review corrections

test/soca/CMakeLists.txt

@@ -53,7 +53,6 @@ function(CREATE_CONFIG_FILE test_config_in test_config_out bufr_input_dir ioda_o
 endfunction()
 
 
-# set(TEST_WORKING_DIR "/scratch1/NCEPDEV/stmp2/Edward.Givelberg/RUNDIRS/GFSv17-3DVAR-C384mx025/prepoceanobs.114138")
 set(TEST_WORKING_DIR ${PROJECT_BINARY_DIR}/test/soca)
 message("bufr to ioda: TEST_WORKING_DIR = ${TEST_WORKING_DIR}")
 
@@ -63,22 +62,22 @@ set(CONFIG_DIR ${PROJECT_SOURCE_DIR}/test/soca/testinput)
 set(TESTREF_DIR ${PROJECT_SOURCE_DIR}/test/soca/testref)
 
 # find the staging directory for bufr test input files ${BUFR_TEST_DIR}
+# checking on orion and hera
 # bufr input files on orion:
 set(BUFR_TEST_DIR
 	"/work/noaa/da/marineda/gfs-marine/data/obs/ci/bufr"
-	# "/work/noaa/da/marineda/gfs-marine/data/obs/ci/obs"
-	# ${TEST_WORKING_DIR}			# temporary fix
 )
 if (NOT EXISTS ${BUFR_TEST_DIR})
 	# bufr input files on hera:
 	set(BUFR_TEST_DIR
 		"/scratch1/NCEPDEV/da/common/ci/bufr"
-		# "/scratch1/NCEPDEV/da/common/ci/obs"
-		# ${TEST_WORKING_DIR}			# temporary fix
 	)
 endif()
 if (NOT EXISTS ${BUFR_TEST_DIR})
-	message(FATAL_ERROR "staging directory for BUFR test files ${BUFR_TEST_DIR} not found")
+	message("staging directory for BUFR test files ${BUFR_TEST_DIR} not found")
+	set(GENERATE_BUFR2IODA_TESTS FALSE)
+else()
+	set(GENERATE_BUFR2IODA_TESTS TRUE)
 endif()
 
 
@@ -120,11 +119,11 @@ function(ADD_INSITU_TEST testname testbufr)
 endfunction()
 
 
-ADD_INSITU_TEST("profile_argo" "subpfl")
-ADD_INSITU_TEST("profile_bathy" "bathy")
-ADD_INSITU_TEST("profile_glider" "subpfl")
-# ADD_INSITU_TEST(profile_marinemammal)
-ADD_INSITU_TEST("profile_tesac" "tesac")
-ADD_INSITU_TEST("profile_xbtctd" "xbtctd")
-# ADD_INSITU_TEST(surface_altkob)
-ADD_INSITU_TEST("surface_trkob" "trkob")
+if (GENERATE_BUFR2IODA_TESTS)
+	ADD_INSITU_TEST("profile_argo" "subpfl")
+	ADD_INSITU_TEST("profile_bathy" "bathy")
+	ADD_INSITU_TEST("profile_glider" "subpfl")
+	ADD_INSITU_TEST("profile_tesac" "tesac")
+	ADD_INSITU_TEST("profile_xbtctd" "xbtctd")
+	ADD_INSITU_TEST("surface_trkob" "trkob")
+endif()

test/soca/testref/bufr2ioda_insitu_profile_bathy_2021063006.ref

@@ -15,6 +15,6 @@ temp hash = c00bbe5d969f8de8232ae22cd0948621e6b3e326e4931cdcfa2f7dd4d2509879
 seqNum: 1751, int32    min, max = 0, 2
 seqNum hash = 7429963169776e1dc0d26732c5053c7e81131cc66654c23aa6393258e9b5b9ae
 PreQC: 1751, int32    min, max = 0, 0
-ObsError_temp: 1751, float32    min, max = 0.0, 0.0
+ObsError_temp: 1751, float32    min, max = 0.23999999463558197, 0.23999999463558197
 OceanBasin: 1751, int32    min, max = 1, 1
 OceanBasin hash = 7de61dfe030e0fabc021c5e1c509cbd2f01afba06ac93959f94c5726d513937f

ush/ioda/bufr2ioda/marine/b2i/bufr2ioda_insitu_profile_bathy.py

@@ -20,8 +20,7 @@
         platform_description)
 
     ioda_vars = BathyIODAVariables()
-    # ??? ioda_vars.SetTemperatureError(0.3)
-    # ??? ioda_vars.SetSalinityError(1.0)
+    ioda_vars.SetTemperatureError(0.24)
     ioda_vars.SetTemperatureVarName("waterTemperature")
 
     bathy = Bufr2ioda_Converter(bufr2ioda_config, ioda_vars, log_file)

ush/ioda/bufr2ioda/marine/b2i/bufr_plot_stations.py

@@ -1,3 +1,10 @@
+# a simple script to plot stations
+# Usage:  python3 bufr_plot_stations.py -i BUFR_FILE_NAME
+# output is produced in the file "stations.png"
+
+# the bufr query strings will not always work;
+# in some cases they need to be changed to CLONH, CLATH
+
 import argparse
 
 from pyiodaconv import bufr
@@ -44,9 +51,6 @@ def plot_points_on_map(latitudes, longitudes, title='Map with Points', marker_co
     plt.savefig(png_file, dpi=300)
 
 
-# bufrfile_path = "/scratch1/NCEPDEV/stmp2/Edward.Givelberg/RUNDIRS/GFSv17-3DVAR-C384mx025/prepoceanobs.114138/xx003"
-
-
 parser = argparse.ArgumentParser()
 parser.add_argument(
     '-i', '--input',