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ensembl-gh-mirror
ensembl
Commits
da44116e
Commit
da44116e
authored
Nov 17, 2011
by
Ian Longden
Browse files
test code to make sure the tutorials on the core api page run okay
parent
5ce05bf5
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misc-scripts/core_tutorial_test/test_code_from_html.pl
misc-scripts/core_tutorial_test/test_code_from_html.pl
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misc-scripts/core_tutorial_test/test_code_from_html.pl
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da44116e
use
strict
;
use
Getopt::
Long
;
my
$path
;
my
$host
;
my
$user
;
my
$ret
=
Getopt::Long::
GetOptions
('
path=s
'
=>
\
$path
,
'
host=s
'
=>
\
$host
,
'
user=s
'
=>
\
$user
,
'
help
'
=>
sub
{
usage
();
exit
(
0
);
}
);
if
(
!
defined
$path
){
print
"
you must defined the path to the ensembl webcode
\n
";
usage
();
exit
(
0
);
}
my
$file
=
$path
.
"
/ensembl-webcode/htdocs/info/docs/api/core/core_tutorial.html
";
my
$code_count
=
0
;
$user
||=
"
ensro
";
$host
||=
"
ens-staging
";
my
$header
=
(
<<
"
HED
");
####### start of insertion #########
use
Bio::EnsEMBL::
Registry
;
my
\
$registry
=
'
Bio::EnsEMBL::Registry
';
\
$registry
->
load_registry_from_db
(
-
host
=>
"
$host
",
-
user
=>
"
$user
");
HED
my
$slice_adaptor
=
(
<<
'
SLI
');
my
$slice_adaptor
=
$registry
->
get_adaptor
(
'
Human
',
'
Core
',
'
Slice
'
);
SLI
open
(
HTML
,"
<
$file
")
||
die
"
Could not open
$file
\n
";
my
$code_mode
=
0
;
my
$code
=
"";
while
(
my
$line
=
<
HTML
>
){
chomp
$line
;
# print $line."DUDE\n";
if
(
$code_mode
){
if
(
$line
=~
m/\<\/pre\>/
){
$code_mode
=
0
;
process_code
();
$code
=
"";
}
else
{
$code
.=
"
\n
"
.
$line
;
}
}
elsif
(
$line
=~
m/pre.*code/
){
# print "CODEMODE*******\n";
$code_mode
=
1
;
}
}
close
HTML
;
sub
process_code
{
$code_count
++
;
$file
=
"
test
"
.
$code_count
.
"
.pl
";
open
(
PERL
,"
>
"
.
$file
)
or
die
"
Could not open
$file
for writing
\n
";
$code
=~
s/\>\;/\>/g
;
my
$prefix
=
"";
if
(
!
(
$code
=~
/load_registry_from_db/m
)){
$prefix
=
$header
;
if
(
!
(
$code
=~
/my\s*\$slice_adaptor/
)){
$prefix
.=
$slice_adaptor
;
if
(
!
(
$code
=~
/fetch_by_region/
)){
$prefix
.=
'
my $slice = $slice_adaptor->fetch_by_region( "clone", "AL031658.11" );
'
.
"
\n
";
}
}
if
(
!
(
$code
=~
/my\s*\$cs_adaptor/
)){
$prefix
.=
'
my $cs_adaptor = $registry->get_adaptor( "Human", "Core", "CoordSystem" );
'
.
"
\n
";;
}
if
(
!
(
$code
=~
/my\s*\$gene_adaptor/
)){
$prefix
.=
'
my $gene_adaptor = $registry->get_adaptor( "Human", "Core", "Gene" );
'
.
"
\n
";;
}
if
(
$code
=~
/\$feature\-\>/
and
!
(
$code
=~
/\$feature_adaptor/
)
){
$prefix
.=
'
my $feat_adaptor = $registry->get_adaptor( "Human", "Core", "Gene" );
'
.
"
\n
";
$prefix
.=
'
my $feature = $feat_adaptor->fetch_by_display_label("COG6");
'
.
"
\n
";
}
if
(
$code
=~
/\$transcript\-\>/
and
!
(
$code
=~
/\$transcript_adaptor/
)
){
$prefix
.=
'
my $transcript_adaptor = $registry->get_adaptor( "Human", "Core", "transcript" );
'
.
"
\n
";
$prefix
.=
'
my $transcript = $transcript_adaptor->fetch_by_stable_id("ENST00000380152");
'
.
"
\n
";
}
if
(
$code
=~
/\$translation\-\>/
and
!
(
$code
=~
/\$translation_adaptor/
)
){
$prefix
.=
'
my $transcript_adaptor = $registry->get_adaptor( "Human", "Core", "transcript" );
'
.
"
\n
";
$prefix
.=
'
my $transcript = $transcript_adaptor->fetch_by_stable_id("ENST00000380152");
'
.
"
\n
";
$prefix
.=
'
my $translation = $transcript->translation;
'
.
"
\n
";
}
if
(
$code
=~
/\$marker\-\>/
and
!
(
$code
=~
/\$marker_adaptor/
)
){
$prefix
.=
'
my $marker_adaptor = $registry->get_adaptor( "Human", "Core", "marker" );
'
.
"
\n
";
$prefix
.=
'
my $marker = $marker_adaptor->fetch_all_by_synonym("D9S1038E")->[0];
'
.
"
\n
";
}
}
$code
=
$prefix
.
"
####### end of insertion#########
\n
"
.
$code
;
print
PERL
$code
.
"
\n
";;
close
PERL
;
sleep
2
;
# print "CODE".$code."\n";
my
$test_val
=
system
("
perl
$file
>& /dev/null
");
# print "VAL is $test_val\n";
# my $test_val = eval {$code};
if
(
$test_val
){
print
"
file
$file
FAILED
$test_val
\n
";
}
else
{
print
"
file
$file
OKAY
$test_val
\n
";
}
}
sub
usage
{
print
<<
"
EOF
";
perl
test_code_from_html
.
pl
This
script
will
strip
and
create
seperate
perl
files
for
any
block
in
the
html
that
is
in
surrounded
by
<
pre
class
=
"
code
"
>
...
</
pre
>
The
script
adds
registry
code
etc
at
the
start
if
is
not
a
full
code
example
.
These
perl
scripts
are
then
executed
and
the
status
of
this
run
reports
if
the
code
as
successfully
executed
.
-
path
The
path
to
the
ensembl
-
webcode
directory
(
Must
be
set
)
-
user
User
name
to
be
used
for
the
mysql
instance
-
host
Host
name
of
the
mysql
instance
(
defualt
ens
-
staging
)
i
.
e
.
perl
test_code_from_html
-
path
~/
src
EOF
}
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