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BUGFIX #56, a new case with extra descriptors & spaces

A new CNV sample file that contains extra descriptors after file_type,
and extra spaces in the end of some lines.

Thanks to @aer205 for proving the cnv sample file.
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castelao committed Sep 1, 2019
1 parent a1f5985 commit ed01688391a1580bac5e54546e36e2c94cea79cc
Showing with 139 additions and 1 deletion.
  1. +2 −1 AUTHORS.rst
  2. +113 −0 aer205.cnv
  3. +24 −0 seabird/rules/cnv4.json
@@ -21,4 +21,5 @@ Contributors
Reported bad path on seabird_dir() for windows machines.
* Mathew Biddle; Reported bug #53 on skipping first line if without header.
* @atorr018; Reported bug #51 on failing to parse due to a empty lines.
* @shaunwbell; Reported bug #55 on typos in cnv rules reference names.
* @shaunwbell; Fixed bug #55 on typos in cnv rules reference names.
* @aer205; Bug #56, provided sample with extra descriptors after file_type.
@@ -0,0 +1,113 @@
* Sea-Bird SBE 9 Data File:
* FileName = C:\LSSL2004-16\ctd_data\200416_001.dat
* Software Version Seasave Win32 V 5.28c
* Temperature SN = 4322
* Conductivity SN = 2809
* Number of Bytes Per Scan = 37
* Number of Voltage Words = 4
* Number of Scans Averaged by the Deck Unit = 1
* System UpLoad Time = Jul 25 2004 07:53:21
* NMEA Latitude = 74 06.98 N
* NMEA Longitude = 089 39.71 W
* NMEA UTC (Time) = Jul 25 2004 14:55:24
* Store Lat/Lon Data = Append to Every Scan
** Ship: CCGS "Louis S. St-Laurent" first
** Cruise: 2004-16
** Station:
** Depth:
# nquan = 14
# nvalues = 3
# units = specified
# name 0 = prDM: Pressure, Digiquartz [db]
# name 1 = t090C: Temperature [ITS-90, deg C]
# name 2 = c0mS/cm: Conductivity [mS/cm]
# name 3 = sbeox0V: Oxygen Voltage, SBE 43
# name 4 = xmiss: Beam Transmission, Chelsea/Seatech/Wetlab CStar [%]
# name 5 = flSP: Fluorescence, Seapoint
# name 6 = altM: Altimeter [m]
# name 7 = sbeox0ML/L: Oxygen, SBE 43 [ml/l]
# name 8 = sbeox0Mm/Kg: Oxygen, SBE 43 [umol/Kg]
# name 9 = sal00: Salinity [PSU]
# name 10 = nbin: Scans Per Bin
# name 11 = potemp090C: Potential Temperature [ITS-90, deg C]
# name 12 = sigma-�00: Density [sigma-theta, Kg/m^3]
# name 13 = flag:
# span 0 = 1.000, 226.000
# span 1 = -1.6787, 1.8923
# span 2 = 25.490845, 27.892963
# span 3 = 2.3272, 3.9163
# span 4 = 67.4294, 89.1811
# span 5 = 2.5525e-02, 4.9016e+00
# span 6 = 0.00, 0.00
# span 7 = 5.88635, 10.71717
# span 8 = 255.930, 466.859
# span 9 = 30.9701, 33.8188
# span 10 = 44, 373
# span 11 = -1.6805, 1.8922
# span 12 = 24.7516, 27.1732
# span 13 = 0.0000e+00, 0.0000e+00
# interval = decibars: 1
# start_time = Jul 25 2004 07:53:21
# bad_flag = -9.990e-29
# sensor 0 = Frequency 0 temperature, primary, 4322, 25-May-04
# sensor 1 = Frequency 1 conductivity, primary, 2809, 25-May-04, cpcor = -9.5700e-08
# sensor 2 = Frequency 2 pressure, 90559, 10/29/02
# sensor 3 = Frequency 3 temperature, secondary, 4239, 25-May-04
# sensor 4 = Frequency 4 conductivity, secondary, 2810, 25-May-04, cpcor = -9.5700e-08
# sensor 5 = Extrnl Volt 0 Fluorometer, Seapoint, primary
# sensor 6 = Extrnl Volt 2 transmissometer, primary, CST-662DR, 20-Mar-2003
# sensor 7 = Extrnl Volt 4 altimeter
# sensor 8 = Extrnl Volt 6 Oxygen, SBE, primary, 0435, 18-Mar-2003, s+v 24jul05
# datcnv_date = Jul 25 2005 15:07:36, 5.32a
# datcnv_in = c:\workdesk\200416_001.dat c:\workdesk\200416-oxycal.CON
# datcnv_skipover = 8750
# alignctd_date = Jul 25 2005 15:07:38, 5.32a
# alignctd_in = c:\workdesk\200416_001-d.cnv
# alignctd_adv = sbeox0V 6.000, xmiss 0.100
# wildedit_date = Jul 25 2005 15:07:41, 5.32a
# wildedit_in = c:\workdesk\200416_001-d-a.cnv
# wildedit_pass1_nstd = 10.0
# wildedit_pass2_nstd = 20.0
# wildedit_pass2_mindelta = 0.000e+000
# wildedit_npoint = 100
# wildedit_vars = prDM t090C t190C c0mS/cm c1mS/cm sbeox0V xmiss flSP altM
# wildedit_excl_bad_scans = yes
# celltm_date = Jul 25 2005 15:07:44, 5.32a
# celltm_in = c:\workdesk\200416_001-d-a-w.cnv
# celltm_alpha = 0.0300, 0.0300
# celltm_tau = 7.0000, 7.0000
# celltm_temp_sensor_use_for_cond = primary, secondary
# filter_date = Jul 25 2005 15:07:47, 5.32a
# filter_in = c:\workdesk\200416_001-d-a-w-c.cnv
# filter_low_pass_tc_A = 0.030
# filter_low_pass_tc_B = 0.150
# filter_low_pass_A_vars = c0mS/cm c1mS/cm
# filter_low_pass_B_vars = prDM
# loopedit_date = Jul 25 2005 15:07:53, 5.32a
# loopedit_in = c:\workdesk\200416_001-d-a-w-c-f.cnv
# loopedit_minVelocity = 0.000
# loopedit_excl_bad_scans = yes
# Derive_date = Jul 25 2005 15:07:57, 5.32a
# Derive_in = c:\workdesk\200416_001-d-a-w-c-f-l.cnv c:\workdesk\200416-oxycal.CON
# derive_time_window_docdt = seconds: 1
# binavg_date = Jul 25 2005 15:08:01, 5.32a
# binavg_in = c:\workdesk\200416_001-d-a-w-c-f-l-d.cnv
# binavg_bintype = decibars
# binavg_binsize = 1
# binavg_excl_bad_scans = yes
# binavg_skipover = 0
# binavg_surface_bin = no, min = 0.000, max = 0.000, value = 0.000
# Derive_date = Jul 25 2005 15:08:04, 5.32a
# Derive_in = c:\workdesk\200416_001-d-a-w-c-f-l-d-b.cnv c:\workdesk\200416-oxycal.CON
# split_date = Jul 25 2005 15:08:04, 5.32a
# split_in = c:\workdesk\200416_001-d-a-w-c-f-l-d-b-d.cnv
# split_excl_bad_scans = yes
# strip_date = Jul 26 2005 20:01:02, 5.32a
# strip_in = C:\workdesk\down\d200416_001-d-a-w-c-f-l-d-b-d.cnv
# file_type = ascii
# Flag_columns = Temperature, Conductivity, Oxygen Voltage
# Flag_code = 2 is good, 6 is interpolated; Added by IOS 27Jul05
*END*
1.00 1.7970 27.4231 3.635 82.076 0.315 0.00 9.39 409.22 31.0125 76 24.7918 1.7970 222
2.00 1.8923 27.4689 3.615 81.839 0.317 0.00 9.31 405.80 30.9753 76 24.7557 1.8922 222
3.00 1.8911 27.4635 3.593 81.951 0.270 0.00 9.25 403.10 30.9692 60 24.7510 1.8910 222
@@ -0,0 +1,24 @@
{
"header": "(?P<intro>\n \\*\\ Sea-Bird\\ SBE\\ ?.*\\ Data\\ File:\\s*\\n\n (\n \\*(?:\\ .*)?\\n # Anything starting with *\n )+\n)\n(?P<notes>\n (\n \\*\\* .*\\n # Anything starting with *\n )*\n)\n# temporary solution just to run while I'm sailing\n# The notes not necessarily are after the intro, they\n# can be in the middle of the intro.\n (\n \\*\\ .*\\n # Anything starting with *\n )*\n\\s*\n(?P<descriptors>\n (\n \\#.*\\n # Anything\n )+\n\\#\\ file_type\\ =\\ ascii\\s*\\n\n (\n \\#.*\\n # Anything\n )+\n)\n",
"sep": "\\*END\\*\\s*\\n\n",
"data": "(?P<data>\n (?:\n (?: # Start of one variable\n \\ *\n -? # Can be a negative number\n \\d+ # Any digits\n (?:\n \\.\\d+ # Real numbers\n (?:\n e[\\+|-]\\d+ # Cientific notation\n )?\n )?\n )+ # Repeat as much variables as there are\n # (?:\n # )?\n \\s* # Following empty spaces, end of line\n )+ # One or more lines\n)\n",
"intro": {
"sbe_model": "\\*\\ Sea-Bird\\ SBE\\ *(?P<value>\\d.*?)\\ +Data\\ File:\\r?\\n",
"LATITUDE": "\\*\\ NMEA\\ Latitude\\ =\\ (?P<value>.*?)\\r?\\n\n",
"LONGITUDE": "\\*\\ NMEA\\ Longitude\\ =\\ (?P<value>.*?)\\r?\\n\n",
"gps_datetime": "\\*\\ NMEA\\ UTC\\ \\(Time\\)\\ =\\ (?P<value>.*?)\\r?\\n\n",
"seasave": "\\*\\ Software\\ Version\\ Seasave\\ (?P<value>.*?)\\r?\\n\n"
},
"descriptors": {
"nquan": "\\#\\ nquan\\ =\\ (?P<value>\\d+)\n",
"nvalues": "\\#\\ nvalues\\ =\\ (?P<value>\\d+)\n",
"start_time": "\\#\\ start_time\\ =\\ (?P<value>.*?)\\r?\\n # Should work, but I'm not happy with this.\n",
"bad_flag": "\\#\\ bad_flag\\ =\\ (?P<value>.*?)\\s\n",
"file_type": "\\#\\ file_type\\ \\=\\ (?P<value>.*?)\\r?\\n\n",
"awkward_xml": "(?P<value>\n \\#\\ \\<\\?xml\\ version=\"\\d+\\.\\d+\"\\ encoding=\"UTF-8\"\\?>\\r?\\n\n (?:\\#\\s+<.*>\\r?\\n)+\n)\n"
},
"fieldname": "\\#\\ name\\ (?P<id>\\d+)\\ =\\ (?P<name>.*)\\:(?:\\ (?P<longname>.*))?\\r?\\s\n",
"fieldspan": "\\#\\ span\\ (?P<id>\\d+)\\ =\\ (?P<valuemin>.*),\\ (?P<valuemax>.*)\\r?\\s\n",
"LATITUDE": "# [LAT|LATITUDE]\n (?:Latitude:?)?\n \\ *\n(?P<degree>\\d{1,2})\n\\ +\n(?P<minute>\\d{1,2}\n [\\.|\\,]\n \\d{1,3})\n\\ *\n(?P<hemisphere>[N|n|S|s])\n",
"LONGITUDE": "# [LON|LONG|LONGITUDE]\n (?:Latitude:?)?\n \\ *\n(?P<degree>\\d{1,3})\n\\ +\n(?P<minute>\\d{1,2}\n [\\.|\\,]\n \\d{1,3})\n\\ *\n(?P<hemisphere>[W|w|E|e])\n"
}

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