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genotoul-bioinfo
D-GENIES
Commits
8c92c3f8
Commit
8c92c3f8
authored
Apr 16, 2018
by
Floreal Cabanettes
Browse files
Fix headers bug
parent
5a472292
Changes
6
Expand all
Hide whitespace changes
Inline
Side-by-side
src/dgenies/lib/functions.py
View file @
8c92c3f8
...
...
@@ -283,3 +283,12 @@ class Functions:
def
query_fasta_file_exists
(
res_dir
):
fasta_file
=
os
.
path
.
join
(
res_dir
,
".query"
)
return
os
.
path
.
exists
(
fasta_file
)
and
os
.
path
.
isfile
(
fasta_file
)
@
staticmethod
def
replace_headers
(
text
):
headers
=
re
.
findall
(
"<h\d id=
\"
[^
\"
]+
\"
>"
,
text
)
for
header
in
headers
:
id_header
=
re
.
search
(
"id=
\"
([^
\"
]+)
\"
"
,
header
).
group
(
1
)
text
=
text
.
replace
(
header
,
"<span class=
\"
anchor
\"
id=
\"
%s
\"
></span>%s"
%
(
id_header
,
re
.
sub
(
r
"id=\"[^\"]+\""
,
"class=
\"
section
\"
"
,
header
)))
return
text
src/dgenies/md/doc_run.md
View file @
8c92c3f8
...
...
@@ -49,7 +49,7 @@ Files must be in fasta format. We recommend using gzipped files to preserve band
Allowed extensions: fa, fasta, fna, fa.gz, fasta.gz, fna.gz
Max file size:
###
size
### (###
size_unc
###
once uncompressed,
###
size_ava
###
in all-vs-all mode)
Max file size:
{{
size
}} ({{
size_unc
}}
once uncompressed,
{{
size_ava
}}
in all-vs-all mode)
{% set puce=puce+1 %}
...
...
@@ -59,7 +59,7 @@ Optional field
Works like the target fasta. If not given, target file will be mapped to itself, in all-vs-all mode.
Max file size:
###
size
### (###
size_unc
###
once uncompressed)
Max file size:
{{
size
}} ({{
size_unc
}}
once uncompressed)
{% set puce=puce+1 %}
...
...
src/dgenies/static/css/dgenies.css
View file @
8c92c3f8
...
...
@@ -4,6 +4,13 @@ body {
padding-top
:
50px
;
}
.anchor
{
display
:
block
;
height
:
50px
;
/*same height as header*/
margin-top
:
-50px
;
/*same height as header*/
visibility
:
hidden
;
}
#main-error
{
display
:
none
;
width
:
100%
;
...
...
src/dgenies/static/css/dgenies.min.css
View file @
8c92c3f8
This diff is collapsed.
Click to expand it.
src/dgenies/templates/documentation.html
View file @
8c92c3f8
...
...
@@ -63,7 +63,7 @@
{% endif %}
<div
id=
"body"
>
{{ content }}
{{ content
| safe
}}
</div>
{% endblock %}
\ No newline at end of file
src/dgenies/views.py
View file @
8c92c3f8
...
...
@@ -325,12 +325,6 @@ def get_file(file, gzip=False): # pragma: no cover
def
documentation_run
():
latest
=
Latest
()
version
=
latest
.
latest
with
open
(
os
.
path
.
join
(
app_folder
,
"md"
,
"doc_run.md"
),
"r"
,
encoding
=
'utf-8'
)
as
install_instr
:
content
=
install_instr
.
read
()
env
=
Environment
()
template
=
env
.
from_string
(
content
)
content
=
template
.
render
(
mode
=
MODE
,
version
=
version
)
md
=
Markdown
(
extensions
=
[
TocExtension
(
baselevel
=
1
)])
max_upload_file_size
=
config_reader
.
max_upload_file_size
if
max_upload_file_size
==
-
1
:
max_upload_file_size
=
"no limit"
...
...
@@ -346,9 +340,14 @@ def documentation_run():
max_upload_size_ava
=
"no limit"
else
:
max_upload_size_ava
=
Functions
.
get_readable_size
(
max_upload_size_ava
,
0
)
content
=
Markup
(
md
.
convert
(
content
)).
replace
(
"###size###"
,
max_upload_file_size
)
\
.
replace
(
"###size_unc###"
,
max_upload_size
)
\
.
replace
(
"###size_ava###"
,
max_upload_size_ava
)
with
open
(
os
.
path
.
join
(
app_folder
,
"md"
,
"doc_run.md"
),
"r"
,
encoding
=
'utf-8'
)
as
install_instr
:
content
=
install_instr
.
read
()
env
=
Environment
()
template
=
env
.
from_string
(
content
)
content
=
template
.
render
(
mode
=
MODE
,
version
=
version
,
size
=
max_upload_file_size
,
size_unc
=
max_upload_size
,
size_ava
=
max_upload_size_ava
)
md
=
Markdown
(
extensions
=
[
TocExtension
(
baselevel
=
1
)])
content
=
Functions
.
replace_headers
(
str
(
Markup
(
md
.
convert
(
content
))))
toc
=
Markup
(
md
.
toc
)
return
render_template
(
"documentation.html"
,
menu
=
"documentation"
,
content
=
content
,
toc
=
toc
)
...
...
@@ -359,7 +358,7 @@ def documentation_result():
encoding
=
'utf-8'
)
as
install_instr
:
content
=
install_instr
.
read
()
md
=
Markdown
(
extensions
=
[
TocExtension
(
baselevel
=
1
)])
content
=
Markup
(
md
.
convert
(
content
))
content
=
Functions
.
replace_headers
(
str
(
Markup
(
md
.
convert
(
content
))
))
toc
=
Markup
(
md
.
toc
)
return
render_template
(
"documentation.html"
,
menu
=
"documentation"
,
content
=
content
,
toc
=
toc
)
...
...
@@ -370,7 +369,7 @@ def documentation_formats():
encoding
=
'utf-8'
)
as
install_instr
:
content
=
install_instr
.
read
()
md
=
Markdown
(
extensions
=
[
TocExtension
(
baselevel
=
1
),
TableExtension
()])
content
=
Markup
(
md
.
convert
(
content
))
content
=
Functions
.
replace_headers
(
str
(
Markup
(
md
.
convert
(
content
))
))
toc
=
Markup
(
md
.
toc
)
return
render_template
(
"documentation.html"
,
menu
=
"documentation"
,
content
=
content
,
toc
=
toc
)
...
...
@@ -381,7 +380,7 @@ def documentation_dotplot():
encoding
=
'utf-8'
)
as
install_instr
:
content
=
install_instr
.
read
()
md
=
Markdown
(
extensions
=
[
TocExtension
(
baselevel
=
1
)])
content
=
Markup
(
md
.
convert
(
content
))
content
=
Functions
.
replace_headers
(
str
(
Markup
(
md
.
convert
(
content
))
))
toc
=
Markup
(
md
.
toc
)
return
render_template
(
"documentation.html"
,
menu
=
"documentation"
,
content
=
content
,
toc
=
toc
)
...
...
@@ -396,7 +395,7 @@ def install():
template
=
env
.
from_string
(
content
)
content
=
template
.
render
(
version
=
latest
.
latest
,
win32
=
latest
.
win32
)
md
=
Markdown
(
extensions
=
[
TocExtension
(
baselevel
=
1
)])
content
=
Markup
(
md
.
convert
(
content
))
content
=
Functions
.
replace_headers
(
str
(
Markup
(
md
.
convert
(
content
))
))
toc
=
Markup
(
md
.
toc
)
return
render_template
(
"documentation.html"
,
menu
=
"install"
,
content
=
content
,
toc
=
toc
)
...
...
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