Merge pull request #5 from cchdo/cnv_sn

Skip CNV generation attempt if the hdr temperature/conductivity sensr…r serial number does not match the first serial number of that sensor type in the xmlcon

Author: asdossant

CHANGELOG.md

@@ -1,5 +1,8 @@
 # Changelog
 
+## v2025.09.1 (2025-09-??)
+* Skip CNV generation attempt if the hdr temperature/conductivity sensor serial number does not match the first serial number of that sensor type in the xmlcon.
+
 ## v2025.09.0 (2025-09-02)
 * Added a timeout to the SBEBatch.exe container wine command, this attempts to work around a issue where the wine process would never exit even though work had finished.
   Right now the timeout is 5 minutes and fixed.

src/r2r_ctd/accessors.py

@@ -37,6 +37,8 @@
     check_time_valid,
 )
 from r2r_ctd.derived import (
+    get_con_report_sn,
+    get_hdr_sn,
     get_latitude,
     get_longitude,
     get_time,
@@ -119,15 +121,79 @@ def con_report(self) -> str | None:
         return None
 
     @cached_property
-    def cnv_24hz(self) -> str | None:
-        """Caching wrapper around :py:func:`~r2r_ctd.derived.make_cnvs`
+    def con_temp_sn(self) -> str | None:
+        """Finds the first temperature sensor serial number in the xmlcon"""
+        if self.con_report is None:
+            return None
+        sns = get_con_report_sn(self.con_report, "Temperature")
+        return sns[0]
 
-        Will generate the :py:meth:`cnv_1db` as a side effect if not already done.
-        """
+    @cached_property
+    def hdr_temp_sn(self) -> str | None:
+        """Finds the temperature sensor serial number in the hdr file"""
+        if "hdr" not in self._obj:
+            return None
+        return get_hdr_sn(self._obj.hdr.item(), "Temperature")
+
+    @cached_property
+    def con_cond_sn(self) -> str | None:
+        """Finds the first conductivity sensor serial number in the xmlcon"""
         if self.con_report is None:
             return None
+        sns = get_con_report_sn(self.con_report, "Conductivity")
+        return sns[0]
+
+    @cached_property
+    def hdr_cond_sn(self) -> str | None:
+        """Finds the conductivity sensor serial number in the hdr file"""
+        if "hdr" not in self._obj:
+            return None
+        return get_hdr_sn(self._obj.hdr.item(), "Conductivity")
+
+    @property
+    def can_make_cnv(self) -> bool:
+        """Test if cnv conversion is likely to succeed
+
+        CNV conversion will be skipped if any of the following are true:
+
+        * missing conreport
+        * missing "all three files"
+        * the hdr temperature serial number is not the same as the first temperature SN in the xmlcon
+        * the hdr conductivity serial number is not the same as the first conductivity SN in the xmlcon
+        """
+        if self.con_report is None:
+            logger.error(
+                f"{self.name}: Unable to make cnv file due to missing conreport"
+            )
+            return False
 
         if self.all_three_files is False:
+            logger.error(
+                f"{self.name}: Unable to make cnv file due to missing all three files"
+            )
+            return False
+
+        if self.con_temp_sn != self.hdr_temp_sn:
+            logger.error(
+                f"{self.name}: Unable to make cnv file due to xmlcon vs hdr Temperature SN mismatch: {self.con_temp_sn} vs {self.hdr_temp_sn}"
+            )
+            return False
+
+        if self.con_cond_sn != self.hdr_cond_sn:
+            logger.error(
+                f"{self.name}: Unable to make cnv file due to xmlcon vs hdr Conductivity SN mismatch: {self.con_cond_sn} vs {self.hdr_cond_sn}"
+            )
+            return False
+
+        return True
+
+    @cached_property
+    def cnv_24hz(self) -> str | None:
+        """Caching wrapper around :py:func:`~r2r_ctd.derived.make_cnvs`
+
+        Will generate the :py:meth:`cnv_1db` as a side effect if not already done.
+        """
+        if not self.can_make_cnv:
             return None
 
         cnv_24hz = get_or_write_derived_file(self._obj, "cnv_24hz", make_cnvs)
@@ -142,10 +208,7 @@ def cnv_1db(self) -> str | None:
 
         Will generate the :py:meth:`cnv_24hz` as a side effect if not already done.
         """
-        if self.con_report is None:
-            return None
-
-        if self.all_three_files is False:
+        if not self.can_make_cnv:
             return None
 
         cnv_1db = get_or_write_derived_file(self._obj, "cnv_1db", make_cnvs)

src/r2r_ctd/derived.py

@@ -207,7 +207,7 @@ def _con_report_extract_sensors(con_report: str) -> list[str]:
     return sensors
 
 
-def get_con_report_sn(con_report: str, instrument: str) -> set[str]:
+def get_con_report_sn(con_report: str, instrument: str) -> list[str]:
     """Get the serial numbers for instruments from the configuration report (XMLCON)."""
     title = ""
     sns = []
@@ -228,10 +228,10 @@ def get_con_report_sn(con_report: str, instrument: str) -> set[str]:
         key = key.strip().lower()
         value = value.strip()
 
-        if key == "serial number":
+        if key == "serial number" and value not in sns:
             sns.append(value)
 
-    return set(sns)
+    return sns
 
 
 def get_hdr_sn(hdr: str, instrument: str) -> str | None:

src/r2r_ctd/reporting.py

@@ -12,16 +12,14 @@
 from functools import cached_property
 from importlib.metadata import metadata, version
 from statistics import mean
-from typing import Literal
+from typing import Literal, cast
 
 from lxml.builder import ElementMaker
 from lxml.etree import _Element
 
 import r2r_ctd.accessors  # noqa: F401
 from r2r_ctd.breakout import Breakout
 from r2r_ctd.derived import (
-    get_con_report_sn,
-    get_hdr_sn,
     get_latitude,
     get_longitude,
     get_model,
@@ -529,32 +527,17 @@ def info_casts_with_dock_deck_test_in_file_name(self):
     @cached_property
     def info_casts_with_temp_sensor_sn_problems(self):
         """List of casts where the serial number in the data header does not
-        match any serial numbers in the xmlcon.
+        match the first serial number for a temperature sensor in the xmlcon.
 
-        .. admonition:: WHOI Divergence
-            :class: warning
-
-            There can be more than one temperature sensor and they will have different serial numbers.
-            The datafile would only have one serial number, but the xmlcon will list all the sensors.
-            The original WHOI code would only check one of the serial numbers found in the xmlcon.
-
-            I'm not sure the exact cause, but there are a lot of false problems in the breakouts I was given
-            to test with, for example: 156405 reports that all the casts have SN problems, but a manual examination
-            and this code, show that there are no mismatches.
-
-            This code checks the serial number in the header file against all the serial numbers in the xmlcon of the
-            same instrument type (e.g. all temperature sensor serial numbers)
+        The seabird software throws an error if the above is not the case, this will prevent the creation of a cnv product
+        even if the serial number is in the secondary channel.
         """
         problem_casts = []
-        for station in self.breakout.stations_hex_paths:
-            data = self.breakout[station]
-            con_report = data.r2r.con_report
-            if con_report is None:
-                continue
-            models = get_con_report_sn(con_report, "Temperature")
-            sn = get_hdr_sn(data.hdr.item(), "Temperature")
-            if sn not in models:
-                problem_casts.append(station.stem)
+        for station in self.breakout:
+            con_sn = station.r2r.con_temp_sn
+            hdr_sn = station.r2r.hdr_temp_sn
+            if con_sn != hdr_sn or None in (con_sn, hdr_sn):
+                problem_casts.append(cast(str, station.r2r.name))
         return Info(
             " ".join(problem_casts),
             name="Casts with temp. sensor serial number problem",
@@ -564,23 +547,17 @@ def info_casts_with_temp_sensor_sn_problems(self):
     @cached_property
     def info_casts_with_cond_sensor_sn_problems(self):
         """List of casts where the serial number in the data header does not
-        match any serial numbers in the xmlcon.
-
-        .. admonition:: WHOI Divergence
-            :class: warning
+        match the first Conductivity sensor serial numbers in the xmlcon.
 
-            See the info_casts_with_temp_sensor_sn_problems divergence note
+        The seabird software throws an error if the above is not the case, this will prevent the creation of a cnv product
+        even if the serial number is in the secondary channel.
         """
         problem_casts = []
-        for station in self.breakout.stations_hex_paths:
-            data = self.breakout[station]
-            con_report = data.r2r.con_report
-            if con_report is None:
-                continue
-            models = get_con_report_sn(con_report, "Conductivity")
-            sn = get_hdr_sn(data.hdr.item(), "Conductivity")
-            if sn not in models:
-                problem_casts.append(station.stem)
+        for station in self.breakout:
+            con_sn = station.r2r.con_cond_sn
+            hdr_sn = station.r2r.hdr_cond_sn
+            if con_sn != hdr_sn or None in (con_sn, hdr_sn):
+                problem_casts.append(cast(str, station.r2r.name))
         return Info(
             " ".join(problem_casts),
             name="Casts with cond. sensor serial number problem",