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vidjil
vidjil
Commits
10e44733
Commit
10e44733
authored
Mar 10, 2020
by
Mathieu Giraud
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Merge branch 'feature-a/4203-with-docker' into 'dev'
Tests algo avec docker Closes
#4203
See merge request
!612
parents
3f88bc20
a481f64c
Pipeline
#127844
failed with stages
in 20 minutes and 3 seconds
Changes
4
Pipelines
7
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4 changed files
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193 additions
and
37 deletions
+193
-37
.gitlab-ci.yml
.gitlab-ci.yml
+1
-27
algo/.gitlab-ci-compilers.yml
algo/.gitlab-ci-compilers.yml
+179
-0
algo/tests/should-get-tests/analysis-ikaros.should
algo/tests/should-get-tests/analysis-ikaros.should
+3
-3
algo/tests/unit-tests/testAffectAnalyser.cpp
algo/tests/unit-tests/testAffectAnalyser.cpp
+10
-7
No files found.
.gitlab-ci.yml
View file @
10e44733
...
...
@@ -55,6 +55,7 @@ test_germlines:
include
:
-
local
:
'
/doc/.gitlab-ci.yml'
-
local
:
'
algo/.gitlab-ci-compilers.yml'
# Stage multiple_tests
# Algorithm
...
...
@@ -177,33 +178,6 @@ deploy_release_prod:
make -C vidjil-algo-${release_name};\
ln -sfT vidjil-algo-${release_name} next"
.testing-compilers
:
&test_various_compilers
stage
:
multiple_tests
tags
:
-
several-compilers
script
:
-
|
for CXX in $COMPILERS; do
echo "**** Using $CXX for compilation ****"
make -C algo clean
make -C algo CXX=$CXX unit
make -C algo CXX=$CXX should
make -C algo CXX=$CXX valgrind_unit
done
test_various_compilers_manual
:
<<
:
*test_various_compilers
when
:
manual
only
:
-
/^feature-.*a.*\/.*$/
-
schedules
test_various_compilers_release
:
<<
:
*test_various_compilers
only
:
-
/^feature-.*a.*\/release$/
# Client
test_browser_unit
:
...
...
algo/.gitlab-ci-compilers.yml
0 → 100644
View file @
10e44733
.testing-compilers
:
stage
:
multiple_tests
tags
:
-
cidocker
before_script
:
-
apt-get update
-
apt-get install -y time valgrind python3 wget tar
script
:
-
$CXX --version
-
make demo data germline
-
make -C algo clean
-
make -C algo CXX=$CXX CC=$CC unit
-
make -C algo CXX=$CXX CC=$CC should
-
make -C algo CXX=$CXX CC=$CC valgrind_unit
.installing-compiler
:
before_script
:
-
apt-get update
-
apt-get install -y time valgrind python3 $COMPILER_PKG-$VERSION zlib1g-dev make wget tar python2.7
-
ln -sf /usr/bin/python2.7 /usr/bin/python
-
export CXX=${COMPILER_CPP}-$VERSION
-
export CC=${COMPILER_C}-$VERSION
.testing-gcc
:
extends
:
.testing-compilers
variables
:
CXX
:
g++
CC
:
gcc
.testing-clang
:
variables
:
COMPILER_PKG
:
"
clang"
COMPILER_CPP
:
"
clang++"
COMPILER_C
:
"
clang"
VERSION
:
$CLANG_VERSION
extends
:
-
.testing-compilers
-
.installing-compiler
# Overrides the before_script to install the compiler
.installing-testing-gcc
:
variables
:
COMPILER_PKG
:
"
g++"
COMPILER_CPP
:
"
g++"
COMPILER_C
:
"
gcc"
VERSION
:
$GCC_VERSION
extends
:
-
.testing-compilers
-
.installing-compiler
.testing_various_compilers_manual
:
when
:
manual
only
:
-
/^feature-.*a.*\/.*$/
-
schedules
.testing_various_compilers_release
:
only
:
-
/^feature-.*a.*\/release$/
test_gcc48_manual
:
image
:
debian:8-slim
variables
:
GCC_VERSION
:
"
4.8"
extends
:
-
.installing-testing-gcc
-
.testing_various_compilers_manual
test_gcc48_release
:
image
:
debian:8-slim
variables
:
GCC_VERSION
:
"
4.8"
extends
:
-
.installing-testing-gcc
-
.testing_various_compilers_release
test_gcc5_manual
:
image
:
gcc:5.3
extends
:
-
.testing-gcc
-
.testing_various_compilers_manual
test_gcc5_release
:
image
:
gcc:5.3
extends
:
-
.testing-gcc
-
.testing_various_compilers_release
test_gcc6_manual
:
image
:
gcc:6.3
extends
:
-
.testing-gcc
-
.testing_various_compilers_manual
test_gcc6_release
:
image
:
gcc:6.3
extends
:
-
.testing-gcc
-
.testing_various_compilers_release
test_gcc7_manual
:
image
:
gcc:7.3
extends
:
-
.testing-gcc
-
.testing_various_compilers_manual
test_gcc7_release
:
image
:
gcc:7.3
extends
:
-
.testing-gcc
-
.testing_various_compilers_release
test_gcc8_manual
:
image
:
gcc:8
extends
:
-
.testing-gcc
-
.testing_various_compilers_manual
test_gcc8_release
:
image
:
gcc:8
extends
:
-
.testing-gcc
-
.testing_various_compilers_release
test_gcc9_manual
:
image
:
gcc:9
extends
:
-
.testing-gcc
-
.testing_various_compilers_manual
test_gcc9_release
:
image
:
gcc:9
extends
:
-
.testing-gcc
-
.testing_various_compilers_release
test_clang34_manual
:
image
:
debian:8-slim
variables
:
CLANG_VERSION
:
"
3.4"
extends
:
-
.testing-clang
-
.testing_various_compilers_manual
test_clang34_release
:
image
:
debian:8-slim
variables
:
CLANG_VERSION
:
"
3.4"
extends
:
-
.testing-clang
-
.testing_various_compilers_release
test_clang4_manual
:
image
:
debian:8-slim
variables
:
CLANG_VERSION
:
"
4.0"
extends
:
-
.testing-clang
-
.testing_various_compilers_manual
test_clang4_release
:
image
:
debian:8-slim
variables
:
CLANG_VERSION
:
"
4.0"
extends
:
-
.testing-clang
-
.testing_various_compilers_release
test_clang6_manual
:
image
:
debian:8-slim
variables
:
CLANG_VERSION
:
"
6.0"
extends
:
-
.testing-clang
-
.testing_various_compilers_manual
test_clang6_release
:
image
:
debian:8-slim
variables
:
CLANG_VERSION
:
"
6.0"
extends
:
-
.testing-clang
-
.testing_various_compilers_release
test_clang7_manual
:
image
:
debian:10-slim
variables
:
CLANG_VERSION
:
"
7"
extends
:
-
.testing-clang
-
.testing_various_compilers_manual
test_clang7_release
:
image
:
debian:10-slim
variables
:
CLANG_VERSION
:
"
7"
extends
:
-
.testing-clang
-
.testing_various_compilers_release
algo/tests/should-get-tests/analysis-ikaros.should
View file @
10e44733
...
...
@@ -6,7 +6,7 @@ $ All sequences have been seen as unique clone
$ All sequences have been seen as different IKZF1 recombinations
1: IKZF1 .* 22
### control sequence given by Debr
é
###
### control sequence given by Debr
e
###
# del4-7__jonction_intron3_intron7
$ Find the correct assignation for the sequence IKZF1-INTRON-3//IKZF1-INTRON-7
1: IKZF1-INTRON-3 16/CCCGCG/8 IKZF1-INTRON-7
...
...
@@ -38,9 +38,9 @@ $ Find the correct assignation for the sequence
### 13922 - sequences ikfz1 ####
$ Find the correct assignation for the sequence (t
é
moin del4-7)
$ Find the correct assignation for the sequence (t
e
moin del4-7)
1: IKZF1-INTRON-3 1//2 IKZF1-INTRON-7
$ Find the correct assignation for the sequence (t
é
moin del2-7)
$ Find the correct assignation for the sequence (t
e
moin del2-7)
1: IKZF1-INTRON-1 8/CCCTTC/3 IKZF1-INTRON-7
$ Find the correct assignation for the sequence (seq 4-7 du patient)
1: IKZF1-INTRON-3 0/TCGG/6 IKZF1-INTRON-7
...
...
algo/tests/unit-tests/testAffectAnalyser.cpp
View file @
10e44733
...
...
@@ -250,8 +250,9 @@ void testGetMaximum() {
// ^^^^^^^^^^
vector
<
KmerAffect
>
affectations
(
a
,
a
+
sizeof
(
a
)
/
sizeof
(
KmerAffect
));
KmerAffectAnalyser
kaa
(
*
index
,
""
,
affectations
);
TAP_TEST_EQUAL
(
kaa
.
getSequence
(),
""
,
TEST_AA_GET_SEQUENCE
,
""
);
string
seq
=
"AAAAAAAAAAAAAA"
;
KmerAffectAnalyser
kaa
(
*
index
,
seq
,
affectations
);
TAP_TEST_EQUAL
(
kaa
.
getSequence
(),
seq
,
TEST_AA_GET_SEQUENCE
,
""
);
affect_infos
results
=
kaa
.
getMaximum
(
AFFECT_J_BWD
,
AFFECT_V_BWD
,
2.
,
0
);
TAP_TEST
(
!
results
.
max_found
,
TEST_AA_GET_MAXIMUM_MAX_FOUND
,
...
...
@@ -288,7 +289,8 @@ void testGetMaximum() {
// V V V V V V V V V V J J J V V V
// ^^^^^^^^^^^^
vector
<
KmerAffect
>
affectations2
(
a2
,
a2
+
sizeof
(
a2
)
/
sizeof
(
KmerAffect
));
KmerAffectAnalyser
kaa2
(
*
index
,
""
,
affectations2
);
seq
=
"AAAAAAAAAAAAAAAA"
;
KmerAffectAnalyser
kaa2
(
*
index
,
seq
,
affectations2
);
results
=
kaa2
.
getMaximum
(
AFFECT_V
,
AFFECT_J
,
2.
,
0
);
TAP_TEST
(
!
results
.
max_found
,
TEST_AA_GET_MAXIMUM_MAX_FOUND
,
"("
<<
results
.
first_pos_max
...
...
@@ -332,7 +334,8 @@ void testGetMaximum() {
// V V V V V V J J J // nb_before_left (6), nb_after_right (3)
// V // nb_before_right (1)
vector
<
KmerAffect
>
affectations3
(
a3
,
a3
+
sizeof
(
a3
)
/
sizeof
(
KmerAffect
));
KmerAffectAnalyser
kaa3
(
*
index
,
""
,
affectations3
);
seq
=
"AAAAAAAAAAAAAAAAAAAAA"
;
KmerAffectAnalyser
kaa3
(
*
index
,
seq
,
affectations3
);
// span = 4, maxOverlap = 0
results
=
kaa3
.
getMaximum
(
AFFECT_V
,
AFFECT_J
,
2.
,
0
);
...
...
@@ -363,7 +366,7 @@ void testGetMaximum() {
// ^^^^^^^^^
// V V V V V V J J J J J J // nb_before_left (6), nb_after_right (6)
vector
<
KmerAffect
>
affectations4
(
a4
,
a4
+
sizeof
(
a4
)
/
sizeof
(
KmerAffect
));
KmerAffectAnalyser
kaa4
(
*
index
,
""
,
affectations4
);
KmerAffectAnalyser
kaa4
(
*
index
,
seq
,
affectations4
);
// span = 4, maxOverlap = 0
results
=
kaa4
.
getMaximum
(
AFFECT_V
,
AFFECT_J
,
2.
,
0
);
...
...
@@ -396,7 +399,7 @@ void testGetMaximum() {
// J J J // nb_after_left (3)
vector
<
KmerAffect
>
affectations5
(
a5
,
a5
+
sizeof
(
a5
)
/
sizeof
(
KmerAffect
));
KmerAffectAnalyser
kaa5
(
*
index
,
""
,
affectations5
);
KmerAffectAnalyser
kaa5
(
*
index
,
seq
,
affectations5
);
results
=
kaa5
.
getMaximum
(
AFFECT_V
,
AFFECT_J
,
2.
,
0
);
TAP_TEST
(
!
results
.
max_found
,
TEST_AA_GET_MAXIMUM_MAX_FOUND
,
...
...
@@ -425,7 +428,7 @@ void testGetMaximum() {
// J-J-J-J-J-J-J-J-V-V-V-V-V-J-J-J-V-V-V-V-
// ^^^^^^^^^^
vector
<
KmerAffect
>
affectations6
(
a6
,
a6
+
sizeof
(
a6
)
/
sizeof
(
KmerAffect
));
KmerAffectAnalyser
kaa6
(
*
index
,
""
,
affectations6
);
KmerAffectAnalyser
kaa6
(
*
index
,
seq
,
affectations6
);
results
=
kaa6
.
getMaximum
(
AFFECT_J_BWD
,
AFFECT_V_BWD
,
2.
,
0
);
TAP_TEST
(
!
results
.
max_found
,
TEST_AA_GET_MAXIMUM_MAX_FOUND
,
...
...
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