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genotoul-bioinfo
jflow
Commits
dae949ca
Commit
dae949ca
authored
Nov 06, 2017
by
Celine Noirot
Browse files
Remove useless lib
parent
ac366bf3
Changes
5
Expand all
Hide whitespace changes
Inline
Side-by-side
src/jflow/featureiolib/gff3.py
View file @
dae949ca
...
...
@@ -15,7 +15,7 @@
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
import
sys
,
re
import
re
class
GFF3Record
:
"""
...
...
src/jflow/seqio.py
View file @
dae949ca
...
...
@@ -26,7 +26,6 @@ __status__ = 'beta'
from
collections
import
namedtuple
import
sys
import
struct
import
os
import
io
str
=
str
from
codecs
import
getreader
,
getwriter
...
...
src/jflow/workflow.py
View file @
dae949ca
...
...
@@ -30,8 +30,6 @@ import datetime
import
logging
import
traceback
from
configparser
import
ConfigParser
,
NoOptionError
from
inspect
import
getcallargs
from
datetime
import
date
as
ddate
from
collections
import
OrderedDict
...
...
@@ -1373,8 +1371,9 @@ class Workflow(threading.Thread):
if
parameter
.
rules
is
not
None
:
rules
[
parameter
.
name
]
=
parameter
.
rules
.
split
(
";"
)
if
isinstance
(
parameter
,
InputFileList
)
and
parameter
.
name
in
user_params
:
if
len
(
set
(
user_params
[
parameter
.
name
]))
<
len
(
user_params
[
parameter
.
name
]):
raise
RuleException
(
"Error for parameter '"
+
parameter
.
name
+
"': some files are duplicated"
)
# if only one element, type is not a list and test doen't works
if
isinstance
(
user_params
[
parameter
.
name
],
list
)
and
len
(
set
(
user_params
[
parameter
.
name
]))
<
len
(
user_params
[
parameter
.
name
]):
raise
RuleException
(
"Error for parameter '"
+
parameter
.
name
+
"': some files are duplicated"
+
user_params
[
parameter
.
name
]
+
":"
+
user_params
[
parameter
.
name
]
+
" "
+
str
(
len
(
parameter
)))
# Check rules:
for
src_arg
,
arg_rules
in
rules
.
items
():
...
...
src/js/jflow-wfform.js
View file @
dae949ca
...
...
@@ -691,10 +691,10 @@ Handsontable.cellTypes["bootdate"] = Handsontable.BootstrapDateCell;
// trigger an event to specify the workflow is loaded
$this
.
$element
.
trigger
(
'
loaded.wfform
'
,
$this
.
workflow
);
$this
.
$element
.
html
(
""
);
$
.
tmpl
(
globalTemplate
,
{
$
.
tmpl
(
globalTemplate
,
{
workflow
:
$this
.
workflow
,
display_form_type
:
$this
.
options
.
displayFormType
,
display_run_button
:
$this
.
options
.
displayRunButton
,
display_reset_button
:
$this
.
options
.
displayResetButton
,
parameters
:
$this
.
options
.
parameters
,
...
...
@@ -936,7 +936,7 @@ Handsontable.cellTypes["bootdate"] = Handsontable.BootstrapDateCell;
JflowBrowser
.
exec
(
fill_files
,
true
);
return
false
;
})
$
(
"
.to-readonly
"
).
on
(
"
focusin
"
,
function
(
event
)
{
$
(
this
).
prop
(
'
readonly
'
,
true
);
});
...
...
@@ -1211,6 +1211,20 @@ Handsontable.cellTypes["bootdate"] = Handsontable.BootstrapDateCell;
if
(
$
(
"
[id^=handsontable_]
"
).
length
==
0
)
{
params
=
JflowWfformRules
.
check_parameters_rules
(
$this
.
workflow
.
parameters
,
$this
);
}
if
(
$this
.
options
.
displayFormType
==
"
collapse
"
)
{
$
(
'
.btn-moreless
'
).
click
(
function
()
{
var
$this
=
$
(
this
);
if
(
$this
.
children
().
hasClass
(
'
glyphicon-chevron-down
'
))
{
$this
.
html
(
'
<span class="glyphicon glyphicon-chevron-up"></span>
'
);
}
else
{
$this
.
html
(
'
<span class="glyphicon glyphicon-chevron-down"></span>
'
);
}
});
}
}
});
}
...
...
@@ -1236,6 +1250,7 @@ Handsontable.cellTypes["bootdate"] = Handsontable.BootstrapDateCell;
}
WFForm
.
prototype
.
_getParameterRule
=
function
(
param
,
server_url
)
{
var
crule
=
{};
crule
[
"
mparam
"
]
=
param
;
if
(
param
.
type
==
"
int
"
&&
param
.
action
==
"
append
"
)
{
...
...
@@ -1249,11 +1264,10 @@ Handsontable.cellTypes["bootdate"] = Handsontable.BootstrapDateCell;
}
else
if
(
param
.
type
.
indexOf
(
"
browsefile
"
)
===
0
)
{
var
size
=
param
.
type
.
split
(
SIZE_LIMIT_SPLITER
)[
1
];
crule
[
"
maxfilesize
"
]
=
[
this
.
getNbOctet
(
size
),
size
];
// if it is not a known type, check from the custom ones, using the validate_field addres
s
// if it's a input file list with choice
s
}
else
if
(
param
.
type
.
indexOf
(
"
inputfiles
"
)
===
0
&&
param
.
action
==
"
append
"
&&
param
.
choices
!=
"
undefined
"
)
{
//ASK Jerome HowTo debug
crule
[
'
inputfiles
'
]
=
true
;
console
.
log
(
param
);
// if it is not a known type, check from the custom ones, using the validate_field address
}
else
if
(
param
.
type
!=
"
str
"
&&
param
.
type
!=
"
password
"
)
{
crule
[
"
remote
"
]
=
{
url
:
server_url
+
'
/validate_field?callback=?
'
,
...
...
@@ -1331,7 +1345,24 @@ Handsontable.cellTypes["bootdate"] = Handsontable.BootstrapDateCell;
'
{{each(gindex, group) workflow.groups}}
'
,
'
<fieldset>
'
,
'
{{if group != "default" }}
'
,
'
<legend>${group}</legend>
'
,
'
<div class="row"><div class="col-sm-8"><legend>
'
,
'
${group}
'
,
'
</legend></div>
'
,
'
<div class="col-sm-4">
'
,
'
{{if display_form_type == "collapse"}}
'
,
'
<button class="btn btn-default btn-moreless" type="button" data-toggle="collapse" data-target="#collapse${gindex}" aria-expanded="false" aria-controls="collapse${gindex}">
'
,
'
{{if gindex <= 1 }}
'
,
'
<span class="glyphicon glyphicon-chevron-up"></span>
'
,
'
{{else}}
'
,
'
<span class="glyphicon glyphicon-chevron-down"></span>
'
,
'
{{/if}}
'
,
'
</button>
'
,
'
{{/if}}
'
,
'
</div>
'
,
'
</div>
'
,
'
{{/if}}
'
,
'
{{if display_form_type == "collapse"}}
'
,
'
<div id="collapse${gindex}" class="collapse {{if gindex <= 1 }} in{{/if}}">
'
,
'
{{/if}}
'
,
'
{{each(index, param) workflow.parameters_per_groups[group]}}
'
,
// it the parameter has not already been settled
...
...
@@ -1382,7 +1413,10 @@ Handsontable.cellTypes["bootdate"] = Handsontable.BootstrapDateCell;
'
{{/if}}
'
,
'
{{/if}}
'
,
'
{{/each}}
'
,
'
</fieldset>
'
,
'
{{if display_form_type == "collapse"}}
'
,
'
</div>
'
,
'
{{/if}}
'
,
'
</fieldset>
'
,
'
{{/each}}
'
,
'
<fieldset>
'
,
// for all workflow add the workflowClass
...
...
@@ -1423,13 +1457,13 @@ Handsontable.cellTypes["bootdate"] = Handsontable.BootstrapDateCell;
'
<input name="browse_${sub_param.name}" id="browse_${sub_param.name}" class="fileupload" type="file">
'
,
'
{{/if}}
'
,
'
{{/if}}
'
,
'
{{/each}}
'
,
'
{{/each}}
'
,
'
{{/if}}
'
,
'
{{/each}}
'
,
'
{{/each}}
'
,
'
</form>
'
,
'
<div id="progress"></div>
'
].
join
(
'
\n
'
);
$
.
fn
.
wfform
.
defaults
=
{
serverURL
:
""
,
dateTemplate
:
[
...
...
@@ -1455,9 +1489,9 @@ Handsontable.cellTypes["bootdate"] = Handsontable.BootstrapDateCell;
'
{{/if}}
'
,
'
{{each(j, choice) param.choices}}
'
,
'
{{if choice == param.default}}
'
,
'
<option
selected>${choice}</option>
'
,
'
<option
{{if $.type(param.choices) === "object"}} value=${j} {{/if}} selected>${choice}</option>
'
,
//Add value= if choices is a dict
'
{{else}}
'
,
'
<option>${choice}</option>
'
,
'
<option
{{if $.type(param.choices) === "object"}} value=${j} {{/if}}
>${choice}</option>
'
,
'
{{/if}}
'
,
'
{{/each}}
'
,
'
</select>
'
,
...
...
@@ -1567,6 +1601,7 @@ Handsontable.cellTypes["bootdate"] = Handsontable.BootstrapDateCell;
'
{{/each}}
'
,
'
</dl>
'
].
join
(
'
\n
'
),
workflowClass
:
null
,
displayFormType
:
"
default
"
,
displayRunButton
:
true
,
displayResetButton
:
true
,
workflow
:
null
,
...
...
src/js/jflow.min.js
View file @
dae949ca
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