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Merge pull request #42 from solgenomics/topic/duplicate_image_warning
2023-07-19
N
a
ama M
e
nda
Mer
g
e
p
u
ll re
q
u
e
st #40 from sol
g
e
nomics/topic/fi
x
_bl
a
s
t
_dbix
.
.
.
commit
|
commitdiff
|
tree
2021-08-16
Naama Menda
M
e
r
ge
p
u
ll requ
e
st
#
3
7 from solgenomics/topic/add_cou
n
t
_
column
commit
|
commitdiff
|
tree
2018-08-24
Naama Me
n
da
M
erge pull requ
e
st #22 from solge
n
omics/topic/fix_ima
g
e_f
i
le
.
.
.
commit
|
commitdiff
|
tree
2018-08-16
Naama Menda
M
e
rge pull
r
equest #
2
0
from solg
e
nom
i
c
s
/topic/image_order
commit
|
commitdiff
|
tree
2018-08-16
Naama Me
n
da
Update Im
a
g
e
.
p
m
commit
|
commitdiff
|
tree
2018-01-26
Naama Menda
Merge pu
l
l request #11 fr
o
m solgenomic
s
/
t
opic/fix_feature_fetch
commit
|
commitdiff
|
tree
2018-01-19
Naa
m
a
M
enda
Merge p
u
ll requ
e
st #10 f
r
om solgeno
m
ics/t
o
pic/fix_
f
eature
_
fetch
commit
|
commitdiff
|
tree
2016-02-09
Na
a
m
a
M
en
d
a
Merge pull req
u
es
t
#8 fr
o
m sol
g
enom
i
cs
/
t
o
p
i
c
/s
y
s
t
em_
c
v
t
erms
commit
|
commitdiff
|
tree
2015-06-17
N
a
ama M
e
nda
fix error in
query
du
e
to
o
rganism_id
column in sgn
.
.
.
commit
|
commitdiff
|
tree
2015-05-20
Naama Menda
store
pu
b
type cvter
m
if
d
oes n
o
t exis
t
in database
commit
|
commitdiff
|
tree
2015-05-13
Na
a
ma Men
d
a
parse DOI from the pubmed XML
.
To b
e
u
s
e
d for banne
r
.
.
.
commit
|
commitdiff
|
tree
2012-12-18
Naa
m
a Menda
option for e
x
clud
i
n
g
clean_marker_name, use
f
u
l wh
e
n
.
.
.
commit
|
commitdiff
|
tree
2012-11-29
Na
a
ma Men
d
a
dump the parentheses
commit
|
commitdiff
|
tree
2012-11-29
N
a
a
m
a Menda
adding o
p
tions fo
r
printing mini-ref
commit
|
commitdiff
|
tree
2012-11-29
Na
a
m
a
Menda
return the pu
b
ob
j
ect
commit
|
commitdiff
|
tree
2012-03-03
Naa
m
a Menda
updated dbic schema objects for sgn
s
c
hema
commit
|
commitdiff
|
tree
2012-03-03
Naama Menda
dbix se
a
rc
h
function takes arguments in a h
a
shref
commit
|
commitdiff
|
tree
2012-02-06
Naama
M
en
d
a
count s
t
oc
k
s instead o
f
deprecated i
n
dividua
l
s
commit
|
commitdiff
|
tree
2011-11-06
Naama Menda
added
m
eth
o
d for a
BCS publication objec
t
.
This is
.
.
.
commit
|
commitdiff
|
tree
2011-10-31
N
a
ama Menda
added acc
e
ssors for spec
i
es na
m
e
commit
|
commitdiff
|
tree
2011-08-31
Naama Menda
check
i
n
g if a schema
object was passed to the or
g
an
i
s
m
.
.
.
commit
|
commitdiff
|
tree
2011-08-25
N
aama Menda
adde
d
an option f
o
r organism functi
o
n to return a
ha
s
h
commit
|
commitdiff
|
tree
2011-06-11
N
a
ama
M
e
nda
added
a functio
n
for storing
stock owners
commit
|
commitdiff
|
tree
2011-04-18
Naama Menda
adding ne
w
met
a
data r
o
w if a row does not exi
s
t
commit
|
commitdiff
|
tree
2011-04-17
Naama M
e
n
da
any u
s
er with db pe
r
miss
i
ons sh
o
uld be able to ca
l
l
.
.
.
commit
|
commitdiff
|
tree
2011-04-17
Naama Mend
a
us
i
ng
n
ew
s
t
oc
k
- phe
n
ome link
i
ng
tabl
e
s
commit
|
commitdiff
|
tree
2011-04-06
Naama
M
end
a
cvterm func
t
ions
f
or cverm p
a
ge moved to
A
J
AX c
o
ntroller
commit
|
commitdiff
|
tree
2011-04-03
Na
a
m
a M
e
nda
add
e
d
function for recur
s
ive annota
t
ed stocks
commit
|
commitdiff
|
tree
2011-04-02
Naam
a
Men
d
a
fun
c
tion
f
or findin
g
ima
g
e
s linked wit
h
t
h
e stock
commit
|
commitdiff
|
tree
2011-04-01
Naama Menda
unused code
.
o
l
d p
h
enotype search
commit
|
commitdiff
|
tree
2011-04-01
Naama Menda
fixed issues with un
d
ef
s
tock object
s
commit
|
commitdiff
|
tree
2011-03-24
Na
a
ma Men
d
a
al
t
ernative constr
u
c
t
o
r
returns an empty object
if
.
.
.
commit
|
commitdiff
|
tree
2011-02-15
N
aama
Menda
got rid of duplicat
e
d funct
i
on
commit
|
commitdiff
|
tree
2011-02-01
Naama
M
enda
remov
e
d duplicated function
commit
|
commitdiff
|
tree
2010-11-20
Naa
m
a Menda
ad
d
ed a check for
e
xisting
pcr_experiment = sequence
.
.
.
commit
|
commitdiff
|
tree
2010-11-16
Naama
M
enda
checking
if the stock exists
b
efore tryi
n
g to fet
c
h
.
.
.
commit
|
commitdiff
|
tree
2010-11-16
Naama M
e
n
da
Merge branch 'master' of
g
ithub
.
com:solgenomics/cxgn
.
.
.
commit
|
commitdiff
|
tree
2010-11-16
Naama Menda
added test for seco
n
d-level BCS stock object
commit
|
commitdiff
|
tree
2010-11-11
Naama Mend
a
changed cv of
s
eq
u
ence types to SO
commit
|
commitdiff
|
tree
2010-11-11
Naa
m
a Menda
fix
e
d s
e
a
r
ch for protocol name
commit
|
commitdiff
|
tree
2010-11-10
N
a
ama Menda
added Indel to protocol
l
is
t
commit
|
commitdiff
|
tree
2010-11-10
Naama Menda
m
erged master
commit
|
commitdiff
|
tree
2010-11-09
Naama Menda
added
funct
i
o
ns
to
add and access sequences linked
.
.
.
commit
|
commitdiff
|
tree
2010-11-06
Naama Menda
removed whi
t
esp
a
ce
commit
|
commitdiff
|
tree
2010-11-06
Naama Menda
got r
i
d o
f
warning
s
c
o
mming from un
d
ef
value in residue
s
.
.
.
commit
|
commitdiff
|
tree
2010-11-04
Naama Menda
a
dded i
n
d
e
l
and ASPE protocols to Mar
k
er subclass
commit
|
commitdiff
|
tree
2010-11-03
Na
a
ma M
e
nda
fixed re
c
ur
s
i
ve_chi
l
d
r
e
n cvterm fu
n
ction, and added
.
.
.
commit
|
commitdiff
|
tree
2010-11-03
Naama Men
d
a
fi
x
ed get-ch
i
ldren me
t
hod to
f
etch only childre
n
of
.
.
.
commit
|
commitdiff
|
tree
2010-11-01
Naama Menda
f
i
x
ed recur
s
ive parents
query
.
This was not workin
g
.
.
.
commit
|
commitdiff
|
tree
2010-11-01
Naa
m
a M
e
nda
r
emovin
g
the pathdistanc
e
filterin
g
w
a
s a bad idea
.
.
.
commit
|
commitdiff
|
tree
2010-11-01
Naama Menda
this should be the right
query for recur
s
ive childre
n
commit
|
commitdiff
|
tree
2010-10-28
Naama Menda
get_recursive_loci s
h
ould return now
lo
c
i
w
i
th d
i
rec
t
.
.
.
commit
|
commitdiff
|
tree
2010-10-28
N
a
ama
Menda
setting
in
d
bh
a
u
tocommit =1
, and
checking
f
or errors
.
.
.
commit
|
commitdiff
|
tree
2010-10-23
Naama Me
n
da
a
d
d
ed
a
trial
o
ption to dbpatch
commit
|
commitdiff
|
tree
2010-10-13
Naam
a
Menda
f
ixed bug in returning feature_
i
d
af
t
er inserting a
.
.
.
commit
|
commitdiff
|
tree
2010-10-11
Naam
a
Menda
a
d
d
e
d h
e
lper functions
f
or BCS organism and cvterm
commit
|
commitdiff
|
tree
2010-10-11
Naama Menda
added acces
s
ors to 2nd le
v
el ch
a
do
S
t
o
c
k object
commit
|
commitdiff
|
tree
2010-10-05
Naama
M
enda
fixed checking o
f
p
r
e
v
io
u
s db patches pre
r
equis
i
te
commit
|
commitdiff
|
tree
2010-10-04
N
aama Menda
cloni
n
g dbh , since the DBIC d
b
h gets disconnected
.
.
.
commit
|
commitdiff
|
tree
2010-10-03
N
a
ama Menda
ad
d
e
d
recu
r
sive_children and recu
r
s
ive_parents methods
.
.
.
commit
|
commitdiff
|
tree
2010-10-03
Naama Menda
get_ch
i
ldr
e
n does
not need
t
o query c
v
termpath, si
n
c
e
.
.
.
commit
|
commitdiff
|
tree
2010-09-29
Naama Menda
chan
g
ed the BCS conne
c
tion
t
o u
s
e
D
BI, inst
e
ad
o
f C
X
GN
.
.
.
commit
|
commitdiff
|
tree
2010-09-29
Naama Men
d
a
changed insert q
u
e
ry to r
e
tu
r
n
f
eature_id
commit
|
commitdiff
|
tree
2010-09-29
Naama Men
d
a
added stock
obsolete acces
s
or
commit
|
commitdiff
|
tree
2010-09-29
N
a
ama
Menda
fixed g
e
t_parents query
commit
|
commitdiff
|
tree
2010-09-28
Naama
Me
n
da
chang
e
d get_parents
query to use
c
v
t
ermpath
commit
|
commitdiff
|
tree
2010-09-28
Naam
a
Menda
chang
e
d
get_chi
l
dren
t
o use cvterm
p
ath
commit
|
commitdiff
|
tree
2010-09-28
Naama
M
e
nda
ad
d
ed stock obsolete accessor
commit
|
commitdiff
|
tree
2010-09-23
Naama M
e
nda
added a
n
o
p
tion to return
an error in
pa
t
c
h{}
commit
|
commitdiff
|
tree
2010-09-22
Naama Menda
some
POD changes
commit
|
commitdiff
|
tree
2010-09-21
Naa
m
a
Menda
r
emoved usage of patch number check
i
n Dbversi
o
n, since
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
Naa
m
a Menda
adde
d
a get_obs
o
l
e
te method
.
Now defaults
t
o
f, but
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
Naama
Menda
remove
d
unnec
e
ssary
p
r
i
nting to STDOUT
commit
|
commitdiff
|
tree
2010-09-20
Naama Menda
ad
d
ed Moo
s
e
X
::Runnable
a
nd
Mo
o
seX::Getopt dependen
c
ies
commit
|
commitdiff
|
tree
2010-09-20
Naama Menda
a
p
arent class for writ
i
ng dbpatches us
i
n
g MooseX:
.
.
.
commit
|
commitdiff
|
tree
2010-09-19
Naama
Menda
a
2nd le
v
el object
for BCS Stcok
.
T
h
is
i
s only for
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Naama Menda
changed
get_
l
a
st_insert_id
to ge
t
ting t
h
e database
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
Naama Menda
removed STDERR printing
commit
|
commitdiff
|
tree
2010-07-15
Naama Menda
fix
e
d query to work w
i
t
h
objec
t
i
d
.
this
i
s
e
quivale
n
t
.
.
.
commit
|
commitdiff
|
tree
2010-07-15
Naama Menda
fixed query f
o
r fetc
h
ing loci and indi
v
i
dual annotatio
n
s
.
.
.
commit
|
commitdiff
|
tree
2010-06-14
Naa
m
a Menda
fi
x
ed CXG
N
::C
h
ado tests
commit
|
commitdiff
|
tree
2010-06-14
Naama Menda
f
i
xed CX
G
N::Chado tests
commit
|
commitdiff
|
tree
2010-05-29
Naama Me
n
da
Merge
branch '
m
ast
e
r
'
of gith
u
b
.
c
om:solgeno
m
ics/cxgn
.
.
.
commit
|
commitdiff
|
tree
2010-05-29
Naama Menda
bug
i
n the
P
henotype module,
s
tore f
u
nction
.
commit
|
commitdiff
|
tree
2010-05-14
Naama Menda
POD t
y
pos
commit
|
commitdiff
|
tree
2010-05-13
Naama
M
enda
refactored the q
u
ery fo
r
fetchin
g
an
n
otated objects
.
.
.
commit
|
commitdiff
|
tree
2010-04-22
Naama M
e
nda
added base c
l
ass to Phylo::Tree
commit
|
commitdiff
|
tree
2010-04-21
N
a
a
ma M
e
nda
c
hanged printing of
n
ode la
b
els dependi
n
g on the
n
umber
.
.
.
commit
|
commitdiff
|
tree
2010-04-19
Naama Menda
printi
n
g
non-le
a
f no
d
e labels ab
o
ve th
e
node line
.
.
.
.
commit
|
commitdiff
|
tree
2010-04-12
Naama Men
d
a
added an option for printing lab
e
l
s
f
o
r
all
t
ree
nodes
commit
|
commitdiff
|
tree
2010-04-09
Naama Menda
adde
d
an option
t
o print
t
he names of non-leaf nodes
.
.
.
commit
|
commitdiff
|
tree
2010-04-05
N
aama Me
n
da
ad
d
ed a funct
i
on or fetching
a
ll direct
childre
n
of
.
.
.
commit
|
commitdiff
|
tree
2010-04-01
Naama Menda
fixed the pod for add_child
.
Th
i
s function
d
oes not
.
.
.
commit
|
commitdiff
|
tree
2010-03-18
Naa
m
a Menda
fixed a bug i
n
Organ
i
sm module
commit
|
commitdiff
|
tree
2010-03-11
N
aama Men
d
a
removed
STDERR s
t
atemen
t
s
commit
|
commitdiff
|
tree
2010-02-26
Naama Menda
a
dded a check t
o
pre
v
ent new_with_c
o
m
m
on_n
a
m
e
from
.
.
.
commit
|
commitdiff
|
tree
2010-02-10
Naama
M
e
nda
m
o
dified
b
ew_with_common_
n
ame to get the
o
r
g
anism
b
ase
d
.
.
.
commit
|
commitdiff
|
tree