handling for status 401. |
ioannis@55 | 450 | |
victor@7 | 451 | if response_dict: |
ioannis@43 | 452 | measurement = Measurement(self.base_url, response_dict) |
victor@7 | 453 | else: |
ioannis@45 | 454 | measurement = None |
victor@7 | 455 | |
ioannis@45 | 456 | return measurement, response.status_code |
victor@7 | 457 | |
ioannis@45 | 458 | def delete_measurement(self, measurement_id, delete_related): |
victor@7 | 459 | """ Deletes a measurement with the provided measurement id. The user |
madrouin@20 | 460 | should have the appropriate permissions. |
madrouin@20 | 461 | |
victor@7 | 462 | The procedures is performed directly through the web interface and |
victor@7 | 463 | NOT through the API. |
victor@7 | 464 | """ |
victor@7 | 465 | # Get the measurement object |
i@31 | 466 | measurement, _ = self.get_measurement(measurement_id) |
victor@7 | 467 | |
victor@7 | 468 | # Check that it exists |
victor@7 | 469 | if measurement is None: |
victor@7 | 470 | logger.warning("Nothing to delete.") |
victor@7 | 471 | return None |
victor@7 | 472 | |
victor@7 | 473 | # Go the the page confirming the deletion |
moritz@29 | 474 | delete_url = self.delete_measurement_pattern.format(measurement_id) |
ioannis@43 | 475 | |
moritz@29 | 476 | confirm_page = self.session.get(delete_url) |
victor@7 | 477 | |
victor@7 | 478 | # Check that the page opened properly |
victor@7 | 479 | if confirm_page.status_code != 200: |
victor@7 | 480 | logger.warning("Could not open delete page. Status: {0}".format(confirm_page.status_code)) |
victor@7 | 481 | return None |
victor@7 | 482 | |
ioannis@43 | 483 | # Get the delete related value |
ioannis@43 | 484 | if delete_related: |
ioannis@43 | 485 | delete_related_option = 'delete_related' |
ioannis@43 | 486 | else: |
ioannis@43 | 487 | delete_related_option = 'not_delete_related' |
ioannis@43 | 488 | |
victor@7 | 489 | # Delete the measurement |
victor@7 | 490 | delete_page = self.session.post(delete_url, |
ioannis@43 | 491 | data={'post': 'yes', |
ioannis@43 | 492 | 'select_delete_related_measurements': delete_related_option}, |
victor@7 | 493 | headers={'X-CSRFToken': confirm_page.cookies['csrftoken'], |
victor@7 | 494 | 'referer': delete_url} |
victor@7 | 495 | ) |
i@31 | 496 | if not delete_page.ok: |
victor@7 | 497 | logger.warning("Something went wrong. Delete page status: {0}".format( |
victor@7 | 498 | delete_page.status_code)) |
victor@7 | 499 | return None |
victor@7 | 500 | |
victor@7 | 501 | logger.info("Deleted measurement {0}".format(measurement_id)) |
victor@7 | 502 | return True |
victor@7 | 503 | |
victor@7 | 504 | def available_measurements(self): |
victor@7 | 505 | """ Get a list of available measurement on the SCC. """ |
i@31 | 506 | response = self.session.get(self.api_measurements_url) |
victor@7 | 507 | response_dict = response.json() |
victor@7 | 508 | |
victor@7 | 509 | if response_dict: |
victor@7 | 510 | measurement_list = response_dict['objects'] |
i@14 | 511 | measurements = [Measurement(self.base_url, measurement_dict) for measurement_dict in measurement_list] |
victor@7 | 512 | logger.info("Found %s measurements on the SCC." % len(measurements)) |
victor@7 | 513 | else: |
victor@7 | 514 | logger.warning("No response received from the SCC when asked for available measurements.") |
ioannis@43 | 515 | measurements = None |
victor@7 | 516 | |
victor@7 | 517 | return measurements |
victor@7 | 518 | |
moritz@29 | 519 | def list_measurements(self, station=None, system=None, start=None, stop=None, upload_status=None, |
moritz@29 | 520 | processing_status=None, optical_processing=None): |
moritz@29 | 521 | |
i@31 | 522 | # TODO: Change this to work through the API |
i@31 | 523 | |
moritz@29 | 524 | # Need to set to empty string if not specified, we won't get any results |
moritz@29 | 525 | params = { |
moritz@29 | 526 | "station": station if station is not None else "", |
moritz@29 | 527 | "system": system if system is not None else "", |
moritz@29 | 528 | "stop": stop if stop is not None else "", |
moritz@29 | 529 | "start": start if start is not None else "", |
moritz@29 | 530 | "upload_status": upload_status if upload_status is not None else "", |
moritz@29 | 531 | "preprocessing_status": processing_status if processing_status is not None else "", |
moritz@29 | 532 | "optical_processing_status": optical_processing if optical_processing is not None else "" |
moritz@29 | 533 | } |
i@31 | 534 | |
i@31 | 535 | response_txt = self.session.get(self.list_measurements_url, params=params).text |
moritz@29 | 536 | tbl_rgx = re.compile(r'<table id="measurements">(.*?)</table>', re.DOTALL) |
moritz@29 | 537 | entry_rgx = re.compile(r'<tr>(.*?)</tr>', re.DOTALL) |
moritz@29 | 538 | measurement_rgx = re.compile( |
moritz@29 | 539 | r'.*?<td><a[^>]*>(\w+)</a>.*?<td>.*?<td>([\w-]+ [\w:]+)</td>.*<td data-order="([-]?\d+),([-]?\d+),([-]?\d+)".*', |
moritz@29 | 540 | re.DOTALL) |
i@31 | 541 | matches = tbl_rgx.findall(response_txt) |
moritz@29 | 542 | if len(matches) != 1: |
moritz@29 | 543 | return [] |
moritz@29 | 544 | |
moritz@29 | 545 | ret = [] |
moritz@29 | 546 | for entry in entry_rgx.finditer(matches[0]): |
moritz@29 | 547 | m = measurement_rgx.match(entry.string[entry.start(0):entry.end(0)]) |
moritz@29 | 548 | if m: |
moritz@29 | 549 | name, date, upload, preproc, optical = m.groups() |
moritz@29 | 550 | ret.append( |
moritz@29 | 551 | Measurement(self.base_url, {"id": name, "upload": int(upload), "pre_processing": int(preproc), |
moritz@29 | 552 | "processing": int(optical)})) |
moritz@29 | 553 | |
moritz@29 | 554 | return ret |
moritz@29 | 555 | |
ioannis@43 | 556 | def measurement_id_for_date(self, t1, call_sign, base_number=0): |
victor@7 | 557 | """ Give the first available measurement id on the SCC for the specific |
madrouin@20 | 558 | date. |
victor@7 | 559 | """ |
victor@7 | 560 | date_str = t1.strftime('%Y%m%d') |
i@31 | 561 | base_id = "%s%s" % (date_str, call_sign) |
i@31 | 562 | search_url = urlparse.urljoin(self.api_base_url, 'measurements/?id__startswith=%s' % base_id) |
victor@7 | 563 | |
moritz@29 | 564 | response = self.session.get(search_url) |
victor@7 | 565 | |
victor@7 | 566 | response_dict = response.json() |
victor@7 | 567 | |
victor@7 | 568 | measurement_id = None |
victor@7 | 569 | |
victor@7 | 570 | if response_dict: |
victor@7 | 571 | measurement_list = response_dict['objects'] |
i@31 | 572 | |
i@31 | 573 | if len(measurement_list) == 100: |
i@31 | 574 | raise ValueError('No available measurement id found.') |
i@31 | 575 | |
victor@7 | 576 | existing_ids = [measurement_dict['id'] for measurement_dict in measurement_list] |
victor@7 | 577 | |
victor@7 | 578 | measurement_number = base_number |
i@31 | 579 | measurement_id = "%s%02i" % (base_id, measurement_number) |
victor@7 | 580 | |
victor@7 | 581 | while measurement_id in existing_ids: |
victor@7 | 582 | measurement_number = measurement_number + 1 |
i@31 | 583 | measurement_id = "%s%02i" % (base_id, measurement_number) |
victor@7 | 584 | |
victor@7 | 585 | return measurement_id |
victor@7 | 586 | |
i@40 | 587 | def get_ancillary(self, file_path, file_type): |
i@38 | 588 | """ |
i@38 | 589 | Try to get the ancillary file data from the SCC API. |
i@38 | 590 | |
i@38 | 591 | The result will always be an API object. If the file does not exist, the .exists property is set to False. |
i@38 | 592 | |
i@38 | 593 | Parameters |
i@38 | 594 | ---------- |
i@40 | 595 | file_path : str |
i@40 | 596 | Path of the uploaded file. |
i@38 | 597 | file_type : str |
i@38 | 598 | Type of ancillary file. One of 'sounding', 'overlap', 'lidarratio'. |
i@38 | 599 | |
i@38 | 600 | Returns |
i@38 | 601 | : AncillaryFile |
i@38 | 602 | The api object. |
i@38 | 603 | """ |
i@38 | 604 | assert file_type in ['sounding', 'overlap', 'lidarratio'] |
i@38 | 605 | |
i@40 | 606 | filename = os.path.basename(file_path) |
i@40 | 607 | |
i@38 | 608 | if file_type == 'sounding': |
i@38 | 609 | file_url = self.api_sounding_search_pattern.format(filename) |
i@38 | 610 | elif file_type == 'overlap': |
i@38 | 611 | file_url = self.api_overlap_search_pattern.format(filename) |
i@38 | 612 | else: |
i@38 | 613 | file_url = self.api_lidarratio_search_pattern.format(filename) |
i@38 | 614 | |
i@38 | 615 | response = self.session.get(file_url) |
i@38 | 616 | |
i@38 | 617 | if not response.ok: |
i@38 | 618 | logger.error('Could not access API. Status code %s.' % response.status_code) |
i@38 | 619 | return None, response.status_code |
i@38 | 620 | |
i@38 | 621 | response_dict = response.json() |
i@38 | 622 | object_list = response_dict['objects'] |
i@38 | 623 | |
i@38 | 624 | logger.debug("Ancillary file JSON: {0}".format(object_list)) |
i@38 | 625 | |
i@38 | 626 | if object_list: |
i@38 | 627 | ancillary_file = AncillaryFile(self.api_base_url, object_list[0]) # Assume only one file is returned |
i@38 | 628 | else: |
i@38 | 629 | ancillary_file = AncillaryFile(self.api_base_url, None) # Create an empty object |
i@38 | 630 | |
i@38 | 631 | return ancillary_file, response.status_code |
i@38 | 632 | |
ioannis@43 | 633 | def __enter__(self): |
ioannis@43 | 634 | return self |
victor@7 | 635 | |
ioannis@43 | 636 | def __exit__(self, *args): |
ioannis@43 | 637 | logger.debug("Closing SCC connection session.") |
ioannis@43 | 638 | self.session.close() |
ioannis@43 | 639 | |
i@31 | 640 | class PageNotAccessibleError(RuntimeError): |
i@31 | 641 | pass |
ioannis@43 | 642 | |
victor@7 | 643 | |
ioannis@17 | 644 | class ApiObject(object): |
victor@7 | 645 | """ A generic class object. """ |
victor@7 | 646 | |
i@14 | 647 | def __init__(self, base_url, dict_response): |
i@14 | 648 | self.base_url = base_url |
victor@7 | 649 | |
victor@7 | 650 | if dict_response: |
victor@7 | 651 | # Add the dictionary key value pairs as object properties |
victor@7 | 652 | for key, value in dict_response.items(): |
ioannis@17 | 653 | # logger.debug('Setting key {0} to value {1}'.format(key, value)) |
ioannis@17 | 654 | try: |
ioannis@17 | 655 | setattr(self, key, value) |
ioannis@17 | 656 | except: |
ioannis@17 | 657 | logger.warning('Could not set attribute {0} to value {1}'.format(key, value)) |
victor@7 | 658 | self.exists = True |
victor@7 | 659 | else: |
victor@7 | 660 | self.exists = False |
victor@7 | 661 | |
victor@7 | 662 | |
victor@7 | 663 | class Measurement(ApiObject): |
ioannis@43 | 664 | """ This class represents the measurement object as returned in the SCC API. |
ioannis@43 | 665 | """ |
victor@7 | 666 | |
i@14 | 667 | def __init__(self, base_url, dict_response): |
victor@7 | 668 | |
ioannis@45 | 669 | # Define expected attributes to assist debugging |
ioannis@53 | 670 | |
ioannis@53 | 671 | self.hirelpp = None |
ioannis@53 | 672 | self.hirelpp_exit_code = None |
ioannis@43 | 673 | self.cloudmask = None |
ioannis@53 | 674 | self.cloudmask_exit_code = None |
ioannis@53 | 675 | self.elpp = None |
ioannis@53 | 676 | self.elpp_exit_code = None |
ioannis@43 | 677 | self.elda = None |
ioannis@53 | 678 | self.elda_exit_code = None |
ioannis@43 | 679 | self.elic = None |
ioannis@53 | 680 | self.elic_exit_code = None |
ioannis@53 | 681 | self.eldec = None |
ioannis@53 | 682 | self.eldec_exit_code = None |
ioannis@53 | 683 | self.elquick = None |
ioannis@53 | 684 | self.elquick_exit_code = None |
ioannis@53 | 685 | |
ioannis@43 | 686 | self.id = None |
ioannis@43 | 687 | self.is_calibration = None |
ioannis@43 | 688 | self.is_running = None |
ioannis@53 | 689 | |
ioannis@43 | 690 | self.resource_uri = None |
ioannis@43 | 691 | self.start = None |
ioannis@43 | 692 | self.stop = None |
ioannis@43 | 693 | self.system = None |
ioannis@43 | 694 | self.upload = None |
ioannis@43 | 695 | |
ioannis@45 | 696 | super().__init__(base_url, dict_response) |
victor@7 | 697 | |
ioannis@53 | 698 | def log_processing_status(self): |
ioannis@53 | 699 | """ Log module status. """ |
ioannis@53 | 700 | logger.info("Measurement is being processed. Status: {}, {}, {}, {}, {}, {}). Please wait.".format( |
ioannis@53 | 701 | self.upload, |
ioannis@53 | 702 | self.hirelpp, |
ioannis@53 | 703 | self.cloudmask, |
ioannis@53 | 704 | self.elpp, |
ioannis@53 | 705 | self.elda, |
ioannis@53 | 706 | self.elic)) |
ioannis@53 | 707 | |
ioannis@53 | 708 | def log_detailed_status(self): |
ioannis@53 | 709 | """ Log module exit and status codes.""" |
ioannis@53 | 710 | logger.info("Measurement exit status:".format(self.id)) |
ioannis@53 | 711 | if self.is_calibration: |
ioannis@53 | 712 | self._log_module_status('ElPP', self.elpp, self.elpp_exit_code) |
ioannis@53 | 713 | self._log_module_status('ElDEC', self.eldec, self.eldec_exit_code) |
ioannis@53 | 714 | else: |
ioannis@53 | 715 | self._log_module_status('HiRElPP', self.hirelpp, self.hirelpp_exit_code) |
ioannis@53 | 716 | self._log_module_status('CloudScreen', self.cloudmask, self.cloudmask_exit_code) |
ioannis@53 | 717 | self._log_module_status('ElPP', self.elpp, self.elpp_exit_code) |
ioannis@53 | 718 | self._log_module_status('ELDA', self.elda, self.elda_exit_code) |
ioannis@53 | 719 | self._log_module_status('ELIC', self.elic, self.elic_exit_code) |
ioannis@53 | 720 | self._log_module_status('ELQuick', self.elquick, self.elquick_exit_code) |
ioannis@53 | 721 | |
ioannis@53 | 722 | def _log_module_status(self, name, status, exit_code): |
ioannis@53 | 723 | if exit_code: |
ioannis@54 | 724 | if exit_code['exit_code'] > 0: |
ioannis@54 | 725 | logger.warning("{0} exit code: {2[exit_code]} - {2[description]}".format(name, status, exit_code)) |
ioannis@54 | 726 | else: |
ioannis@54 | 727 | logger.info("{0} exit code: {2[exit_code]} - {2[description]}".format(name, status, exit_code)) |
ioannis@53 | 728 | else: |
ioannis@53 | 729 | logger.info("{0} exit code: {2}".format(name, status, exit_code)) |
ioannis@53 | 730 | |
ioannis@43 | 731 | @property |
ioannis@43 | 732 | def rerun_elda_url(self): |
ioannis@43 | 733 | url_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/rerun-elda/') |
ioannis@43 | 734 | return url_pattern.format(self.id) |
victor@7 | 735 | |
victor@7 | 736 | @property |
ioannis@43 | 737 | def rerun_elpp_url(self): |
ioannis@43 | 738 | url_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/rerun-elpp/') |
i@14 | 739 | return url_pattern.format(self.id) |
victor@7 | 740 | |
victor@7 | 741 | @property |
victor@7 | 742 | def rerun_all_url(self): |
i@14 | 743 | ulr_pattern = urlparse.urljoin(self.base_url, 'data_processing/measurements/{0}/rerun-all/') |
i@14 | 744 | return ulr_pattern.format(self.id) |
victor@7 | 745 | |
victor@7 | 746 | def __str__(self): |
ioannis@43 | 747 | return "Measurement {}".format(self.id) |
victor@7 | 748 | |
victor@7 | 749 | |
i@38 | 750 | class AncillaryFile(ApiObject): |
i@38 | 751 | """ This class represents the ancilalry file object as returned in the SCC API. |
i@38 | 752 | """ |
i@38 | 753 | @property |
i@38 | 754 | def already_on_scc(self): |
i@38 | 755 | if self.exists is False: |
i@38 | 756 | return False |
i@38 | 757 | |
i@38 | 758 | return not self.status == 'missing' |
i@38 | 759 | |
i@38 | 760 | def __str__(self): |
i@38 | 761 | return "%s: %s, %s" % (self.id, |
i@38 | 762 | self.filename, |
i@38 | 763 | self.status) |
i@38 | 764 | |
i@38 | 765 | |
ioannis@45 | 766 | def process_file(filename, system_id, settings, force_upload, delete_related, |
ioannis@54 | 767 | delay=0, monitor=True, rs_filename=None, lr_filename=None, ov_filename=None): |
ioannis@32 | 768 | """ Shortcut function to process a file to the SCC. """ |
ioannis@32 | 769 | logger.info("Processing file %s, using system %s" % (filename, system_id)) |
victor@7 | 770 | |
ioannis@43 | 771 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@43 | 772 | scc.login(settings['website_credentials']) |
ioannis@45 | 773 | measurement = scc.process(filename, system_id, |
ioannis@45 | 774 | force_upload=force_upload, |
ioannis@45 | 775 | delete_related=delete_related, |
ioannis@54 | 776 | delay=delay, |
ioannis@45 | 777 | monitor=monitor, |
ioannis@45 | 778 | rs_filename=rs_filename, |
ioannis@45 | 779 | lr_filename=lr_filename, |
ioannis@45 | 780 | ov_filename=ov_filename) |
ioannis@43 | 781 | scc.logout() |
victor@7 | 782 | return measurement |
victor@7 | 783 | |
victor@7 | 784 | |
ioannis@45 | 785 | def delete_measurements(measurement_ids, delete_related, settings): |
moritz@29 | 786 | """ Shortcut function to delete measurements from the SCC. """ |
ioannis@45 | 787 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@45 | 788 | scc.login(settings['website_credentials']) |
ioannis@45 | 789 | for m_id in measurement_ids: |
ioannis@54 | 790 | logger.info("Deleting %s." % m_id) |
ioannis@45 | 791 | scc.delete_measurement(m_id, delete_related) |
ioannis@45 | 792 | scc.logout() |
moritz@29 | 793 | |
moritz@29 | 794 | |
moritz@29 | 795 | def rerun_all(measurement_ids, monitor, settings): |
moritz@29 | 796 | """ Shortcut function to rerun measurements from the SCC. """ |
i@14 | 797 | |
ioannis@43 | 798 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@43 | 799 | scc.login(settings['website_credentials']) |
ioannis@45 | 800 | for m_id in measurement_ids: |
ioannis@54 | 801 | logger.info("Rerunning all products for %s." % m_id) |
ioannis@45 | 802 | scc.rerun_all(m_id, monitor) |
ioannis@43 | 803 | scc.logout() |
victor@7 | 804 | |
victor@7 | 805 | |
moritz@29 | 806 | def rerun_processing(measurement_ids, monitor, settings): |
victor@7 | 807 | """ Shortcut function to delete a measurement from the SCC. """ |
i@14 | 808 | |
ioannis@43 | 809 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@43 | 810 | scc.login(settings['website_credentials']) |
ioannis@45 | 811 | for m_id in measurement_ids: |
ioannis@45 | 812 | logger.info("Rerunning (optical) processing for %s" % m_id) |
ioannis@45 | 813 | scc.rerun_elpp(m_id, monitor) |
ioannis@45 | 814 | scc.logout() |
moritz@29 | 815 | |
moritz@29 | 816 | |
moritz@29 | 817 | def list_measurements(settings, station=None, system=None, start=None, stop=None, upload_status=None, |
moritz@29 | 818 | preprocessing_status=None, |
moritz@29 | 819 | optical_processing=None): |
moritz@29 | 820 | """List all available measurements""" |
ioannis@45 | 821 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@45 | 822 | scc.login(settings['website_credentials']) |
ioannis@45 | 823 | ret = scc.list_measurements(station=station, system=system, start=start, stop=stop, upload_status=upload_status, |
ioannis@45 | 824 | processing_status=preprocessing_status, optical_processing=optical_processing) |
ioannis@45 | 825 | for entry in ret: |
ioannis@45 | 826 | print("%s" % entry.id) |
ioannis@43 | 827 | scc.logout() |
victor@7 | 828 | |
victor@7 | 829 | |
moritz@29 | 830 | def download_measurements(measurement_ids, download_preproc, download_optical, download_graph, settings): |
moritz@29 | 831 | """Download all measurements for the specified IDs""" |
ioannis@43 | 832 | with SCC(settings['basic_credentials'], settings['output_dir'], settings['base_url']) as scc: |
ioannis@43 | 833 | scc.login(settings['website_credentials']) |
ioannis@45 | 834 | for m_id in measurement_ids: |
ioannis@45 | 835 | if download_preproc: |
ioannis@45 | 836 | logger.info("Downloading preprocessed files for '%s'" % m_id) |
ioannis@45 | 837 | scc.download_elpp(m_id) |
ioannis@45 | 838 | logger.info("Complete") |
ioannis@45 | 839 | if download_optical: |
ioannis@45 | 840 | logger.info("Downloading optical files for '%s'" % m_id) |
ioannis@45 | 841 | scc.download_elda(m_id) |
ioannis@45 | 842 | logger.info("Complete") |
ioannis@45 | 843 | if download_graph: |
ioannis@45 | 844 | logger.info("Downloading profile graph files for '%s'" % m_id) |
ioannis@45 | 845 | scc.download_plots(m_id) |
ioannis@45 | 846 | logger.info("Complete") |
ioannis@43 | 847 | scc.logout() |
i@14 | 848 | |
i@14 | 849 | |
moritz@29 | 850 | def settings_from_path(config_file_path): |
i@14 | 851 | """ Read the configuration file. |
i@14 | 852 | |
i@14 | 853 | The file should be in YAML syntax.""" |
i@14 | 854 | |
i@14 | 855 | if not os.path.isfile(config_file_path): |
moritz@29 | 856 | raise argparse.ArgumentTypeError("Wrong path for configuration file (%s)" % config_file_path) |
i@14 | 857 | |
i@14 | 858 | with open(config_file_path) as yaml_file: |
i@14 | 859 | try: |
i@14 | 860 | settings = yaml.safe_load(yaml_file) |
i@14 | 861 | logger.debug("Read settings file(%s)" % config_file_path) |
moritz@29 | 862 | except Exception: |
moritz@29 | 863 | raise argparse.ArgumentTypeError("Could not parse YAML file (%s)" % config_file_path) |
i@14 | 864 | |
i@14 | 865 | # YAML limitation: does not read tuples |
i@14 | 866 | settings['basic_credentials'] = tuple(settings['basic_credentials']) |
i@14 | 867 | settings['website_credentials'] = tuple(settings['website_credentials']) |
i@14 | 868 | return settings |
i@14 | 869 | |
i@14 | 870 | |
moritz@29 | 871 | # Setup for command specific parsers |
moritz@29 | 872 | def setup_delete(parser): |
moritz@29 | 873 | def delete_from_args(parsed): |
ioannis@45 | 874 | delete_measurements(parsed.IDs, |
ioannis@45 | 875 | delete_related=False, |
ioannis@45 | 876 | settings=parsed.config) |
moritz@29 | 877 | |
moritz@29 | 878 | parser.add_argument("IDs", nargs="+", help="measurement IDs to delete.") |
moritz@29 | 879 | parser.set_defaults(execute=delete_from_args) |
moritz@29 | 880 | |
moritz@29 | 881 | |
moritz@29 | 882 | def setup_rerun_all(parser): |
moritz@29 | 883 | def rerun_all_from_args(parsed): |
moritz@29 | 884 | rerun_all(parsed.IDs, parsed.process, parsed.config) |
moritz@29 | 885 | |
moritz@29 | 886 | parser.add_argument("IDs", nargs="+", help="Measurement IDs to rerun.") |
moritz@29 | 887 | parser.add_argument("-p", "--process", help="Wait for the results of the processing.", |
moritz@29 | 888 | action="store_true") |
moritz@29 | 889 | parser.set_defaults(execute=rerun_all_from_args) |
moritz@29 | 890 | |
moritz@29 | 891 | |
ioannis@45 | 892 | def setup_rerun_elpp(parser): |
moritz@29 | 893 | def rerun_processing_from_args(parsed): |
moritz@29 | 894 | rerun_processing(parsed.IDs, parsed.process, parsed.config) |
moritz@29 | 895 | |
moritz@29 | 896 | parser.add_argument("IDs", nargs="+", help="Measurement IDs to rerun the processing on.") |
moritz@29 | 897 | parser.add_argument("-p", "--process", help="Wait for the results of the processing.", |
moritz@29 | 898 | action="store_true") |
moritz@29 | 899 | parser.set_defaults(execute=rerun_processing_from_args) |
moritz@29 | 900 | |
moritz@29 | 901 | |
ioannis@45 | 902 | def setup_upload_file(parser): |
ioannis@45 | 903 | """ Upload but do not monitor processing progress. """ |
ioannis@45 | 904 | def upload_file_from_args(parsed): |
ioannis@45 | 905 | process_file(parsed.filename, parsed.system, parsed.config, |
ioannis@54 | 906 | delay=parsed.delay, |
ioannis@45 | 907 | monitor=parsed.process, |
ioannis@45 | 908 | force_upload=parsed.force_upload, |
ioannis@45 | 909 | delete_related=False, # For now, use this as default |
ioannis@32 | 910 | rs_filename=parsed.radiosounding, |
ioannis@32 | 911 | ov_filename=parsed.overlap, |
ioannis@32 | 912 | lr_filename=parsed.lidarratio) |
moritz@29 | 913 | |
ioannis@54 | 914 | def delay(arg): |
ioannis@54 | 915 | try: |
ioannis@54 | 916 | int_arg = int(arg) |
ioannis@54 | 917 | except ValueError: |
ioannis@54 | 918 | raise argparse.ArgumentTypeError("Could not convert delay argument {} to integer.".format(arg)) |
ioannis@54 | 919 | |
ioannis@54 | 920 | if 0 <= int_arg <= 96: |
ioannis@54 | 921 | return int_arg |
ioannis@54 | 922 | else: |
ioannis@54 | 923 | raise argparse.ArgumentTypeError("Delay should be an integer between 0 and 96.") |
ioannis@54 | 924 | |
moritz@29 | 925 | parser.add_argument("filename", help="Measurement file name or path.") |
moritz@29 | 926 | parser.add_argument("system", help="Processing system id.") |
ioannis@54 | 927 | parser.add_argument("--delay", help="Delay processing by the specified number of hours (0 to 96).", |
ioannis@54 | 928 | default=0, type=delay) |
ioannis@45 | 929 | parser.add_argument("-p", "--process", help="Wait for the processing results.", |
ioannis@45 | 930 | action="store_true") |
ioannis@45 | 931 | parser.add_argument("--force_upload", help="If measurement ID exists on SCC, delete before uploading.", |
ioannis@45 | 932 | action="store_true") |
i@30 | 933 | parser.add_argument("--radiosounding", default=None, help="Radiosounding file name or path") |
ioannis@32 | 934 | parser.add_argument("--overlap", default=None, help="Overlap file name or path") |
ioannis@32 | 935 | parser.add_argument("--lidarratio", default=None, help="Lidar ratio file name or path") |
i@30 | 936 | |
moritz@29 | 937 | parser.set_defaults(execute=upload_file_from_args) |
moritz@29 | 938 | |
moritz@29 | 939 | |
moritz@29 | 940 | def setup_list_measurements(parser): |
moritz@29 | 941 | def list_measurements_from_args(parsed): |
ioannis@45 | 942 | # TODO: Fix this |
ioannis@45 | 943 | logger.warning("This method needs to be updated. Cross-chceck any results.") |
ioannis@45 | 944 | |
moritz@29 | 945 | list_measurements(parsed.config, station=parsed.station, system=parsed.system, start=parsed.start, |
moritz@29 | 946 | stop=parsed.stop, |
moritz@29 | 947 | upload_status=parsed.upload_status, preprocessing_status=parsed.preprocessing_status, |
moritz@29 | 948 | optical_processing=parsed.optical_processing_status) |
moritz@29 | 949 | |
moritz@29 | 950 | def status(arg): |
moritz@29 | 951 | if -127 <= int(arg) <= 127: |
moritz@29 | 952 | return arg |
moritz@29 | 953 | else: |
moritz@29 | 954 | raise argparse.ArgumentTypeError("Status must be between -127 and 127") |
moritz@29 | 955 | |
moritz@29 | 956 | def date(arg): |
moritz@29 | 957 | if re.match(r'\d{4}-\d{2}-\d{2}', arg): |
moritz@29 | 958 | return arg |
moritz@29 | 959 | else: |
moritz@29 | 960 | raise argparse.ArgumentTypeError("Date must be in format 'YYYY-MM-DD'") |
moritz@29 | 961 | |
moritz@29 | 962 | parser.add_argument("--station", help="Filter for only the selected station") |
moritz@29 | 963 | parser.add_argument("--system", help="Filter for only the selected station") |
moritz@29 | 964 | parser.add_argument("--start", help="Filter for only the selected station", type=date) |
moritz@29 | 965 | parser.add_argument("--stop", help="Filter for only the selected station", type=date) |
moritz@29 | 966 | parser.add_argument("--upload-status", help="Filter for only the selected station", type=status) |
moritz@29 | 967 | parser.add_argument("--preprocessing-status", help="Filter for only the selected station", type=status) |
moritz@29 | 968 | parser.add_argument("--optical-processing-status", help="Filter for only the selected station", type=status) |
moritz@29 | 969 | parser.set_defaults(execute=list_measurements_from_args) |
moritz@29 | 970 | |
moritz@29 | 971 | |
moritz@29 | 972 | def setup_download_measurements(parser): |
moritz@29 | 973 | def download_measurements_from_args(parsed): |
ioannis@45 | 974 | # TODO: Fix this |
ioannis@45 | 975 | logger.warning("This method needs to be updated. Cross-chceck any results.") |
ioannis@45 | 976 | |
ioannis@45 | 977 | preproc = parsed.download_elpp |
ioannis@45 | 978 | optical = parsed.download_elda |
moritz@29 | 979 | graphs = parsed.download_profile_graphs |
moritz@29 | 980 | if not preproc and not graphs: |
moritz@29 | 981 | optical = True |
moritz@29 | 982 | download_measurements(parsed.IDs, preproc, optical, graphs, parsed.config) |
moritz@29 | 983 | |
moritz@29 | 984 | parser.add_argument("IDs", help="Measurement IDs that should be downloaded.", nargs="+") |
moritz@29 | 985 | parser.add_argument("--download-preprocessed", action="store_true", help="Download preprocessed files.") |
moritz@29 | 986 | parser.add_argument("--download-optical", action="store_true", |
moritz@29 | 987 | help="Download optical files (default if no other download is used).") |
moritz@29 | 988 | parser.add_argument("--download-profile-graphs", action="store_true", help="Download profile graph files.") |
moritz@29 | 989 | parser.set_defaults(execute=download_measurements_from_args) |
moritz@29 | 990 | |
moritz@29 | 991 | |
victor@7 | 992 | def main(): |
victor@7 | 993 | # Define the command line arguments. |
victor@7 | 994 | parser = argparse.ArgumentParser() |
moritz@29 | 995 | subparsers = parser.add_subparsers() |
moritz@29 | 996 | |
moritz@29 | 997 | delete_parser = subparsers.add_parser("delete", help="Deletes a measurement.") |
ioannis@45 | 998 | rerun_all_parser = subparsers.add_parser("rerun-all", help="Rerun all processing steps for the provided measurement IDs.") |
ioannis@45 | 999 | rerun_processing_parser = subparsers.add_parser("rerun-elpp", |
ioannis@45 | 1000 | help="Rerun low-resolution processing steps for the provided measurement ID.") |
ioannis@45 | 1001 | upload_file_parser = subparsers.add_parser("upload-file", help="Submit a file and, optionally, download the output products.") |
ioannis@32 | 1002 | list_parser = subparsers.add_parser("list", help="List measurements registered on the SCC.") |
moritz@29 | 1003 | download_parser = subparsers.add_parser("download", help="Download selected measurements.") |
moritz@29 | 1004 | |
moritz@29 | 1005 | setup_delete(delete_parser) |
moritz@29 | 1006 | setup_rerun_all(rerun_all_parser) |
ioannis@45 | 1007 | setup_rerun_elpp(rerun_processing_parser) |
ioannis@45 | 1008 | |
moritz@29 | 1009 | setup_upload_file(upload_file_parser) |
moritz@29 | 1010 | setup_list_measurements(list_parser) |
moritz@29 | 1011 | setup_download_measurements(download_parser) |
victor@7 | 1012 | |
victor@7 | 1013 | # Verbosity settings from http://stackoverflow.com/a/20663028 |
victor@7 | 1014 | parser.add_argument('-d', '--debug', help="Print debugging information.", action="store_const", |
victor@7 | 1015 | dest="loglevel", const=logging.DEBUG, default=logging.INFO, |
victor@7 | 1016 | ) |
victor@7 | 1017 | parser.add_argument('-s', '--silent', help="Show only warning and error messages.", action="store_const", |
victor@7 | 1018 | dest="loglevel", const=logging.WARNING |
victor@7 | 1019 | ) |
victor@7 | 1020 | |
ioannis@32 | 1021 | # Setup default config location |
moritz@29 | 1022 | home = os.path.expanduser("~") |
moritz@29 | 1023 | default_config_location = os.path.abspath(os.path.join(home, ".scc_access.yaml")) |
moritz@29 | 1024 | parser.add_argument("-c", "--config", help="Path to the config file.", type=settings_from_path, |
moritz@29 | 1025 | default=default_config_location) |
victor@7 | 1026 | |
victor@7 | 1027 | args = parser.parse_args() |
ioannis@43 | 1028 | |
victor@7 | 1029 | # Get the logger with the appropriate level |
victor@7 | 1030 | logging.basicConfig(format='%(levelname)s: %(message)s', level=args.loglevel) |
victor@7 | 1031 | |
moritz@29 | 1032 | # Dispatch to appropriate function |
moritz@29 | 1033 | args.execute(args) |
moritz@29 | 1034 | |
i@14 | 1035 | |
moritz@29 | 1036 | # When running through terminal |
moritz@29 | 1037 | if __name__ == '__main__': |
moritz@29 | 1038 | main() |