Removed deprecated source files previously used for tests
This commit is contained in:
Celine Mercier
@ -1,51 +0,0 @@
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import sys
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import argparse
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from obitools3.obidms._obidms import OBIDMS
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(description='Pseudo obigrep.')
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parser.add_argument('-V', '--view', dest='view', type=str,
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help='Name of the view that should be considered')
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parser.add_argument('-N', '--new_view', dest='new_view', type=str,
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help='Name of the new view that should be created')
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# parser.add_argument('-k', '--key', dest='key', type=str,
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# help='Name of the key that should be considered')
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#
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# parser.add_argument('-c', '--comp', dest='comparison', type=int,
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# help='Comparison to be made: -1:< ; 0:== ; 1:>')
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#
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# parser.add_argument('-v', '--value', dest='value', type=object,
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# help='Value to be compared')
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args = parser.parse_args()
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d = OBIDMS('tdms')
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#condition = 1
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line_selec = []
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v = d.open_view(args.view)
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i = 0
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for l in v :
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if l['score'] > 350 :
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line_selec.append(i)
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i+=1
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new_v = d.new_view(args.new_view, view_to_clone=v, line_selection=line_selec, view_type="NUC_SEQS_VIEW", comments="obigrep "+args.view+" to "+args.new_view) #args.key+" "+str(args.comparison)+" "+str(args.value)+" "+)
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print("\n")
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print(new_v.__repr__())
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v.save_and_close()
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new_v.save_and_close()
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d.close()
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print("\nDone.")
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@ -1,43 +0,0 @@
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import sys
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import argparse
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from obitools3.obidms._obidms import OBIDMS
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(description='Pseudo obihead.')
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parser.add_argument('-V', '--view', dest='view', type=str,
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help='Name of the view that should be considered')
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parser.add_argument('-N', '--new_view', dest='new_view', type=str,
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help='Name of the new view that should be created')
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parser.add_argument('-n', '--nb', dest='nb_lines', type=int,
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help='Number of lines that should be taken')
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args = parser.parse_args()
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d = OBIDMS('tdms')
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#condition = 1
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line_selec = []
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v = d.open_view(args.view)
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for i in range(0, args.nb_lines) :
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line_selec.append(i)
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new_v = d.new_view(args.new_view, view_to_clone=v, line_selection=line_selec, view_type="NUC_SEQS_VIEW", comments="obihead "+str(args.nb_lines)+", "+args.view+" to "+args.new_view) #args.key+" "+str(args.comparison)+" "+str(args.value)+" "+)
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print("\n")
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print(new_v.__repr__())
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v.save_and_close()
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new_v.save_and_close()
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d.close()
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print("\nDone.")
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@ -1,199 +0,0 @@
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import sys
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import argparse
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import time
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from obitools3.obidms._obidms import OBIDMS
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def bufferedRead(fileobj,size=209715200): ## 200 MB
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buffer = fileobj.readlines(size)
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while buffer:
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for l in buffer:
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yield l
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buffer = fileobj.readlines(size)
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(description='Convert a fasta file in an OBIDMS.')
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parser.add_argument('-i', '--input', dest='input_file', type=str,
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help='Name of the file containing the sequences')
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args = parser.parse_args()
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d = OBIDMS('tdms')
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view = d.new_view('uniq view', view_type="NUC_SEQS_VIEW")
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# for i in range(35000000) :
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# if (not (i%500000)) :
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# print(str(time.time())+'\t'+str(i))
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# id = "@HWI-D00405:142:C71BAANXX:4:1101:1234:2234_CONS_SUB_SUB_"+str(i)
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# view[i].set_id(id)
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# if id != view[i]["ID"] :
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# print("nope", id, view[i]["ID"])
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input_file = open(args.input_file, 'r')
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input_file_buffered = bufferedRead(input_file)
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#
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# if args.input_file[-1:] == "a" :
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#
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# i = 0
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# next = False
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# first = True
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#
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# for line in input_file :
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#
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# if line[0] == ">" :
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#
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# if not first :
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# # save seq
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# #print(i, id, seq)
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# view[i].set_sequence(seq)
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# i+=1
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#
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# first = False
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#
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# #id = line.split(" ", 1)[0][1:]
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# #rest = (line[:-1].split(" ", 1)[1]).split(";")
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# #view[i].set_id(id)
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#
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# # description = ""
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# # for j in range(len(rest)) :
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# # if "=" in rest[j] :
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# # rest[j] = rest[j].strip()
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# # rest[j] = rest[j].split("=", 1)
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# # column_name = rest[j][0]
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# # v = rest[j][1]
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# # if ((not v.isalpha()) and (v.isalnum())) :
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# # conv_v = int(v)
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# # elif (v == "True") or (v == "False") :
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# # conv_v = bool(v)
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# # else :
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# # f = True
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# # for letter in v :
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# # if ((not letter.isalnum()) or (letter != ".")) :
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# # f = False
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# # if f :
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# # conv_v = float(v)
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# # else :
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# # conv_v = v
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# # view[i][column_name] = conv_v
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# # else :
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# # description+=rest[j]
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# #
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# # if description != "" :
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# # description = description.strip()
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# # view[i].set_description(description)
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#
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# #print(id)
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# #print(rest)
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# #print(description)
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#
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# next = True
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#
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# elif next == True :
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#
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# # if not (i % 1E5) :
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# # print(i)
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#
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# seq = line[:-1]
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# next = False
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#
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# elif not next :
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#
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# seq += line[:-1]
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#
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#
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# elif args.input_file[-1:] == "q" :
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#
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# i = 0
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# l = 0
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# next = False
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#
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l=0
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i=0
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# while (True):
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# l+=1
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# line = input_file.readline()
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# if line=="":
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# break
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for line in input_file_buffered :
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#
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#if i > 1E7 :
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# # print('hmm?')
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#
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# if i == 6000000 :
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# break
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#
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if l%4 == 0 :
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#
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if (not (i%500000)) :
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print(str(time.time())+'\t'+str(i))
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# #
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# # #print("header", line)
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# #
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id = line.split(" ", 1)[0][1:]
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# print(id)
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# # #rest = (line[:-1].split(" ", 1)[1]).split(";")
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view[i].set_id(id)
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# print(view[i]["ID"])
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#
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# i+=1
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# l+=1
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#
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# # description = ""
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# # for j in range(len(rest)) :
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# # if "=" in rest[j] :
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# # rest[j] = rest[j].strip()
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# # rest[j] = rest[j].split("=", 1)
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# # column_name = rest[j][0]
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# # #print("COLUMN", column_name)
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# # v = rest[j][1]
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# # if (v == "") and (column_name in view) and (view[column_name].get_data_type() == "OBI_SEQ") :
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# # #print(">>>>>>YUP")
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# # conv_v = "aa"
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# # else :
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# # if ((not v.isalpha()) and (v.isalnum())) :
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# # conv_v = int(v)
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# # elif (v == "True") or (v == "False") :
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# # conv_v = bool(v)
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# # else :
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# # f = True
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# # for letter in v :
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# # if ((not letter.isalnum()) or (letter != ".")) :
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# # f = False
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# # if f :
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# # conv_v = float(v)
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# # else :
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# # conv_v = v
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# # view[i][column_name] = conv_v
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# # else :
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# # description+=rest[j]
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# #
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# # if description != "" :
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# # description = description.strip()
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# # view[i].set_description(description)
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#
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elif l%4 == 1 :
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# #
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seq = line[:-1]
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# #print("seq", seq)
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view[i].set_sequence(seq)
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i+=1
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#
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l+=1
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#
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#
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input_file.close()
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#print(view)
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print(view.__repr__())
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view.save_and_close()
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d.close()
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print("Done.")
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@ -1,311 +0,0 @@
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import os
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import sys
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import shutil
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import unittest
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from random import randint, uniform, choice
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import string
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from obitools3.obidms._obidms import OBIDMS
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LINE_COUNT_FOR_TEST_COLUMN = 10000 # TODO randomize?
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SMALLER_LINE_COUNT_FOR_TEST_COLUMN = 1000 # TODO randomize?
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NB_ELEMENTS_PER_LINE = 10 # TODO randomize?
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DMS_NAME = "unit_test_dms"
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def create_test_obidms():
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dms_name = DMS_NAME
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dms_dir_name = dms_name+'.obidms'
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dms = OBIDMS(dms_name)
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return (dms, dms_name, dms_dir_name)
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def create_test_column(dms, data_type, multiple_elements_per_line=False):
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col_name = "unit_test_"+data_type
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if multiple_elements_per_line :
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elts_names = elements_names()
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col = dms.open_column(col_name,
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create=True,
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type=data_type,
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nb_elements_per_line=NB_ELEMENTS_PER_LINE,
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elements_names=elts_names)
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return (col, col_name, elts_names)
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else :
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col = dms.open_column(col_name,
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create=True,
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type=data_type)
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return (col, col_name)
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def elements_names():
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names = [str(i) for i in range(NB_ELEMENTS_PER_LINE)]
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return names
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def random_obivalue(data_type):
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r = 1000000
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if data_type == "OBI_INT" :
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return randint(-r,r)
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elif data_type == "OBI_FLOAT" :
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return uniform(-r,r)
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elif data_type == "OBI_BOOL" :
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return randint(0,1)
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elif data_type == "OBI_CHAR" :
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return choice(string.ascii_lowercase)
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elif data_type == "OBI_STR" :
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length = randint(1,200)
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randoms = ''.join(choice(string.ascii_lowercase) for i in range(length))
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return randoms
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elif data_type == "OBI_SEQ" :
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length = randint(1,200)
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randoms = ''.join(choice("atgcryswkmdbhvn") for i in range(length))
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return randoms
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class OBIDMS_Column_TestCase(unittest.TestCase):
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def tearDown(self):
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self.col.close()
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self.dms.close()
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shutil.rmtree(self.dms_dir_name, ignore_errors=True)
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def test_OBIDMS_column_type(self):
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assert self.col.get_data_type() == self.data_type, 'Wrong data type associated with column'
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def test_OBIDMS_column_cloning(self):
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for i in range(LINE_COUNT_FOR_TEST_COLUMN):
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self.col[i]= random_obivalue(self.data_type)
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self.col.close()
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clone = self.dms.open_column(self.col_name, clone=True)
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self.col = self.dms.open_column(self.col_name)
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assert clone.get_nb_lines_used() == self.col.get_nb_lines_used(), "Cloned column doesn't have the same number of lines used"
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i=0
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for i in range(clone.get_nb_lines_used()) :
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assert clone[i] == self.col[i], "Different value in original column and cloned column"
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assert clone[i] is not None, "None value"
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clone.close()
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def test_OBIDMS_column_set_and_get(self):
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for i in range(LINE_COUNT_FOR_TEST_COLUMN):
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v = random_obivalue(self.data_type)
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self.col[i] = v
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assert self.col[i] == v, "Different value than the set value"
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assert self.col[i] is not None, "None value"
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def test_OBIDMS_referring_column(self):
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for i in range(LINE_COUNT_FOR_TEST_COLUMN):
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self.col[i] = random_obivalue(self.data_type)
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ref_col = self.dms.open_column(self.col_name, referring=True)
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j = 0
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for i in range(LINE_COUNT_FOR_TEST_COLUMN):
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if i%2 : # TODO randomize
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ref_col.grep_line(i)
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assert ref_col[j] == self.col[i], "Different value in original column and returned by referring column"
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assert ref_col[j] is not None, "None value"
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j+=1
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class OBIDMS_Column_multiple_elements_TestCase(OBIDMS_Column_TestCase):
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def test_OBIDMS_column_cloning(self):
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pass
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for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
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v = {}
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for e in self.elts_names :
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v[e] = random_obivalue(self.data_type)
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self.col[i] = v
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self.col.close()
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clone = self.dms.open_column(self.col_name, clone=True)
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self.col = self.dms.open_column(self.col_name)
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assert clone.get_nb_lines_used() == self.col.get_nb_lines_used(), "Cloned column doesn't have the same number of lines used"
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i=0
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for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
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assert self.col[i] == clone[i], "Different value in original column and cloned column"
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assert self.col[i] is not None, "None value"
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clone.close()
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def test_OBIDMS_column_set_and_get_with_elements_names(self):
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for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
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for e in range(NB_ELEMENTS_PER_LINE) :
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v = random_obivalue(self.data_type)
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self.col.set_item(i, self.elts_names[e], v)
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assert self.col.get_item(i, self.elts_names[e]) == v, "Different value than the set value"
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assert self.col.get_item(i, self.elts_names[e]) is not None, "None value"
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def test_OBIDMS_column_set_and_get(self):
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for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
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v = {}
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for e in self.elts_names :
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v[e] = random_obivalue(self.data_type)
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self.col[i] = v
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assert self.col[i] == v, "Different value than the set value"
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assert self.col[i] is not None, "None value"
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def test_OBIDMS_referring_column(self):
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for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
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v = {}
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for e in self.elts_names :
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v[e] = random_obivalue(self.data_type)
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self.col[i] = v
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ref_col = self.dms.open_column(self.col_name, referring=True)
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j = 0
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for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
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if i%2 : # TODO randomize
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ref_col.grep_line(i)
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assert ref_col[j] == self.col[i], "Different value in original column and returned by referring column"
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assert ref_col[j] is not None, "None value"
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j+=1
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ref_col.close()
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class OBIDMS_Column_OBI_INT_TestCase(OBIDMS_Column_TestCase):
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def setUp(self):
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self.data_type = 'OBI_INT'
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self.dms, \
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self.dms_name, \
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self.dms_dir_name = create_test_obidms()
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self.col, \
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self.col_name = create_test_column(self.dms,
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self.data_type)
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class OBIDMS_Column_OBI_INT_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
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def setUp(self):
|
||||
self.data_type = 'OBI_INT'
|
||||
self.dms, \
|
||||
self.dms_name, \
|
||||
self.dms_dir_name = create_test_obidms()
|
||||
self.col, \
|
||||
self.col_name, \
|
||||
self.elts_names = create_test_column(self.dms,
|
||||
self.data_type,
|
||||
multiple_elements_per_line=True)
|
||||
|
||||
|
||||
class OBIDMS_Column_OBI_FLOAT_TestCase(OBIDMS_Column_TestCase):
|
||||
def setUp(self):
|
||||
self.data_type = 'OBI_FLOAT'
|
||||
self.dms, \
|
||||
self.dms_name, \
|
||||
self.dms_dir_name = create_test_obidms()
|
||||
self.col, \
|
||||
self.col_name = create_test_column(self.dms,
|
||||
self.data_type)
|
||||
|
||||
|
||||
class OBIDMS_Column_OBI_FLOAT_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
|
||||
def setUp(self):
|
||||
self.data_type = 'OBI_FLOAT'
|
||||
self.dms, \
|
||||
self.dms_name, \
|
||||
self.dms_dir_name = create_test_obidms()
|
||||
self.col, \
|
||||
self.col_name, \
|
||||
self.elts_names = create_test_column(self.dms,
|
||||
self.data_type,
|
||||
multiple_elements_per_line=True)
|
||||
|
||||
|
||||
class OBIDMS_Column_OBI_BOOL_TestCase(OBIDMS_Column_TestCase):
|
||||
def setUp(self):
|
||||
self.data_type = 'OBI_BOOL'
|
||||
self.dms, \
|
||||
self.dms_name, \
|
||||
self.dms_dir_name = create_test_obidms()
|
||||
self.col, \
|
||||
self.col_name = create_test_column(self.dms,
|
||||
self.data_type)
|
||||
|
||||
|
||||
class OBIDMS_Column_OBI_BOOL_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
|
||||
def setUp(self):
|
||||
self.data_type = 'OBI_BOOL'
|
||||
self.dms, \
|
||||
self.dms_name, \
|
||||
self.dms_dir_name = create_test_obidms()
|
||||
self.col, \
|
||||
self.col_name, \
|
||||
self.elts_names = create_test_column(self.dms,
|
||||
self.data_type,
|
||||
multiple_elements_per_line=True)
|
||||
|
||||
|
||||
class OBIDMS_Column_OBI_CHAR_TestCase(OBIDMS_Column_TestCase):
|
||||
def setUp(self):
|
||||
self.data_type = 'OBI_CHAR'
|
||||
self.dms, \
|
||||
self.dms_name, \
|
||||
self.dms_dir_name = create_test_obidms()
|
||||
self.col, \
|
||||
self.col_name = create_test_column(self.dms,
|
||||
self.data_type)
|
||||
|
||||
|
||||
class OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
|
||||
def setUp(self):
|
||||
self.data_type = 'OBI_CHAR'
|
||||
self.dms, \
|
||||
self.dms_name, \
|
||||
self.dms_dir_name = create_test_obidms()
|
||||
self.col, \
|
||||
self.col_name, \
|
||||
self.elts_names = create_test_column(self.dms,
|
||||
self.data_type,
|
||||
multiple_elements_per_line=True)
|
||||
|
||||
|
||||
class OBIDMS_Column_OBI_STR_TestCase(OBIDMS_Column_TestCase):
|
||||
def setUp(self):
|
||||
self.data_type = 'OBI_STR'
|
||||
self.dms, \
|
||||
self.dms_name, \
|
||||
self.dms_dir_name = create_test_obidms()
|
||||
self.col, \
|
||||
self.col_name = create_test_column(self.dms,
|
||||
self.data_type)
|
||||
|
||||
|
||||
class OBIDMS_Column_OBI_STR_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
|
||||
def setUp(self):
|
||||
self.data_type = 'OBI_STR'
|
||||
self.dms, \
|
||||
self.dms_name, \
|
||||
self.dms_dir_name = create_test_obidms()
|
||||
self.col, \
|
||||
self.col_name, \
|
||||
self.elts_names = create_test_column(self.dms,
|
||||
self.data_type,
|
||||
multiple_elements_per_line=True)
|
||||
|
||||
class OBIDMS_Column_OBI_SEQ_TestCase(OBIDMS_Column_TestCase):
|
||||
def setUp(self):
|
||||
self.data_type = 'OBI_SEQ'
|
||||
self.dms, \
|
||||
self.dms_name, \
|
||||
self.dms_dir_name = create_test_obidms()
|
||||
self.col, \
|
||||
self.col_name = create_test_column(self.dms,
|
||||
self.data_type)
|
||||
|
||||
|
||||
class OBIDMS_Column_OBI_SEQ_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
|
||||
def setUp(self):
|
||||
self.data_type = 'OBI_SEQ'
|
||||
self.dms, \
|
||||
self.dms_name, \
|
||||
self.dms_dir_name = create_test_obidms()
|
||||
self.col, \
|
||||
self.col_name, \
|
||||
self.elts_names = create_test_column(self.dms,
|
||||
self.data_type,
|
||||
multiple_elements_per_line=True)
|
||||
|
||||
if __name__ == '__main__':
|
||||
unittest.main(verbosity=2, defaultTest=["OBIDMS_Column_OBI_INT_TestCase",
|
||||
"OBIDMS_Column_OBI_INT_multiple_elements_TestCase",
|
||||
"OBIDMS_Column_OBI_FLOAT_TestCase",
|
||||
"OBIDMS_Column_OBI_FLOAT_multiple_elements_TestCase",
|
||||
"OBIDMS_Column_OBI_BOOL_TestCase",
|
||||
"OBIDMS_Column_OBI_BOOL_multiple_elements_TestCase",
|
||||
"OBIDMS_Column_OBI_CHAR_TestCase",
|
||||
"OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase",
|
||||
"OBIDMS_Column_OBI_STR_TestCase",
|
||||
"OBIDMS_Column_OBI_STR_multiple_elements_TestCase",
|
||||
"OBIDMS_Column_OBI_SEQ_TestCase",
|
||||
"OBIDMS_Column_OBI_SEQ_multiple_elements_TestCase"])
|
||||
|
||||
|
||||
Reference in New Issue
Block a user