Save log reading options

Save the log file checkbox and option to add mass-positions to SOH messages in log file.

#94 (closed)

sohstationviewer/model/reftek_data/reftek_reader/log_file_reader.py

@@ -12,6 +12,14 @@ RT130_PACKETS = ['SH', 'SC', 'OM', 'DS', 'AD', 'CD', 'FD', 'EH', 'ET']
 SeparatedPacketLines = Tuple[List[str], List[str], List[str]]
 
 
+class LogReadError(ValueError):
+    """
+    Error to raise when there is a problem when reading a log file.
+    """
+    def __init__(self, message: str):
+        self.message = message
+
+
 def detect_log_packet_format(packet: List[str]) -> Optional[LogFileFormat]:
     """
     Detect the format of a log file packet. The format can be either rt2ms',
@@ -197,6 +205,33 @@ PACKET_PARSERS: Dict[Optional[LogFileFormat], Parser] = {
 }
 
 
+def validate_soh_lines(soh_lines: List[str]):
+    """
+    Validate a list of SOH lines by examining its header.
+    :param soh_lines: a list of SOH lines
+    :return: whether soh_lines is valid
+    """
+    valid_packet_types = {
+        'Auxiliary Data Parameter',
+        'Calibration Definition',
+        'Data Stream Definition',
+        'Filter Description',
+        'Operating Mode Definition',
+        'Station Channel Definition',
+        'State of Health',
+    }
+    if not any(soh_lines[0].startswith(packet_type)
+               for packet_type in valid_packet_types):
+        return False
+    splitted_header = soh_lines[0].split()
+    if not (len(splitted_header[-1]) == 4 and splitted_header[-1].isalnum()):
+        return False
+    if splitted_header[-2] != 'ST:':
+        return False
+
+    return True
+
+
 def get_experiment_number(soh_lines: List[str]):
     """
     Get the experiment number from the list of SOH lines in a packet.
@@ -253,12 +288,11 @@ class LogFileReader:
             parser = PACKET_PARSERS[self.log_file_type]
             eh_et_lines, soh_lines, masspos_lines = parser(packet)
             if self.station_code is None and soh_lines:
-                split_packet_header = soh_lines[0].strip().split(' ')
-                possible_programs = ['logpeek:', 'SOHStationViewer:', 'rt2ms:']
-                # We want to skip the file header, which contains the program
-                # used to generate the file.
-                if split_packet_header[0] not in possible_programs:
-                    self.station_code = split_packet_header[-1]
+                if validate_soh_lines(soh_lines):
+                    self.station_code = soh_lines[0].split()[-1]
+            if self.station_code is None and eh_et_lines:
+                # Each event info line stores the station code as second word
+                self.station_code = eh_et_lines[0].split()[1]
             if self.experiment_number is None and soh_lines:
                 found_experiment_number = get_experiment_number(soh_lines)
                 self.experiment_number = found_experiment_number
@@ -269,6 +303,16 @@ class LogFileReader:
             # separate the SOH lines blocks during processing.
             self.soh_lines.append('\n')
             self.masspos_lines.extend(masspos_lines)
+        # In cases where there is no SOH data, we are going to assume that the
+        # experiment number is 0.
+        if self.experiment_number is None:
+            self.experiment_number = '0'
+        if self.station_code is None:
+            msg = (f'The log file {self.file_path.name} does not contain a '
+                   f'station code. Please make sure it is a valid RT130 log '
+                   f'file. RT130 log files can be generated with rt2ms, '
+                   f'logpeek, or this program.')
+            raise LogReadError(msg)
 
 
 def process_mass_poss_line(masspos_lines: List[str]