add unit test for mascot feeder

[cpanse]

No description provided.

[cpanse]

import bfabric

B = bfabric.Bfabric()


query={'resource': {'status': 'available', 'size': 56530266, 'name': 'data/20201020/F290274.dat', 'relativepath': 'data/20201020/F290274.dat', 'filechecksum': '26e2295015ed85e60f3825510083eb62', 'storageid': 4}, 'containerid': '23023', 'name': '20201020_C23023_002_S269992_RH1408_Recombinant_protein_FTHCD.mgf PAG_AutoSearch_swissprot BF10 full storage; F290274.dat; \\\\fgcz-r-035.fgcz-net.unizh.ch\\Data2San\\p23023\\Proteomics\\QEXACTIVE_1\\analytic_20201020\\mgf__pd21_separate_IMP_charged_deconvolution\\', 'applicationid': 19, 'inputresource': [{'relativepath': 'p23023/Proteomics/QEXACTIVE_1/analytic_20201020/20201020_C23023_002_S269992_RH1408_Recombinant_protein.raw', 'storageid': 2}], 'description': 'COM=20201020_C23023_002_S269992_RH1408_Recombinant_protein_FTHCD.mgf PAG_AutoSearch_swissprot BF10 full storage; TOL=10; TOLU=ppm; ITOL=0.03; ITOLU=Da; FILE=\\\\fgcz-r-035.fgcz-net.unizh.ch\\Data2San\\p23023\\Proteomics\\QEXACTIVE_1\\analytic_20201020\\mgf__pd21_separate_IMP_charged_deconvolution\\20201020_C23023_002_S269992_RH1408_Recombinant_protein_FTHCD.mgf; USERNAME=daemon; CHARGE=2+ and 3+; IT_MODS=Oxidation (M); INSTRUMENT=Q-Exactive (Deconv); USERID=4; DECOY=1; release=SwissProt_autoup_20200812.fasta; feeder = http://fgcz-svn.uzh.ch/repos/fgcz/computer/fgcz-c-064/bfabric-feeder/fgcz_dataFeederMascot.py'}



rv = B.checkandinsert_object('workunit', query)
print(rv)
print(rv[0])


query={'resource': {'status': 'available', 'size': 69399582, 'name': 'data/20201018/F290245.dat', 'relativepath': 'data/20201018/F290245.dat', 'filechecksum': '233c47a66e5cc1a367770fc68162102f', 'storageid': 4}, 'containerid': '22976', 'name': '20201016_C22976_026_S269780_12_Recombinant_protein_FTHCD.mgf PAG_AutoSearch_swissprot BF10 full storage; F290245.dat; \\\\fgcz-r-035.fgcz-net.unizh.ch\\Data2San\\p22976\\Proteomics\\QEXACTIVE_1\\analytic_20201016\\mgf__pd21_separate_IMP_charged_deconvolution\\2020', 'applicationid': 19, 'inputresource': [{'relativepath': 'p22976/Proteomics/QEXACTIVE_1/analytic_20201016/20201016_C22976_026_S269780_12_Recombinant_protein.raw', 'storageid': 2}], 'description': 'COM=20201016_C22976_026_S269780_12_Recombinant_protein_FTHCD.mgf PAG_AutoSearch_swissprot BF10 full storage; TOL=10; TOLU=ppm; ITOL=0.03; ITOLU=Da; FILE=\\\\fgcz-r-035.fgcz-net.unizh.ch\\Data2San\\p22976\\Proteomics\\QEXACTIVE_1\\analytic_20201016\\mgf__pd21_separate_IMP_charged_deconvolution\\20201016_C22976_026_S269780_12_Recombinant_protein_FTHCD.mgf; USERNAME=daemon; CHARGE=2+ and 3+; IT_MODS=Oxidation (M); INSTRUMENT=Q-Exactive (Deconv); USERID=4; DECOY=1; release=SwissProt_autoup_20200812.fasta; feeder = http://fgcz-svn.uzh.ch/repos/fgcz/computer/fgcz-c-064/bfabric-feeder/fgcz_dataFeederMascot.py'}

rv = B.checkandinsert_object('workunit', query)
print(rv)
print(rv[0])


query={'resource': {'status': 'available', 'size': 193698609, 'name': 'data/20191202/F282658.dat', 'relativepath': 'data/20191202/F282658.dat', 'filechecksum': 'bfc39b5df6836f8f32896ceb0bda03ab', 'storageid': 4}, 'containerid': '3000', 'name': 'Lumos2_Hela02_DDA_GT90_RT110min_HCD_IT_08IW_adGradient_adIT; F282658.dat; Hela02_DDA_GT90_RT110min_HCD_IT_08IW_adGradient_adIT.mgf', 'applicationid': 19, 'inputresource': [{'relativepath': 'p3000/Proteomics/LUMOS_2/cfortes_20191128_FirstRuns/Hela02_DDA_GT90_RT110min_HCD_IT_08IW_adGradient_adIT.raw', 'storageid': 2}], 'description': 'COM=Lumos2_Hela02_DDA_GT90_RT110min_HCD_IT_08IW_adGradient_adIT; TOL=10; TOLU=ppm; ITOL=0.6; ITOLU=Da; MODS=Carbamidomethyl (C); FILE=Hela02_DDA_GT90_RT110min_HCD_IT_08IW_adGradient_adIT.mgf; USERNAME=cfortes; CHARGE=2+; IT_MODS=Oxidation (M); INSTRUMENT=LTQ-ORBI-Default; USERID=1274; QUANTITATION=None; release=fgcz_9606_reviewed_cnl_20190709.fasta; feeder = http://fgcz-svn.uzh.ch/repos/fgcz/computer/fgcz-c-064/bfabric-feeder/fgcz_dataFeederMascot.py'}

rv = B.checkandinsert_object('workunit', query)
print(rv)
print(rv[0])

OUTPUT

[<suds.sudsobject.xmlWorkunit object at 0x7f8b6956f278>]
(xmlWorkunit){
   errorreport = "Resource(s) with the specified attribute combination not found: storage id: 2 relative path: p23023/Proteomics/QEXACTIVE_1/analytic_20201020/20201020_C23023_002_S269992_RH1408_Recombinant_protein.raw"
 }
[<suds.sudsobject.xmlWorkunit object at 0x7f8b69583128>]
(xmlWorkunit){
   errorreport = "Resource(s) with the specified attribute combination not found: storage id: 2 relative path: p22976/Proteomics/QEXACTIVE_1/analytic_20201016/20201016_C22976_026_S269780_12_Recombinant_protein.raw"
 }
[<suds.sudsobject.xmlWorkunit object at 0x7f8b6958c358>]
(xmlWorkunit){
   errorreport = "There already exists a resource with the following attributes: relativepath=data/20191202/F282658.dat storageid=4 containerid=3000 applicationid=19"
 }