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vidjil
vidjil
Commits
7b073b43
Commit
7b073b43
authored
Apr 13, 2016
by
marc
Browse files
pre_process: reup pre_process files lost during rebase
parent
bf323460
Changes
4
Hide whitespace changes
Inline
Side-by-side
server/web2py/applications/vidjil/controllers/pre_process.py
0 → 100644
View file @
7b073b43
# coding: utf8
import
gluon.contrib.simplejson
if
request
.
env
.
http_origin
:
response
.
headers
[
'Access-Control-Allow-Origin'
]
=
request
.
env
.
http_origin
response
.
headers
[
'Access-Control-Allow-Credentials'
]
=
'true'
response
.
headers
[
'Access-Control-Max-Age'
]
=
86400
ACCESS_DENIED
=
"access denied"
def
index
():
if
not
auth
.
user
:
res
=
{
"redirect"
:
"default/user/login"
}
return
gluon
.
contrib
.
simplejson
.
dumps
(
res
,
separators
=
(
','
,
':'
))
query
=
db
((
auth
.
accessible_query
(
'read'
,
db
.
pre_process
)
|
auth
.
accessible_query
(
'admin'
,
db
.
pre_process
)
)
).
select
(
orderby
=~
db
.
pre_process
.
name
)
return
dict
(
message
=
T
(
'Pre-process list'
),
query
=
query
,
isAdmin
=
auth
.
is_admin
())
def
add
():
return
dict
(
message
=
T
(
'Add pre-process'
))
def
add_form
():
error
=
""
required_fields
=
[
'config_name'
,
'config_command'
,
'config_fuse_command'
,
'config_program'
]
for
field
in
required_fields
:
if
request
.
vars
[
field
]
==
""
:
error
+=
field
+
" needed, "
if
error
==
""
:
db
.
config
.
insert
(
name
=
request
.
vars
[
'config_name'
],
info
=
request
.
vars
[
'config_info'
],
command
=
request
.
vars
[
'config_command'
],
fuse_command
=
request
.
vars
[
'config_fuse_command'
],
program
=
request
.
vars
[
'config_program'
]
)
res
=
{
"redirect"
:
"config/index"
,
"message"
:
"config '%s' added"
%
request
.
vars
[
'config_name'
]}
log
.
admin
(
res
)
return
gluon
.
contrib
.
simplejson
.
dumps
(
res
,
separators
=
(
','
,
':'
))
else
:
res
=
{
"success"
:
"false"
,
"message"
:
error
}
log
.
error
(
res
)
return
gluon
.
contrib
.
simplejson
.
dumps
(
res
,
separators
=
(
','
,
':'
))
def
edit
():
return
dict
(
message
=
T
(
'edit config'
))
def
edit_form
():
error
=
""
required_fields
=
[
'id'
,
'config_name'
,
'config_command'
,
'config_fuse_command'
,
'config_program'
]
for
field
in
required_fields
:
if
request
.
vars
[
field
]
==
""
:
error
+=
field
+
" needed, "
if
error
==
""
:
db
.
config
[
request
.
vars
[
"id"
]]
=
dict
(
name
=
request
.
vars
[
'config_name'
],
info
=
request
.
vars
[
'config_info'
],
command
=
request
.
vars
[
'config_command'
],
fuse_command
=
request
.
vars
[
'config_fuse_command'
],
program
=
request
.
vars
[
'config_program'
]
)
res
=
{
"redirect"
:
"config/index"
,
"message"
:
"config '%s' updated"
%
request
.
vars
[
'config_name'
]}
log
.
admin
(
res
)
return
gluon
.
contrib
.
simplejson
.
dumps
(
res
,
separators
=
(
','
,
':'
))
else
:
res
=
{
"success"
:
"false"
,
"message"
:
error
}
log
.
error
(
res
)
return
gluon
.
contrib
.
simplejson
.
dumps
(
res
,
separators
=
(
','
,
':'
))
def
confirm
():
return
dict
(
message
=
T
(
'confirm config deletion'
))
def
delete
():
#delete results_file using this config
db
(
db
.
results_file
.
config_id
==
request
.
vars
[
"id"
]).
delete
()
#delete config
db
(
db
.
config
.
id
==
request
.
vars
[
"id"
]).
delete
()
res
=
{
"redirect"
:
"config/index"
,
"message"
:
"config '%s' deleted"
%
request
.
vars
[
"id"
]}
log
.
admin
(
res
)
return
gluon
.
contrib
.
simplejson
.
dumps
(
res
,
separators
=
(
','
,
':'
))
server/web2py/applications/vidjil/views/pre_process/add.html
0 → 100644
View file @
7b073b43
{{extend 'db_layout.html'}}
<form
id=
"data_form"
action=
"DB_ADDRESS/pre_process/add_form"
enctype=
"multipart/form-data"
method=
"post"
>
<table>
<tbody>
<tr>
<td
>
<label
for=
"pre_process_name"
id=
"pre_process_name__label"
>
Name:
</label>
</td>
<td
>
<input
class=
"string"
id=
"pre_process_name"
name=
"pre_process_name"
type=
"text"
value=
""
>
</td>
<td
>
</td>
</tr>
<tr>
<td>
<label
for=
"pre_process_command"
id=
"pre_process_command__label"
>
Command:
</label>
</td>
<td>
<textarea
class=
"text"
cols=
"60"
id=
"pre_process_command"
name=
"pre_process_command"
rows=
"10"
></textarea>
</td>
<td>
Describe the command usage of your script to help Vidjil to use it correctly.
</br>
replace in your command input file paths with
&
file1
&
and
&
file2
&
and result file path with
&
result
&
<br>
for exemple the command:
<br>
<span
style=
"font-family: 'courier'"
>
python myReadMergerScript.py -n 50 sample_r1.fastq sample_r2.fastq -o result.fastq
</span><br>
must be described as:
<br>
<span
style=
"font-family: 'courier'"
>
python myReadMergerScript.py -n 50
&
file1
&
&
file2
&
-o
&
result
&
</span><br>
</td>
</tr>
<tr>
<td>
<label
for=
"pre_process_info"
id=
"pre_process_info__label"
>
Info:
</label>
</td>
<td>
<textarea
class=
"text"
cols=
"60"
id=
"pre_process_info"
name=
"pre_process_info"
rows=
"10"
></textarea>
</td>
<td>
</td>
</tr>
<tr>
<td>
</td>
<td
><input
type=
"submit"
value=
"Soumettre"
class=
"btn"
>
</td>
<td>
</td>
</tr>
</tbody>
</table>
</form>
server/web2py/applications/vidjil/views/pre_process/edit.html
0 → 100644
View file @
7b073b43
{{extend 'db_layout.html'}}
{{
info = db.pre_process[request.vars["id"]]
}}
<form
id=
"data_form"
action=
"DB_ADDRESS/pre_process/edit_form"
enctype=
"multipart/form-data"
method=
"post"
>
<input
type=
"HIDDEN"
id=
"pre_process_id"
name=
"id"
value=
"{{=request.vars["
id
"]}}"
>
<table>
<tbody>
<tr>
<td
>
<label
for=
"pre_process_name"
id=
"pre_process_name__label"
>
Name:
</label>
</td>
<td
>
<input
class=
"string"
id=
"pre_process_name"
name=
"pre_process_name"
type=
"text"
value=
"{{=info.name}}"
>
</td>
<td
>
</td>
</tr>
<tr>
<td>
<label
for=
"pre_process_command"
id=
"pre_process_command__label"
>
Command:
</label>
</td>
<td>
<textarea
class=
"text"
cols=
"60"
id=
"pre_process_command"
name=
"pre_process_command"
rows=
"10"
>
{{=info.command}}
</textarea>
</td>
<td>
</td>
</tr>
<tr>
<tr>
<td>
<label
for=
"pre_process_info"
id=
"pre_process_info__label"
>
Info:
</label>
</td>
<td>
<textarea
class=
"text"
cols=
"80"
id=
"pre_process_info"
name=
"pre_process_info"
rows=
"10"
>
{{=info.info}}
</textarea>
</td>
<td>
</td>
</tr>
<tr>
<td>
</td>
<td
><input
type=
"submit"
value=
"Soumettre"
class=
"btn"
>
</td>
<td>
</td>
</tr>
</tbody>
</table>
</form>
server/web2py/applications/vidjil/views/pre_process/index.html
0 → 100644
View file @
7b073b43
{{extend 'db_layout.html'}}
{{('message' in globals())}}
{{if 'message' in globals():}}
<h3>
{{=message}}
</h3>
<div
id=
"db_table_container"
>
<table
class=
"db_table"
id=
"table"
>
<thead>
<tr><td
class=
"column_50"
></td>
<td
class=
"column2"
>
name
</td>
<td>
command
</td>
<td>
info
</td>
<td
class=
"column5"
>
</td>
<td
class=
"column5"
>
</td>
<td
class=
"column5"
>
</td>
</tr>
</thead>
{{ for row in query :}}
<tr>
<td>
{{=row.id }}
</td>
<td>
{{=row.name }}
</td>
<td>
{{=row.command }}
</td>
<td>
{{=row.info }}
</td>
{{if isAdmin:}}
<td
onclick=
"db.call('pre_process/permission', {'id' :'{{=row.id}}'} )"
>
<i
class=
"icon-key"
title=
"set permissions"
></i>
</td>
{{else:}}
<td></td>
{{pass}}
<td
onclick=
"db.call('pre_process/edit', {'id' :'{{=row.id}}'} )"
>
<i
class=
"icon-pencil-2"
title=
"edit pre-process"
></i>
</td>
<td
onclick=
"db.call('pre_process/confirm', {'id' :'{{=row.id}}'} )"
>
<i
class=
"icon-erase"
title=
"delete pre-process"
></i>
</td>
</tr>
{{pass}}
</table>
<table
class=
"db_table"
id=
"db_fixed_header"
></table>
</div>
<span
class=
"button2"
onclick=
"db.call('pre_process/add')"
>
+ new pre-process
</span>
{{elif 'content' in globals():}}
{{=content}}
{{else:}}
{{=BEAUTIFY(response._vars)}}
{{pass}}
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