Commit 1ed5edc8 authored by emarti2's avatar emarti2
Browse files

Metrics computation improvements

parent 31180b32
This diff is collapsed.
......@@ -3,10 +3,10 @@ repeatmodeler,False,True,True,False,True,False,False,False,False,False,False,Fal
prigsa2,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False
popstr2,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False
nanosatellite,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False
tricolor,True,True,True,True,False,False,True,False,False,True,True,False,False,False,True,True,True,False,False,False,True,False,False,True,True
repet,True,True,True,True,True,False,True,False,False,True,True,True,False,False,True,True,True,False,False,False,True,False,False,True,False
tricolor,True,True,True,True,False,False,True,True,False,True,True,False,False,False,True,True,True,False,False,False,True,False,False,True,True
repet,True,True,True,True,True,False,True,True,False,True,True,True,False,False,True,True,True,False,False,False,True,False,False,True,False
kmasker,True,True,True,True,True,False,False,False,False,False,False,False,False,False,True,True,True,False,False,False,True,False,False,True,True
kmasker,True,True,True,True,True,False,True,False,False,False,True,True,False,False,True,True,True,False,False,False,True,False,False,True,True
kmasker,True,True,True,True,True,False,True,True,False,False,True,True,False,False,True,True,True,False,False,False,True,False,False,True,True
ostrfpd,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
ultra,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
pipealign2,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False
......@@ -45,8 +45,8 @@ interpro,False,True,True,False,True,False,False,False,False,False,False,False,Fa
pfam,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False,False,True,False
repeatsdb,True,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False,False,True,False
reputer,False,True,True,True,True,True,False,False,False,False,False,False,False,False,True,True,True,True,False,False,True,False,False,True,False
reputer,False,True,True,True,True,False,True,False,False,True,True,True,False,False,True,True,True,True,False,False,True,False,False,True,False
radar,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,False,True,False
reputer,False,True,True,True,True,False,True,True,False,True,True,True,False,False,True,True,True,True,False,False,True,False,False,True,False
radar,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,True,True,False
trdistiller,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
gcat,True,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
kmer-ssr,False,True,True,False,True,False,False,False,False,False,True,False,False,False,False,False,False,False,False,False,True,False,False,True,False
......@@ -56,7 +56,7 @@ vivaxgen,False,True,True,False,True,False,False,False,False,False,False,False,Fa
lrrsearch,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
detectir,False,True,True,False,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
esap plus,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False
spotyping,True,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
spotyping,True,True,True,False,True,False,False,True,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
sewer,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False
gream,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
mreps,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
......@@ -87,7 +87,7 @@ protinfo ppc,False,True,True,False,True,False,False,False,False,False,False,Fals
repeatoire,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
eslpred,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
strap,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
genebreak,True,True,True,False,True,False,True,False,False,True,True,True,False,False,False,False,True,True,False,False,True,False,False,True,False
genebreak,True,True,True,False,True,False,True,True,False,True,True,True,False,False,False,False,True,True,False,False,True,False,False,True,False
subseqer,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
adgo,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
barcode generator,False,True,True,False,False,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
......@@ -101,41 +101,41 @@ pbil,False,True,True,False,True,False,False,False,False,False,False,False,False,
uniqueprot,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
rjprimers,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
tmsoc,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
oddcomp,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
palindrome,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
cpgreport,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
newcpgreport,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
freak,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
density,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
geecee,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
compseq,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
chaos,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
oddcomp,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
palindrome,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
cpgreport,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
newcpgreport,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
freak,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
density,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
geecee,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
compseq,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
chaos,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
seqentropy,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
sbars,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
equicktandem,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
sbars,False,True,True,False,True,False,False,True,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
equicktandem,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
genes by isoelectric point,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False,False,True,False
mwcontam,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
wordcount,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
emowse,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
etandem,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
iva,False,True,True,False,True,False,False,False,False,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False
newcpgseek,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
mwcontam,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
wordcount,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
emowse,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
etandem,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
iva,False,True,True,False,True,False,False,False,False,False,True,False,False,False,False,False,False,False,False,False,False,False,True,False,False
newcpgseek,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
trust,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,False,False
peptide match,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False,False,True,False
mwfilter,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
mwfilter,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
repdenovo,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
cpgplot,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
isochore,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
einverted,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,False,True,False
cpgplot,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
isochore,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
einverted,False,True,True,True,True,False,True,False,False,True,True,True,False,False,False,False,False,False,False,False,True,False,True,True,False
pssrdb,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False
lalign,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,False,True,False
censor,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,False,True,False
lalign,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,True,True,False
censor,False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,True,True,False
satellog,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
newcpgreport (ebi),False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,False,True,False
cpgplot (ebi),False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,False,True,False
newcpgreport (ebi),False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,True,True,False
cpgplot (ebi),False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,True,True,False
polyq,False,True,True,False,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,False,False,True,False
tral,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,True,False,False,True,False,False,True,False
isochore (ebi),False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,False,True,False
isochore (ebi),False,True,True,False,True,True,False,False,False,False,False,False,False,False,False,False,False,False,False,False,True,True,True,True,False
reupred,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,True,False,False,True,False,False,False,False
trap,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
vntrfinder,False,True,True,False,True,False,False,False,False,False,True,True,False,False,False,False,False,False,False,False,True,False,False,False,False
......
......@@ -3,10 +3,10 @@ repeatmodeler,0.54,0.0,0.0,0.0,0.135
prigsa2,0.54,0.0,0.0,0.0,0.135
popstr2,0.54,0.0,0.0,0.0,0.135
nanosatellite,0.54,0.0,0.0,0.2,0.185
tricolor,0.9400000000000002,0.565,0.6,0.7,0.7012499999999999
repet,1.0,0.6399999999999999,0.6,0.5,0.6849999999999999
tricolor,0.9400000000000002,0.7049999999999998,0.6,0.7,0.7362500000000001
repet,1.0,0.7799999999999999,0.6,0.5,0.72
kmasker,1.0,0.0,0.6,0.7,0.575
kmasker,1.0,0.5,0.6,0.7,0.7
kmasker,1.0,0.6399999999999999,0.6,0.7,0.7349999999999999
ostrfpd,0.54,0.15,0.0,0.5,0.2975
ultra,0.54,0.15,0.0,0.5,0.2975
pipealign2,0.54,0.0,0.0,0.0,0.135
......@@ -45,7 +45,7 @@ interpro,0.54,0.0,0.0,0.5,0.26
pfam,0.54,0.42,0.1,0.5,0.39
repeatsdb,0.9400000000000002,0.0,0.1,0.5,0.38500000000000006
reputer,0.6000000000000001,0.42,0.7,0.5,0.5549999999999999
reputer,0.6000000000000001,0.6399999999999999,0.7,0.5,0.61
reputer,0.6000000000000001,0.7799999999999999,0.7,0.5,0.645
radar,0.54,0.42,0.0,0.8,0.44
trdistiller,0.54,0.15,0.0,0.3,0.2475
gcat,0.9400000000000002,0.15,0.0,0.3,0.34750000000000003
......@@ -56,7 +56,7 @@ vivaxgen,0.54,0.0,0.0,0.5,0.26
lrrsearch,0.54,0.0,0.0,0.5,0.26
detectir,0.54,0.6399999999999999,0.0,0.5,0.42
esap plus,0.54,0.0,0.0,0.2,0.185
spotyping,0.9400000000000002,0.15,0.0,0.5,0.3975
spotyping,0.9400000000000002,0.29,0.0,0.5,0.43250000000000005
sewer,0.54,0.0,0.0,0.2,0.185
gream,0.54,0.0,0.0,0.5,0.26
mreps,0.54,0.0,0.0,0.5,0.26
......@@ -87,7 +87,7 @@ protinfo ppc,0.54,0.0,0.0,0.5,0.26
repeatoire,0.54,0.15,0.0,0.3,0.2475
eslpred,0.54,0.0,0.0,0.5,0.26
strap,0.54,0.0,0.0,0.5,0.26
genebreak,0.9400000000000002,0.6399999999999999,0.22,0.5,0.575
genebreak,0.9400000000000002,0.7799999999999999,0.22,0.5,0.6100000000000001
subseqer,0.54,0.0,0.0,0.5,0.26
adgo,0.54,0.0,0.0,0.5,0.26
barcode generator,0.48,0.15,0.0,0.5,0.2825
......@@ -101,32 +101,32 @@ pbil,0.54,0.0,0.0,0.5,0.26
uniqueprot,0.54,0.0,0.0,0.5,0.26
rjprimers,0.54,0.0,0.0,0.5,0.26
tmsoc,0.54,0.0,0.0,0.5,0.26
oddcomp,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
palindrome,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
cpgreport,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
newcpgreport,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
freak,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
density,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
geecee,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
compseq,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
chaos,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
oddcomp,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
palindrome,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
cpgreport,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
newcpgreport,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
freak,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
density,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
geecee,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
compseq,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
chaos,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
seqentropy,0.54,0.15,0.0,0.3,0.2475
sbars,0.54,0.15,0.0,0.3,0.2475
equicktandem,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
sbars,0.54,0.29,0.0,0.3,0.28250000000000003
equicktandem,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
genes by isoelectric point,0.48,0.0,0.1,0.5,0.27
mwcontam,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
wordcount,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
emowse,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
etandem,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
iva,0.54,0.075,0.0,0.0,0.15375
newcpgseek,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
mwcontam,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
wordcount,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
emowse,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
etandem,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
iva,0.54,0.075,0.0,0.3,0.22875
newcpgseek,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
trust,0.54,0.42,0.0,0.3,0.315
peptide match,0.54,0.0,0.1,0.5,0.28500000000000003
mwfilter,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
mwfilter,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
repdenovo,0.54,0.15,0.0,0.3,0.2475
cpgplot,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
isochore,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
einverted,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
cpgplot,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
isochore,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
einverted,0.6000000000000001,0.6399999999999999,0.0,0.8,0.51
pssrdb,0.54,0.0,0.0,0.2,0.185
lalign,0.54,0.42,0.0,0.8,0.44
censor,0.54,0.42,0.0,0.8,0.44
......
......@@ -4,6 +4,9 @@ import yaml
import sys
global webTypes
webTypes = ['Web API', 'Web application', 'Web service', 'Suite', 'Workbench', 'Database portal']
def prepFAIRcomp(instances):
global stdFormats
......@@ -129,8 +132,6 @@ class instance(object):
##============== Accessibility metrics computation functions ================
global webTypes
webTypes = ['Web API', 'Web application', 'Web service', 'Suite', 'Workbench', 'Database portal']
def compA1_1(self):
'''
WEB
......@@ -252,7 +253,8 @@ class instance(object):
if self.super_type == 'no_web':
eInfra = ['vre.multiscalegenomics.eu', 'galaxy.', 'usegalaxy.']
for url in self.links:
if True in [a in url for a in eInfra]:
for e in eInfra:
if e in url['url']:
return(True)
else:
return(False)
......@@ -268,10 +270,11 @@ class instance(object):
Whether the software can be used in several e-infrastructure
'''
if self.super_type == 'no_web':
eInfra = ['vre.multiscalegenomics.eu', 'galaxy.', 'usegalaxy.']
count = 0
eInfra = ['vre.multiscalegenomics.eu', 'galaxy.', 'usegalaxy.']
for url in self.links:
if True in [a in url for a in eInfra]:
for e in eInfra:
if e in url['url']:
count += 1
if count>1:
return(True)
......@@ -424,6 +427,8 @@ class instance(object):
for doc in self.documentation:
if doc[0][0].lower() == 'conditions of use':
return(True)
if doc[0][0].lower() == 'terms of use':
return(True)
return(False)
......@@ -509,7 +514,7 @@ class instance(object):
self.metrics.A3_2 = self.compA3_2()
self.metrics.A3_3 = self.compA3_3()
self.metrics.A3_4 = self.compA3_4()
self.metrics.A3_5 = self.compA3_4()
self.metrics.A3_5 = self.compA3_5()
self.metrics.I1_1 = self.compI1_1() # TO DO
#self.metrics.I1_2 = False # NOT FOR NOW
......@@ -531,6 +536,7 @@ class instance(object):
self.metrics.R2_2 = self.compR2_2()
#self.metrics.R3_1 = False # Not for now
self.metrics.R3_2 = self.compR3_2()
self.metrics.R4_1 = self.compR4_1()
......@@ -738,7 +744,8 @@ class biotoolsToolsGenerator(toolGenerator):
return(doc)
def parse_install_instr(self, tool, newInst):
if 'Manual' in [ doc[0] for doc in newInst.documentation ]:
for d in newInst.documentation:
if 'manual' in d[0][0].lower():
return(True)
else:
return(False)
......
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