add file_extractor.py

update test_config
reorganize folders

.vstags

+!_TAG_FILE_FORMAT	2	/extended format; --format=1 will not append ;" to lines/
+!_TAG_FILE_SORTED	1	/0=unsorted, 1=sorted, 2=foldcase/
+!_TAG_PROGRAM_AUTHOR	Darren Hiebert	/dhiebert@users.sourceforge.net/
+!_TAG_PROGRAM_NAME	Exuberant Ctags	//
+!_TAG_PROGRAM_URL	http://ctags.sourceforge.net	/official site/
+!_TAG_PROGRAM_VERSION	5.8	//
+display_version	.\btl-all.pl	107;"	s
+entete_odv	.\btl-all.pl	282;"	s
+get_options	.\btl-all.pl	131;"	s
+position	.\btl-all.pl	259;"	s
+read_config	.\btl-all.pl	161;"	s
+read_config_string	.\btl-all.pl	148;"	s
+usage	.\btl-all.pl	115;"	s
+usage	.\sta-fr22.pl	35;"	s
+write_xml_header	.\btl-all.pl	211;"	s

Readme-python.txt

@@ -486,5 +486,24 @@ Developpement:
 
 Tests avec unittest:
 --------------------
+Voir: https://docs.python.org/3.7/library/unittest.html?highlight=unittest
+
 Les fichiers de tests sont sous tests
-> python -m unittest -v tests/test_roscop.py
+Run test in single file
+> python - m unittest - v tests/test_roscop.py
+
+Run all test_ * in dir tests:
+> python - m unittest  discover tests - v
+> python - m unittest  discover - s tests - p 'test_*.py' - v
+
+Methods name:
+assertEqual() 	
+assertNotEqual() 
+assertTrue() 	
+assertFalse() 	
+assertRaises() 	
+assertAlmostEqual() 	
+assertNotAlmostEqual() 	
+assertRegex() 	  	
+assertNotRegex() 	
+assertRaisesRegex()
\ No newline at end of file

__init__.py

 __version__ = '0.10.0'
 
-from physicalParameter import Roscop
+#from physicalParameter import Roscop

config.py

@@ -2,18 +2,34 @@ import toml
 
 # some examples:
 # https://www.programcreek.com/python/example/93872/toml.load
-cfg = toml.load('cruise.toml')
+cfg = toml.load('tests/test.toml')
 
 print(cfg['global']['author'])
 
+d = cfg['global']
+print(d, end='\n')
+
+d = cfg['cruise']
+print(d, end='\n')
+
+d = cfg['ctd']
+print(d, end='\n')
+
 for key in cfg['cruise'].keys():
     print(cfg['cruise'][key])
-    print(cfg['cruise'].get(key))
-
-ctd = cfg['ctd']
-s = ctd['split']
-for key in s.keys():
-    print("{}: {}".format(key, s[key]))
-s = ctd['splitAll']
-for key in s.keys():
-    print("{}: {}".format(key, s[key]))
+    # print(cfg['cruise'].get(key))
+
+d = cfg['split']['ctd']
+print(d, end='\n')
+for key in d.keys():
+    print("{}: {}".format(key, d[key]))
+
+d = cfg['split']['ctdAll']
+print(d, end='\n')
+for key in d.keys():
+    print("{}: {}".format(key, d[key]))
+
+d = cfg['split']['btl']
+print(d, end='\n')
+for key in d.keys():
+    print("{}: {}".format(key, d[key]))

file_extractor.py

+'''
+file_extractor.py
+'''
+import fileinput
+
+
+class FileExtractor:
+
+    '''
+    This class read an ASCII file, extract physical parameter with ROSCOP codification from the given column
+    '''
+
+    # constructor with values by default
+    def __init__(self, file):
+        # attibutes
+        # public:
+        self.file = file
+        # private:
+        self.__hash = {}
+        # constructor build objet by reading the file
+        self.read()
+
+    # overloading operators
+    def __str__(self):
+        ''' overload string representation '''
+        return 'Class FileExtractor, file: %s, size = %d' % (self.file, len(self))
+
+   # read code roscop file
+    def read(self):
+        for line in fileinput.input(
+                self.file, openhook=fileinput.hook_encoded("ISO-8859-1")):
+
+            # iterate over the lines of opened file "fileName"
+            # ------------------------------------------------
+            print(line)
+
+
+# for testing in standalone context
+# ---------------------------------
+if __name__ == "__main__":
+    fe = FileExtractor('data/cnv/fr29001.cnv')
+    fe.read()

cruise.toml → tests/test.toml

@@ -16,7 +16,6 @@ creator        = "Jacques.Grelet@ird.fr"
 
 [ctd]
 cruisePrefix   = "fr29"
-# profile name : fr29xxx
 station = 'Station\s*:\s*\D*(\d*)'
 stationPrefixLength  = 3
 titleSummary  = "CTD profiles processed during PIRATA-FR29 cruise"
@@ -32,47 +31,78 @@ bottomDepth = 'Bottom Depth\s*:\s*(\d*\.?\d+?)\s*\S*'
 operator = 'Operator\s*:\s*(.*)'
 type = 'Type\s*:\s*(.*)'
 
-split.ETDD = 2
-split.PRES = 3
-split.DEPTH = 4
-split.TEMP = 5
-split.PSAL = 18
-split.DENS = 20
-split.SVEL = 22
-split.DOX2 = 16
-split.FLU2 = 14
-split.FLU3 = 15
-split.TUR3 = 13
-split.NAVG = 24
 
-splitAll.ETDD = 2
-splitAll.PRES = 3
-splitAll.DEPH = 4
-splitAll.TE01 = 5
-splitAll.TE02 = 6
-splitAll.CND1 = 7
-splitAll.CND2 = 8
-splitAll.DOV1 = 9
-splitAll.DOV2 = 10
-splitAll.DVT1 = 11
-splitAll.DVT2 = 12
-splitAll.TUR3 = 13
-splitAll.FLU2 = 14
-splitAll.FLU3 = 15
-splitAll.DO12 = 16
-splitAll.DO22 = 17
-splitAll.PSA1 = 18
-splitAll.PSA2 = 19
-splitAll.DEN1 = 20
-splitAll.DEN2 = 21
-splitAll.SVEL = 22
-splitAll.NAVG = 24
 
 [btl]
 typeInstrument           = "SBE32 standard 24 Niskin bottles"
-instrumentNumber             = "unknown"
+instrumentNumber         = "unknown"
 titleSummary   = "Water sample during PIRATA-FR29 cruise with 20 levels"
 comment        = "CTD bottles water sampling with temperature, salinity and oxygen from primary and secondary sensors"
-split = ' BOTL,1,month,2,day,3,year,4,PSA1,5,PSA2,6,DO11,7,DO12,8,DO21,9,DO22,10,Potemp090C,11,Potemp190C,12,ETDD,13,PRES,14,DEPH,15,TE01,16,TE02,17,CND1,18,CND2,19,DOV1,20,DOV2,21,DVT1,22,DVT2,23,TUR3,24,FLU2,25'
 
+[split]
+	[split.ctd]
+	ETDD = 2
+	PRES = 3
+	DEPTH = 4
+	TEMP = 5
+	PSAL = 18
+	DENS = 20
+	SVEL = 22
+	DOX2 = 16
+	FLU2 = 14
+	FLU3 = 15
+	TUR3 = 13
+	NAVG = 24
 
+	[split.ctdAll]
+	ETDD = 2
+	PRES = 3
+	DEPTH = 4
+	TE01 = 5
+	TE02 = 6
+	CND1 = 7
+	CND2 = 8
+	DOV1 = 9
+	DOV2 = 10
+	DVT1 = 11
+	DVT2 = 12
+	TUR3 = 13
+	FLU2 = 14
+	FLU3 = 15
+	DO12 = 16
+	DO22 = 17
+	PSA1 = 18
+	PSA2 = 19
+	DEN1 = 20
+	DEN2 = 21
+	SVEL = 22
+	NAVG = 24
+
+	[split.btl]
+	BOTL = 1
+	month = 2
+	day = 3
+	year = 4
+	PSA1 = 5
+	PSA2 = 6
+	DO11 = 7
+	DO12 = 8
+	DO21 = 9
+	DO22 = 10
+	Potemp090C = 11
+	Potemp190C = 12
+	ETDD = 13
+	PRES = 14
+	DEPH = 15
+	TE01 = 16
+	TE02 = 17
+	CND1 = 18
+	CND2 = 19
+	DOV1 = 20
+	DOV2 = 21
+	DVT1 = 22
+	DVT2 = 23
+	TUR3 = 24
+	FLU2 = 25
+	
+	

tests/test_config.py

+import unittest
+import toml
+
+'''
+Run all test_* in dir test:
+> python -m unittest  discover tests -v
+> python -m unittest  discover -s tests -p 'test_*.py' -v
+'''
+
+
+class testConfig(unittest.TestCase):
+
+    def setUp(self):
+        """Initialisation des tests."""
+        self.cfg = toml.load('tests/test.toml')
+        self.glob = {'author': 'jgrelet IRD March 2019 PIRATA-FR29 cruise',
+                     'debug': False, 'echo': True}
+        self.cruise = {'cycleMesure': 'PIRATA-FR29', 'plateforme': 'THALASSA', 'callsign': 'FNFP', 'institute': 'IRD',
+                       'timezone': 'GMT', 'beginDate': '01/03/2019', 'endDate': '04/04/2019', 'pi': 'BOURLES',
+                       'creator': 'Jacques.Grelet@ird.fr'}
+        self.ctd = {'cruisePrefix': 'fr29', 'station': 'Station\\s*:\\s*\\D*(\\d*)', 'stationPrefixLength': 3,
+                    'titleSummary': 'CTD profiles processed during PIRATA-FR29 cruise', 'typeInstrument': 'SBE911+',
+                    'instrumentNumber': '09P1263', 'isHeader': '^[*#]', 'isDevice': ['^\\*\\s+(Sea-Bird)', '(\\*END\\*)'],
+                    'latitude': ['Latitude\\s*:\\s*(\\d+)\\s+(\\d+.\\d+)\\s+(\\w)', 'NMEA Latitude\\s*=\\s*(\\d+\\s+\\d+.\\d+\\s+\\w)'],
+                    'longitude': ['Longitude\\s*:\\s*(\\d+)\\s+(\\d+.\\d+)\\s+(\\w)', 'NMEA Longitude\\s*=\\s*(\\d+\\s+\\d+.\\d+\\s+\\w)'],
+                    'date': 'Date\\s*:\\s*(\\d+)/(\\d+)/(\\d+)', 'hour': '[Heure|Hour]\\s*:\\s*(\\d+)[:hH](\\d+):(\\d+)',
+                    'bottomDepth': 'Bottom Depth\\s*:\\s*(\\d*\\.?\\d+?)\\s*\\S*', 'operator': 'Operator\\s*:\\s*(.*)',
+                    'type': 'Type\\s*:\\s*(.*)'}
+        self.splitCtd = {'ETDD': 2, 'PRES': 3, 'DEPTH': 4, 'TEMP': 5, 'PSAL': 18,
+                         'DENS': 20, 'SVEL': 22, 'DOX2': 16, 'FLU2': 14, 'FLU3': 15, 'TUR3': 13, 'NAVG': 24}
+        self.splitCtdAll = {'ETDD': 2, 'PRES': 3, 'DEPTH': 4, 'TE01': 5, 'TE02': 6, 'CND1': 7, 'CND2': 8, 'DOV1': 9, 'DOV2': 10, 'DVT1': 11, 'DVT2': 12,
+                            'TUR3': 13, 'FLU2': 14, 'FLU3': 15, 'DO12': 16, 'DO22': 17, 'PSA1': 18, 'PSA2': 19, 'DEN1': 20, 'DEN2': 21, 'SVEL': 22, 'NAVG': 24}
+        self.splitBtl = {'BOTL': 1, 'month': 2, 'day': 3, 'year': 4, 'PSA1': 5, 'PSA2': 6, 'DO11': 7,
+                         'DO12': 8, 'DO21': 9, 'DO22': 10, 'Potemp090C': 11, 'Potemp190C': 12,
+                         'ETDD': 13, 'PRES': 14, 'DEPH': 15, 'TE01': 16, 'TE02': 17, 'CND1': 18, 'CND2': 19,
+                         'DOV1': 20, 'DOV2': 21, 'DVT1': 22, 'DVT2': 23, 'TUR3': 24, 'FLU2': 25}
+
+    def test_global(self):
+        ''' test block [GLOBAL]'''
+        d = self.cfg['global']
+        for k in d.keys():
+            self.assertEqual(d[k], self.glob[k])
+
+    def test_cruise(self):
+        ''' test block [CRUISE]'''
+        d = self.cfg['cruise']
+        for k in d.keys():
+            self.assertEqual(d[k], self.cruise[k])
+
+    def test_ctd(self):
+        ''' test block [CTD]'''
+        d = self.cfg['ctd']
+        for k in d.keys():
+            self.assertEqual(d[k], self.ctd[k])
+
+    def test_split_ctd(self):
+        """ Test if all value  in block [SPLIT.CTD] are correct """
+        d = self.cfg['split']['ctd']
+        for k in d.keys():
+            self.assertEqual(d[k], self.splitCtd[k])
+
+    def test_split_ctdAll(self):
+        """ Test if all value  in block [SPLIT.CTDALL] are correct """
+        d = self.cfg['split']['ctdAll']
+        for k in d.keys():
+            self.assertEqual(d[k], self.splitCtdAll[k])
+
+    def test_split_btl(self):
+        """ Test if all value  in block [SPLIT.BTL] are correct """
+        d = self.cfg['split']['btl']
+        for k in d.keys():
+            self.assertEqual(d[k], self.splitBtl[k])
+
+
+if __name__ == '__main__':
+    unittest.main()

tests/test_roscop.py

@@ -3,14 +3,19 @@ import unittest
 from physicalParameter import Roscop
 
 '''
-> python -m unittest -v tests/test_roscop.py
+Run test in single file
+> python - m unittest - v tests/test_roscop.py
+
+Run all test_ * in dir tests:
+> python - m unittest  discover tests - v
+> python - m unittest  discover - s tests - p 'test_*.py' - v
 '''
 
 
-class RoscopTest(unittest.TestCase):
+class testRoscop(unittest.TestCase):
 
     def setUp(self):
-        """Initialisation des tests."""
+        """ Test initialisation """
 
         self.file = 'code_roscop.csv'
         self.r = Roscop(self.file)