Merge branch 'sesam' into 'master' (7ec7ad7b) · Commits · CAMS / CSO

config/tutorial/tutorial.rc

+6 −1

Original line number	Diff line number	Diff line
		@@ -308,6 +308,8 @@ cso.tutorial.inquire-table-dataspace.url : https://stac.data
		! collection name:
		cso.tutorial.inquire-table-dataspace.collections : sentinel-5p-l2-no2-rpro \
		sentinel-5p-l2-no2-offl
		!!~ near-real time processing:
		!cso.tutorial.inquire-table-dataspace.collections : sentinel-5p-l2-no2-nrti

		! target area;
		!!~ empty for no limitation:
		@@ -375,6 +377,8 @@ my.tutorial.selection : C03
		!
		cso.tutorial.convert.selection : (%{collection} == '03') and (%{processing} == 'RPRO') ; \
		(%{collection} == '03') and (%{processing} == 'OFFL')
		!!~ for near-real-time processing:
		!cso.tutorial.convert.selection : %{collection} == '03'

		! input directory;
		! files are searched here or downloaded to if not present yet;
		@@ -425,7 +429,8 @@ cso.tutorial.convert.filter.quality.units : 1
		! - times are taken from mid of selection, rounded to hours
		! - use '%{processing}' for the processing name
		! - use '%{orbit}' for orbit number
		cso.tutorial.convert.output.filename : ${my.work}/CSO-data/${my.region}/S5p/NO2/${my.tutorial.selection}/%Y/%m/S5p_%{processing}_NO2_%{orbit}.nc
		! - include start time to have different files if orbit is stored in patches
		cso.tutorial.convert.output.filename : ${my.work}/CSO-data/${my.region}/S5p/NO2/${my.tutorial.selection}/%Y/%m/S5p_%{processing}_NO2_%{orbit}_%Y%m%dT%H%M%S.nc

		! pack variables on output:
		cso.tutorial.convert.output.packed : True

src/cso/cso_colhub.py

+90 −29

Original line number	Diff line number	Diff line
		@@ -29,6 +29,8 @@
		#
		# 2026-04, Arjo Segers
		# Initialize columns of listing file.
		# Added production time of data files to listings.
		# Select file with latest production time if multiple are found.
		#

		########################################################################
		@@ -185,7 +187,7 @@ class CSO_ColHubMirror_Inquire(utopya.UtopyaRc):

		# initiallize for (re)creation,
		# define extra columns to ensure correct content even for empty files:
		listing = cso_file.CSO_Listing( columns=["orbit","processing","collection","processor_version","href"] )
		listing = cso_file.CSO_Listing( columns=["orbit","processing","collection","processor_version","production_time","href"] )

		# archive directories
		archive_dirs = self.GetSetting("dir").split()
		@@ -242,7 +244,7 @@ class CSO_ColHubMirror_Inquire(utopya.UtopyaRc):
		orbit,
		collection,
		processor_version,
		prod_time,
		production_time,
		) = rest.split("_")
		except:
		logging.error(
		@@ -267,6 +269,7 @@ class CSO_ColHubMirror_Inquire(utopya.UtopyaRc):
		data["processing"] = processing
		data["collection"] = collection
		data["processor_version"] = processor_version
		data["production_time"] = production_time
		data["href"] = os.path.join(root, fname)
		# update record:
		listing.UpdateRecord(fname, data, indent=f"{indent} ")
		@@ -413,8 +416,10 @@ class CSO_ColHubMirror_Missing(utopya.UtopyaRc):
		# info ..
		logging.info(f"{indent}create %s ..." % lst_file)

		# initiallize for (re)creation:
		listing = cso_file.CSO_Listing()
		# initiallize for (re)creation,
		# define extra columns to ensure correct content even for empty files:
		listing = cso_file.CSO_Listing( columns=["orbit","processing","collection","processor_version","production_time","href"] )


		# table with all available files:
		listfile_all = self.GetSetting("all.file")
		@@ -460,6 +465,8 @@ class CSO_ColHubMirror_Missing(utopya.UtopyaRc):
		logging.info(f"{indent}loop over available orbits ...")
		# loop:
		for orbit in orbits:
		## testing ...
		#if orbit != '40182' : continue
		# info ..
		logging.info(f"{indent} orbit '{orbit}' ...")

		@@ -469,11 +476,66 @@ class CSO_ColHubMirror_Missing(utopya.UtopyaRc):
		# nothing selected?
		if len(xlst) == 0:
		continue
		#
		elif len(xlst) == 1:
		# single record:
		rec = xlst.GetRecord(irec=0)
		#
		else:
		# multiple records ...
		# init name of selected file:
		selected_filename = None
		#
		# 1st adhoc fix ...
		# check if these are the same data but file was recreated later (and forgotten to be removed ...)
		# S5P_RPRO_L2__CO_____20250715T142651_20250715T161018_40182_03_020800_20251103T112819.nc
		# S5P_RPRO_L2__CO_____20250715T142651_20250715T161018_40182_03_020800_20251030T133312.nc
		# init basenames:
		basenames = []
		# loop over filenames:
		for filename in xlst.df.index:
		# basename without production time:
		basename = filename.rsplit(sep="_",maxsplit=1)[0]
		# store:
		if basename not in basenames:
		basenames.append( basename )
		#endif
		# first?
		if selected_filename is None:
		# store first values:
		selected_filename = filename
		else:
		# newer?
		if filename > selected_filename:
		selected_filename = filename
		#endif
		#endif
		#endfor # filenames
		# should be the same ..
		if len(basenames) == 1:
		# info ...
		logging.info(f"{indent} selected single file based on latest production time:")
		logging.info(f"{indent} {selected_filename}")
		else:
		# info ...
		logging.warning(f"{indent} checked on production time, but found multiple base names:")
		for basename in basenames:
		logging.warning(f"{indent} {basename}")
		#endfor
		# reset selected name, check below:
		selected_filename = None
		#endif
		#
		# none of the adhoc fix lead to selection of a single file ...
		if selected_filename is None:
		logging.error(f"multiple records selected, something wrong with files or selection?")
		raise Exception
		#endif
		#
		# extract record:
		rec = xlst.GetRecord( name=selected_filename )
		# endif

		# loop over selected records:
		for irec in range(len(xlst)):
		# current:
		rec = xlst.GetRecord(irec)
		## info ..
		# logging.info( f"{indent} {fname}" )
		# set flag:
		@@ -497,7 +559,6 @@ class CSO_ColHubMirror_Missing(utopya.UtopyaRc):
		# add record to list:
		listing.UpdateRecord(rec["filename"], rec)
		# endif
		# endfor

		## TESTING ...
		# if len(listing) > 0 :

src/cso/cso_dataspace.py

+17 −4

Original line number	Diff line number	Diff line
		@@ -55,6 +55,8 @@
		# Fixed definition of bounding box for global selection.
		# Added increasing delays to avoid rate limit errors from STAC catalogue inquiry.
		# Check on different paths to 'href' attribute in stac inquiry.
		# Trap files that could not be downloaded.
		# Added production time of data files to listings.
		#


		@@ -378,7 +380,7 @@ class CSO_DataSpace_Inquire(utopya.UtopyaRc):
		platform_name, processing, rest = product_id.split("_", 2)
		product_type = rest[0:10]
		parts = rest[11:].split("_")
		start_time, end_time, orbit, collection, processor_version, prod_time = parts
		start_time, end_time, orbit, collection, processor_version, production_time = parts

		# convert:
		tfmt = "%Y%m%dT%H%M%S"
		@@ -427,6 +429,7 @@ class CSO_DataSpace_Inquire(utopya.UtopyaRc):
		"processing": [processing],
		"collection": [collection],
		"processor_version": [processor_version],
		"production_time": [production_time],
		"filename": [filename],
		"href": [href],
		}
		@@ -783,8 +786,12 @@ class CSO_DataSpace_Downloader(object):
		# check ...
		if npfile != 1:
		print(f"ERROR - found {npfile} files in S3 bucket for product: {product}")
		if npfile == 0:
		raise Exception(f"file not found in S3 bucket")
		else:
		raise Exception
		#endif
		#endif

		# loop over (single) files:
		for pfile in pfiles:
		@@ -893,8 +900,14 @@ class CSO_DataSpace_Downloader(object):

		# unknown ...
		except Exception as err:
		# check on known errors ..
		if "file not found in S3 bucket" in str(err):
		logging.warning(f"{indent} WARNING - could not download: {href}")
		break
		else:
		logging.error(f"{indent}unknown error:")
		logging.error(f"{indent} {str(err)}")
		#endif

		# endtry

src/cso/cso_file.py

+21 −6

Original line number	Diff line number	Diff line
		@@ -68,6 +68,9 @@
		# 2026-04, Arjo Segers
		# Added optional "columns" argument to initialize empty listing object.
		#
		# 2026-05, Arjo Segers
		# Support `name` argument for GetRecord method.
		#

		########################################################################
		###
		@@ -1407,11 +1410,24 @@ class CSO_Listing(object):

		# *

		def GetRecord(self, irec):
		def GetRecord(self, irec=None, name=None):
		"""
		Return record for corresponding 0-based row index.
		Return record for corresponding 0-based row index or index name.
		"""

		# modules:
		import numpy

		# by name?
		if name is not None:
		indx, = numpy.where( self.df.index == name )
		if len(indx) == 0:
		logging.error(f"value `{name}` not found in index")
		raise Exception
		#endif
		irec = indx[0]
		#endif

		# extract:
		rec = self.df.iloc[irec].copy()
		# add index values:
		@@ -1604,8 +1620,7 @@ class CSO_Listing(object):
		(%{processor_version} == '020400') & (%{processing} == 'RPRO') ; ...

		This is evaluted after the previously described selections.
		The result should be None or exactly one record.
		Eventually skip files in ``blacklists``.
		Eventually skip files in ``blacklist``.

		"""

		@@ -1650,7 +1665,7 @@ class CSO_Listing(object):
		# endif
		# select:
		df = df[df[key] == value]
		# endfor
		# endfor # key/value pairs

		# *

		@@ -1734,7 +1749,7 @@ class CSO_Listing(object):
		df = df.loc[selected]
		# endif

		# endif
		# endif # expr defined

		# *

src/cso/cso_s5p.py

+301 −259

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