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genotoul-bioinfo
ng6
Commits
f982c9b4
Commit
f982c9b4
authored
Dec 01, 2014
by
Penom Nom
Browse files
Update to bootstrap 3
parent
dc08c829
Changes
123
Hide whitespace changes
Inline
Side-by-side
ui/felogin.html
View file @
f982c9b4
...
...
@@ -48,49 +48,50 @@
<!--###TEMPLATE_LOGIN###-->
<div
class=
"sub-content sc-top-bottom"
>
<div
class=
"ng6-content-header-left"
>
<h2>
###STATUS_HEADER###
</h2>
<p>
###STATUS_MESSAGE###
</p>
<!-- ###LOGIN_FORM### -->
<form
action=
"###ACTION_URI###"
target=
"_top"
method=
"post"
onsubmit=
"###ON_SUBMIT###"
class=
"form-horizontal"
>
<fieldset>
<legend>
###LEGEND###
</legend>
<div
class=
"control-group"
>
<label
class=
"control-label"
for=
"user"
>
###USERNAME_LABEL###
</label>
<div
class=
"controls"
>
<input
type=
"text"
class=
"input-small"
id=
"user"
name=
"user"
placeholder=
"User name"
>
</div>
</div>
<div
class=
"control-group"
>
<label
class=
"control-label"
for=
"pass"
>
###PASSWORD_LABEL###
</label>
<div
class=
"controls"
>
<input
type=
"password"
class=
"input-small"
id=
"pass"
name=
"pass"
placeholder=
"Password"
>
</div>
</div>
<!--###PERMALOGIN_VALID###-->
<div>
<label
for=
"permalogin"
>
###PERMALOGIN###
</label>
<input
name=
"permalogin"
value=
"0"
type=
"hidden"
###PERMALOGIN_HIDDENFIELD_ATTRIBUTES###
id=
"permaloginHiddenField"
/>
<input
name=
"permalogin"
value=
"1"
type=
"checkbox"
###PERMALOGIN_CHECKBOX_ATTRIBUTES###
id=
"permalogin"
onclick=
"document.getElementById('permaloginHiddenField').disabled = this.checked;"
/>
</div>
<!--###PERMALOGIN_VALID###-->
<legend>
###LEGEND###
</legend>
<div
class=
"form-group"
>
<label
class=
"col-sm-offset-1 col-sm-4 control-label"
for=
"user"
>
###USERNAME_LABEL###
</label>
<div
class=
"col-sm-6"
>
<input
type=
"text"
class=
"input-sm form-control"
id=
"user"
name=
"user"
placeholder=
"User name"
>
</div>
</div>
<div
class=
"form-group"
>
<label
class=
"col-sm-offset-1 col-sm-4 control-label"
for=
"pass"
>
###PASSWORD_LABEL###
</label>
<div
class=
"col-sm-6"
>
<input
type=
"password"
class=
"input-sm form-control"
id=
"pass"
name=
"pass"
placeholder=
"Password"
>
</div>
</div>
<div
class=
"control-group"
>
<div
class=
"controls"
>
<input
type=
"submit"
name=
"submit"
class=
"btn"
value=
"###LOGIN_LABEL###"
/>
</div>
</div>
<!--###PERMALOGIN_VALID###-->
<div>
<label
for=
"permalogin"
>
###PERMALOGIN###
</label>
<input
name=
"permalogin"
value=
"0"
type=
"hidden"
###PERMALOGIN_HIDDENFIELD_ATTRIBUTES###
id=
"permaloginHiddenField"
/>
<input
name=
"permalogin"
value=
"1"
type=
"checkbox"
###PERMALOGIN_CHECKBOX_ATTRIBUTES###
id=
"permalogin"
onclick=
"document.getElementById('permaloginHiddenField').disabled = this.checked;"
/>
</div>
<!--###PERMALOGIN_VALID###-->
<div
class=
"form-group"
>
<div
class=
"col-sm-offset-5 col-sm-6"
>
<input
type=
"submit"
name=
"submit"
class=
"btn btn-default"
value=
"###LOGIN_LABEL###"
/>
</div>
</div>
<div
class=
"felogin-hidden"
>
<input
type=
"hidden"
name=
"logintype"
value=
"login"
/>
<input
type=
"hidden"
name=
"pid"
value=
"###STORAGE_PID###"
/>
<input
type=
"hidden"
name=
"redirect_url"
value=
"###REDIRECT_URL###"
/>
<input
type=
"hidden"
name=
"###PREFIXID###[noredirect]"
value=
"###NOREDIRECT###"
/>
###EXTRA_HIDDEN###
</div>
<div
class=
"felogin-hidden"
>
<input
type=
"hidden"
name=
"logintype"
value=
"login"
/>
<input
type=
"hidden"
name=
"pid"
value=
"###STORAGE_PID###"
/>
<input
type=
"hidden"
name=
"redirect_url"
value=
"###REDIRECT_URL###"
/>
<input
type=
"hidden"
name=
"###PREFIXID###[noredirect]"
value=
"###NOREDIRECT###"
/>
###EXTRA_HIDDEN###
</div>
</fieldset>
</form>
</div>
...
...
@@ -108,7 +109,7 @@
<dt>
August 2nd 2011
</dt>
<dd>
New functionalities are available to browse your projects/runs/analyses. A hierarchical display is now available for analysis. For project administrators new functionalities are also available.
</dd>
</dl>
</div>
<div
style=
"clear:both"
></div>
</div>
...
...
@@ -133,17 +134,17 @@
<form
action=
"###ACTION_URI###"
target=
"_top"
method=
"post"
onsubmit=
"###ON_SUBMIT###"
class=
"form-horizontal"
>
<fieldset>
<legend>
###LEGEND###
</legend>
<div
class=
"
control
-group"
>
<label
class=
"control-label"
for=
"user"
>
###USERNAME_LABEL###
</label>
<div
class=
"co
ntrols
"
>
<input
type=
"text"
class=
"input-sm
al
l"
value=
"###USERNAME###"
disabled
>
<div
class=
"
form
-group"
>
<label
class=
"
col-sm-offset-1 col-sm-4
control-label"
for=
"user"
>
###USERNAME_LABEL###
</label>
<div
class=
"co
l-sm-6
"
>
<input
type=
"text"
class=
"input-sm
form-contro
l"
value=
"###USERNAME###"
disabled
>
</div>
</div>
<div
class=
"
control
-group"
>
<div
class=
"co
ntrols
"
>
<input
type=
"submit"
name=
"submit"
class=
"btn"
value=
"###LOGOUT_LABEL###"
/>
<div
class=
"
form
-group"
>
<div
class=
"co
l-sm-offset-5 col-sm-6
"
>
<input
type=
"submit"
name=
"submit"
class=
"btn
btn-default
"
value=
"###LOGOUT_LABEL###"
/>
</div>
</div>
<div
class=
"felogin-hidden"
>
...
...
@@ -256,4 +257,5 @@
###BACKLINK_LOGIN###
<!--###TEMPLATE_CHANGEPASSWORD###-->
</body>
</html>
ui/nG6/lib/class.tx_nG6_db.php
View file @
f982c9b4
...
...
@@ -1842,8 +1842,20 @@ class tx_nG6_db {
function
is_ng6_administrator
(
$user_id
){
$is_ng6_admin
=
false
;
if
(
$user_id
!=
null
){
$user_group
=
tx_nG6_db
::
get_user_usergroup
(
$user_id
);
$groups
=
explode
(
','
,
$user_group
)
;
$usergroup
=
null
;
$queryParts
=
Array
(
'SELECT'
=>
'fe_users.usergroup'
,
'FROM'
=>
'fe_users'
,
'WHERE'
=>
'fe_users.uid='
.
$user_id
,
'GROUPBY'
=>
''
,
'ORDERBY'
=>
''
,
'LIMIT'
=>
''
,
);
$res
=
$GLOBALS
[
'TYPO3_DB'
]
->
exec_SELECT_queryArray
(
$queryParts
);
while
(
$res_row
=
$GLOBALS
[
'TYPO3_DB'
]
->
sql_fetch_assoc
(
$res
))
{
$usergroup
=
$res_row
[
'usergroup'
];
}
$groups
=
explode
(
','
,
$usergroup
)
;
if
(
in_array
(
'1'
,
$groups
)){
$is_ng6_admin
=
true
;
}
...
...
ui/nG6/pi1/analysis_table.tpl
View file @
f982c9b4
...
...
@@ -18,8 +18,10 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<table
class=
"table table-striped table-bordered dataTable"
id=
"analysis_data_table"
>
<thead>
<tr>
{
assign
var
=
"acolspan"
value
=
5
}
{
if
$is_admin
&&
$login_user
&&
$display_analysis_result
}
<th><center><input
type=
"checkbox"
id=
"chk_all_analysis"
></center></th>
<th><center><input
type=
"checkbox"
id=
"chk_all_analysis"
></center></th>
{
assign
var
=
"acolspan"
value
=
$acolspan
+
1
}
{/
if
}
<th
nowrap
>
Name
</th>
<th>
Description
</th>
...
...
@@ -34,18 +36,18 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
if
$is_admin
}
<tfoot>
<tr>
<th
align=
"left"
colspan=
"
6
"
>
<th
align=
"left"
colspan=
"
{
$acolspan
}
"
>
With selection :
<div
class=
"btn-group"
>
<button
id=
"hide_analysis"
type=
"button"
class=
"btn multiplea-selection-btn btn-sm
all"
><i
class=
"
icon-eye-close"
></i>
hide
</button>
<button
id=
"unhide_analysis"
type=
"button"
class=
"btn multiplea-selection-btn btn-sm
all"
><i
class=
"
icon-eye-open"
></i>
unhide
</button>
<button
id=
"hide_analysis"
type=
"button"
class=
"btn multiplea-selection-btn btn-sm
btn-default"
><i
class=
"glyphicon glyph
icon-eye-close"
></i>
hide
</button>
<button
id=
"unhide_analysis"
type=
"button"
class=
"btn multiplea-selection-btn btn-sm
btn-default"
><i
class=
"glyphicon glyph
icon-eye-open"
></i>
unhide
</button>
</div>
<div
class=
"btn-group"
>
<button
id=
"add_analysis"
type=
"button"
class=
"btn noa-selection-btn btn-sm
all"
><i
class=
"
icon-plus"
></i>
add
</button>
<button
id=
"delete_analysis"
type=
"button"
class=
"btn multiplea-selection-btn btn-sm
all"
><i
class=
"
icon-minus"
></i>
delete
</button>
<button
id=
"add_analysis"
type=
"button"
class=
"btn noa-selection-btn btn-sm
btn-default"
><i
class=
"glyphicon glyph
icon-plus"
></i>
add
</button>
<button
id=
"delete_analysis"
type=
"button"
class=
"btn multiplea-selection-btn btn-sm
btn-default"
><i
class=
"glyphicon glyph
icon-minus"
></i>
delete
</button>
</div>
</th>
</tr>
</tfoot>
{/
if
}
</table>
\ No newline at end of file
</table>
ui/nG6/pi1/analyzes/AnalysisTemplate.tpl
View file @
f982c9b4
...
...
@@ -21,6 +21,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<input
type=
"hidden"
id=
"server_url"
value=
"
{
$server_url
}
"
/>
<input
type=
"hidden"
id=
"user_login"
value=
"
{
$user_login
}
"
/>
<input
type=
"hidden"
id=
"user_id"
value=
"
{
$user_id
}
"
/>
<input
type=
"hidden"
id=
"user_email"
value=
"
{
$user_email
}
"
/>
<div
class=
"sub-content sc-top"
>
{
block
name
=
description
}
...
...
@@ -138,40 +139,4 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/
block
}
</div>
{* Modal initialization *}
{* Global tmpl *}
<div
id=
"ng6modal"
class=
"modal hide fade"
tabindex=
"-1"
role=
"dialog"
aria-labelledby=
"modal-label-tmpl"
aria-hidden=
"true"
>
<div
class=
"modal-header"
>
<button
type=
"button"
class=
"close"
data-dismiss=
"modal"
aria-hidden=
"true"
>
x
</button>
<h3
id=
"modal-label-tmpl"
>
Modal header
</h3>
</div>
<div
id=
"modal-body-tmpl"
class=
"modal-body"
></div>
<div
id=
"modal-foot-tmpl"
class=
"modal-footer"
></div>
</div>
{* setAndRunModal *}
<div
id=
"setAndRunModal"
class=
"modal hide fade"
tabindex=
"-1"
role=
"dialog"
aria-labelledby=
"setAndRunModalLabel"
aria-hidden=
"true"
>
<div
class=
"modal-header"
>
<button
type=
"button"
class=
"close"
data-dismiss=
"modal"
aria-hidden=
"true"
>
x
</button>
<h3
id=
"setAndRunModalLabel"
></h3>
</div>
<div
id=
"setAndRunModalBody"
class=
"modal-body"
></div>
<div
class=
"modal-footer"
>
<button
id=
"reset_workflow"
class=
"btn"
><i
class=
"icon-refresh"
></i>
Reset
</button>
<button
id=
"run_workflow"
class=
"btn btn-primary"
><i
class=
"icon-cog icon-white"
></i>
Run
</button>
</div>
</div>
{* Error only 1 raw modal *}
<div
id=
"ng6modal-1raw"
class=
"modal hide fade"
tabindex=
"-1"
role=
"dialog"
aria-labelledby=
"modalLabel-1raw"
aria-hidden=
"true"
>
<div
class=
"modal-header"
>
<button
type=
"button"
class=
"close"
data-dismiss=
"modal"
aria-hidden=
"true"
>
x
</button>
<h3>
Error
</h3>
</div>
<div
class=
"modal-body"
>
<div
class=
'tx-nG6-pi1-error'
>
Only one row should be selected to access this fonctionality.
</div>
</div>
<div
class=
"modal-footer"
>
<button
class=
"btn"
data-dismiss=
"modal"
aria-hidden=
"true"
><i
class=
"icon-remove"
></i>
Close
</button>
</div>
</div>
{
include
file
=
'../modals.tpl'
}
ui/nG6/pi1/analyzes/BasicAnalyse.tpl
View file @
f982c9b4
...
...
@@ -21,7 +21,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<br/>
<div
style=
"float:right;"
>
{
if
$is_project_admin
}
<button
id=
"add_file"
type=
"button"
class=
"btn btn-sm
all
btn-primary"
><i
class=
"
icon-plus icon-white
"
></i>
add files
</button>
<button
id=
"add_file"
type=
"button"
class=
"btn btn-sm btn-primary"
><i
class=
"
glyphicon glyphicon-plus
"
></i>
add files
</button>
{/
if
}
</div>
{/
block
}
...
...
ui/nG6/pi1/analyzes/BismarkMethylationExtractor.js
View file @
f982c9b4
...
...
@@ -36,23 +36,6 @@ function resize(elt, ratio) {
}
$
(
function
()
{
$
(
"
.largeimglink
"
).
click
(
function
()
{
$
(
"
#modal-label-tmpl
"
).
html
(
"
NG6 <small>
"
+
$
(
"
#analyse_name
"
).
val
()
+
"
</small>
"
);
$
(
"
#modal-body-tmpl
"
).
html
(
'
<div id="img_container"><img id="modal_img" src="
'
+
$
(
this
).
attr
(
'
href
'
)
+
'
" onload=vertical_centering("ng6modal") alt="Cannot display"></div>
'
);
$
(
"
#modal-foot-tmpl
"
).
html
(
'
<button class="btn" data-dismiss="modal" aria-hidden="true"><i class="icon-remove"></i> Close</button>
'
);
$
(
"
#ng6modal
"
).
css
(
'
margin-left
'
,
'
-400px
'
);
// Width
$
(
"
#modal_img
"
).
css
(
"
max-width
"
,
"
2000px
"
);
$
(
"
#ng6modal
"
).
css
(
'
width
'
,
'
800px
'
);
// Height
$
(
"
#modal-body-tmpl
"
).
css
(
'
max-height
'
,
modal_height
(
200
,
50
)
+
'
px
'
);
// Display
$
(
"
#ng6modal
"
).
modal
();
return
false
;
});
/* Opens a window that all the element in the selected column */
$
(
"
#columns_extract
"
).
click
(
function
()
{
var
samples
=
new
Array
()
;
...
...
ui/nG6/pi1/analyzes/BismarkMethylationExtractor.tpl
View file @
f982c9b4
...
...
@@ -87,8 +87,8 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<td
id=
"sample_
{
$i
}
_col_9"
>
{
$sample_results
[
"default"
].
totalMethylatedCinCHH
|
number_format
:
0
:
' '
:
' '
}
</td>
<td
id=
"sample_
{
$i
}
_col_10"
>
{
$sample_results
[
"default"
].
totalUnmethylatedCinCHH
|
number_format
:
0
:
' '
:
' '
}
</td>
<td
id=
"sample_
{
$i
}
_col_11"
>
{
round
((
$sample_results
[
"default"
].
totalMethylatedCinCHH
/(
$sample_results
[
"default"
].
totalMethylatedCinCHH
+
$sample_results
[
"default"
].
totalUnmethylatedCinCHH
))*
100
,
2
)
}
</td>
<td
id=
"sample_
{
$i
}
_col_12"
><a
class=
"
large
imglink"
href=
"
{
$sample_results
[
"R1"
].
img
}
"
>
M-bias
</a></td>
<td
id=
"sample_
{
$i
}
_col_13"
><a
class=
"
large
imglink"
href=
"
{
$sample_results
[
"R2"
].
img
}
"
>
M-bias
</a></td>
<td
id=
"sample_
{
$i
}
_col_12"
><a
class=
"imglink"
href=
"
{
$sample_results
[
"R1"
].
img
}
"
>
M-bias
</a></td>
<td
id=
"sample_
{
$i
}
_col_13"
><a
class=
"imglink"
href=
"
{
$sample_results
[
"R2"
].
img
}
"
>
M-bias
</a></td>
</tr>
{
$i
=
$i
+
1
}
{
else
}
...
...
ui/nG6/pi1/analyzes/FastQC.js
View file @
f982c9b4
...
...
@@ -36,23 +36,6 @@ function resize(elt, ratio) {
}
$
(
function
()
{
$
(
"
.largeimglink
"
).
click
(
function
()
{
$
(
"
#modal-label-tmpl
"
).
html
(
"
NG6 <small>
"
+
$
(
"
#analyse_name
"
).
val
()
+
"
</small>
"
);
$
(
"
#modal-body-tmpl
"
).
html
(
'
<div id="img_container"><img id="modal_img" src="
'
+
$
(
this
).
attr
(
'
href
'
)
+
'
" onload=vertical_centering("ng6modal") alt="Cannot display"></div>
'
);
$
(
"
#modal-foot-tmpl
"
).
html
(
'
<button class="btn" data-dismiss="modal" aria-hidden="true"><i class="icon-remove"></i> Close</button>
'
);
$
(
"
#ng6modal
"
).
css
(
'
margin-left
'
,
'
-400px
'
);
// Width
$
(
"
#modal_img
"
).
css
(
"
max-width
"
,
"
2000px
"
);
$
(
"
#ng6modal
"
).
css
(
'
width
'
,
'
800px
'
);
// Height
$
(
"
#modal-body-tmpl
"
).
css
(
'
max-height
'
,
modal_height
(
200
,
50
)
+
'
px
'
);
// Display
$
(
"
#ng6modal
"
).
modal
();
return
false
;
});
/* Opens a window that all the element in the selected column */
$
(
"
#columns_extract
"
).
click
(
function
()
{
var
samples
=
new
Array
()
;
...
...
@@ -130,14 +113,14 @@ $(function () {
// Display images table
$
(
"
#modal-label-tmpl
"
).
html
(
"
NG6 <small>
"
+
$
(
"
#analyse_name
"
).
val
()
+
"
</small>
"
);
$
(
"
#modal-body-tmpl
"
).
html
(
'
<div id="table_container"></div>
'
);
$
(
"
#modal-foot-tmpl
"
).
html
(
'
<button class="btn" data-dismiss="modal" aria-hidden="true"><i class="icon-remove"></i> Close</button>
'
);
$
(
"
#ng6modal
"
).
css
(
'
width
'
,
'
870px
'
);
$
(
"
#ng6modal
"
).
css
(
'
top
'
,
'
0%
'
);
$
(
"
#ng6modal
"
).
css
(
'
margin-top
'
,
'
20
px
'
);
$
(
"
#modal-body-tmpl
"
).
css
(
'
max-height
'
,
modal_height
(
200
,
50
)
+
'
px
'
);
$
(
"
#ng6modal
"
).
css
(
'
margin-left
'
,
'
-
4
35px
'
);
$
(
"
#table_container
"
).
append
(
'
<table class="table table-striped table-bordered
dataTable
">
'
+
thead
+
tbody
+
'
</table>
'
);
$
(
"
#modal-body-tmpl
"
).
html
(
'
<div id="table_container"
style="overflow-x : auto"
></div>
'
);
$
(
"
#modal-foot-tmpl
"
).
html
(
'
<button class="btn
btn-default
" data-dismiss="modal" aria-hidden="true"><i class="
glyphicon glyph
icon-remove"></i> Close</button>
'
);
$
(
"
#ng6modal
.modal-content
"
).
css
({
'
width
'
:
'
870px
'
,
'
max-height
'
:
modal_height
(
200
,
50
)
+
'
px
'
}
);
$
(
"
#ng6modal
"
).
css
(
'
margin-left
'
,
'
-
1
35px
'
);
$
(
"
#table_container
"
).
append
(
'
<table class="table table-striped table-bordered ">
'
+
thead
+
tbody
+
'
</table>
'
);
$
(
"
#ng6modal
"
).
modal
();
}
...
...
ui/nG6/pi1/analyzes/FastQC.tpl
View file @
f982c9b4
...
...
@@ -65,10 +65,10 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{
if
$analyse_results
|@
count
>
1
}
<td
id=
'sample_
{
$i
}
_col_1'
class=
"sample_name"
>
{
$sample
|
get_description
:
$descriptions
}
</td>
{/
if
}
<td
id=
"sample_
{
$i
}
_col_2"
><a
class=
"
large
imglink"
href=
"
{
$sample_results
[
"pbqpng"
].
img
}
"
>
{
$sample_results
[
"pbqpng"
].
result
}
</a></td>
<td
id=
"sample_
{
$i
}
_col_3"
><a
class=
"
large
imglink"
href=
"
{
$sample_results
[
"pbgcpng"
].
img
}
"
>
{
$sample_results
[
"pbgcpng"
].
result
}
</a></td>
<td
id=
"sample_
{
$i
}
_col_4"
><a
class=
"
large
imglink"
href=
"
{
$sample_results
[
"pbnspng"
].
img
}
"
>
{
$sample_results
[
"pbnspng"
].
result
}
</a></td>
<td
id=
"sample_
{
$i
}
_col_5"
><a
class=
"
large
imglink"
href=
"
{
$sample_results
[
"pbspng"
].
img
}
"
>
{
$sample_results
[
"pbspng"
].
result
}
</a></td>
<td
id=
"sample_
{
$i
}
_col_2"
><a
class=
"imglink"
href=
"
{
$sample_results
[
"pbqpng"
].
img
}
"
>
{
$sample_results
[
"pbqpng"
].
result
}
</a></td>
<td
id=
"sample_
{
$i
}
_col_3"
><a
class=
"imglink"
href=
"
{
$sample_results
[
"pbgcpng"
].
img
}
"
>
{
$sample_results
[
"pbgcpng"
].
result
}
</a></td>
<td
id=
"sample_
{
$i
}
_col_4"
><a
class=
"imglink"
href=
"
{
$sample_results
[
"pbnspng"
].
img
}
"
>
{
$sample_results
[
"pbnspng"
].
result
}
</a></td>
<td
id=
"sample_
{
$i
}
_col_5"
><a
class=
"imglink"
href=
"
{
$sample_results
[
"pbspng"
].
img
}
"
>
{
$sample_results
[
"pbspng"
].
result
}
</a></td>
<td
id=
"sample_
{
$i
}
_col_6"
>
{
$sample_results
[
"default"
].
nbseq
|
number_format
:
0
:
' '
:
' '
}
</td>
<td
id=
"sample_
{
$i
}
_col_7"
><a
class=
"imglink"
href=
"
{
$sample_results
[
"psqpng"
].
img
}
"
>
{
$sample_results
[
"psqpng"
].
result
}
</a></td>
<td
id=
"sample_
{
$i
}
_col_8"
>
{
$sample_results
[
"psgcpng"
].
value
}
(
<a
class=
"imglink"
href=
"
{
$sample_results
[
"psgcpng"
].
img
}
"
>
{
$sample_results
[
"psgcpng"
].
result
}
</a>
)
</td>
...
...
@@ -102,7 +102,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<tr>
<th
align=
"left"
colspan=
"
{
if
$analyse_results
|@
count
>
1
}
13
{
else
}
12
{/
if
}
"
>
With selection :
<button
type=
"button"
class=
"btn multiple-selection-btn"
id=
"columns_extract"
><i
class=
"icon-picture"
></i>
Compare
</button>
<button
type=
"button"
class=
"btn
btn-default
multiple-selection-btn"
id=
"columns_extract"
><i
class=
"
glyphicon glyph
icon-picture"
></i>
Compare
</button>
</th>
</tr>
</tfoot>
...
...
ui/nG6/pi1/class.tx_nG6_pi1.php
View file @
f982c9b4
...
...
@@ -62,31 +62,40 @@ class tx_nG6_pi1 extends tslib_pibase {
// Add the ng6 plugins css
$GLOBALS
[
'TSFE'
]
->
additionalHeaderData
[
$this
->
prefixId
]
=
'
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jquery-1.8.3.min.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jquery.min.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jquery.dataTables.min.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jquery.tmpl.min.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jquery.ui.widget.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jquery.iframe-transport.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jquery.fileupload.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jquery.fileupload-process.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jquery.fileupload-validate.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jquery.validate.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/wysihtml5-0.3.0.min.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/bootstrap.min.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/bootstrap-editable.min.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/bootstrap-datepicker.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/bootstrap-typeahead.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/wysihtml5-0.3.0.min.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/bootstrap-wysihtml5-0.0.2.min.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jquery.dataTables.min.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/DT_bootstrap.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jquery.validate.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/bootstrap3-wysihtml5.all.min.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/dataTables.bootstrap.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/cytoscape.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/cytoscape.js-panzoom.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/typeahead.bundle.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jflow-activewf.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jflow-availablewf.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jflow-wfform.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jflow-wfoutputs.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jflow-wfstatus.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/jquery.tmpl.min.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/tx_nG6_pi1.js"></script>
<script type="text/javascript" src="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/js/tx_nG6_utils.js"></script>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/jflow.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/bootstrap.min.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/bootstrap-responsive.min.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/bootstrap-wysihtml5-0.0.2.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/DT_bootstrap.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/bootstrap-editable.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/bootstrap3-wysihtml5.min.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/dataTables.bootstrap.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/bootstrap-editable.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/typeaheadjs.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/datepicker.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/cytoscape.js-panzoom.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/font-awesome.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/jflow.css"/>
<link type="text/css" rel="stylesheet" media="screen" href="'
.
t3lib_extMgm
::
siteRelPath
(
$this
->
extKey
)
.
'res/css/tx_nG6.css"/>'
;
tx_nG6_db
::
check_db_rights_level
();
...
...
@@ -192,6 +201,8 @@ class tx_nG6_pi1 extends tslib_pibase {
$smarty
->
assign
(
'server_url'
,
$this
->
conf
[
'server_url'
]);
$smarty
->
assign
(
'single_project_display'
,
$single_project_display
);
$smarty
->
assign
(
'is_ng6_admin'
,
tx_nG6_db
::
is_ng6_administrator
(
$user_id
)
?
true
:
false
);
$userval
=
tx_nG6_db
::
get_user_informations
(
$user_id
);
$smarty
->
assign
(
'user_email'
,
$userval
[
'email'
]);
// If it's a single project, add runs and analysis information
if
(
$single_project_display
)
{
...
...
@@ -281,6 +292,8 @@ class tx_nG6_pi1 extends tslib_pibase {
$smarty
->
assign
(
'server_url'
,
$this
->
conf
[
'server_url'
]);
$smarty
->
assign
(
'run_ids'
,
substr
(
$run_ids
,
0
,
-
1
));
$smarty
->
assign
(
'single_run_display'
,
$single_run_display
);
$userval
=
tx_nG6_db
::
get_user_informations
(
$user_id
);
$smarty
->
assign
(
'user_email'
,
$userval
[
'email'
]);
// If it's a single run, add analysis information
if
(
$single_run_display
)
{
...
...
@@ -354,6 +367,8 @@ class tx_nG6_pi1 extends tslib_pibase {
$smarty
->
assign
(
'server_url'
,
$this
->
conf
[
'server_url'
]);
$smarty
->
assign
(
'user_login'
,
$GLOBALS
[
'TSFE'
]
->
fe_user
->
user
[
'username'
]);
$smarty
->
assign
(
'user_id'
,
$GLOBALS
[
'TSFE'
]
->
fe_user
->
user
[
'uid'
]);
$userval
=
tx_nG6_db
::
get_user_informations
(
$user_id
);
$smarty
->
assign
(
'user_email'
,
$userval
[
'email'
]);
// Then select analyse results
$results
=
tx_nG6_db
::
select_analyse_results
(
$this
->
piVars
[
'analyze_id'
]);
...
...
ui/nG6/pi1/comments.tpl
View file @
f982c9b4
...
...
@@ -18,8 +18,8 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<div
class=
"tab-pane fade comment-tab"
id=
"
{
$tab_id
}
"
>
{
if
$comments
}
{
foreach
from
=
$comments
key
=
comm_id
item
=
cdata
}
<div
class=
"comment-block"
id=
"comment_id_
{
$cdata.id
}
"
>
<div
class=
'comment-block-header'
>
<div
class=
"comment-block
ng6-block-box
"
id=
"comment_id_
{
$cdata.id
}
"
>
<div
class=
'comment-block-header
ng6-block-box-header
'
>
<i
class=
"icon-user"
></i>
{
$cdata.cruser_info.username
}
{
$cdata.date
}
{
if
$cdata.cruser_info.uid
==
$user_id
}
...
...
@@ -27,7 +27,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/
if
}
</div>
<div
class=
"comment-block-body"
>
{
$cdata.comment
}
</div>
<div
class=
"comment-block-body
ng6-block-box-body
"
>
{
$cdata.comment
}
</div>
</div>
{/
foreach
}
{
else
}
...
...
@@ -38,7 +38,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<div
class=
"new-comment-block"
>
New comment
<textarea
class=
"wysihtml5-textarea"
></textarea>
<div
style=
"text-align : right;"
><button
id=
"post-comment"
type=
"button"
class=
"btn btn-sm
all
btn-primary"
>
Post comment
</button></div>
<div
style=
"text-align : right;
margin-top : 5px
"
><button
id=
"post-comment"
type=
"button"
class=
"btn btn-sm btn-primary"
>
Post comment
</button></div>
</div>
{/
if
}
</div>
ui/nG6/pi1/install_view.tpl
View file @
f982c9b4
...
...
@@ -35,76 +35,76 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<input
type=
"hidden"
id=
"server_url"
value=
"
{
$server_url
}
"
/>
<input
type=
"hidden"
id=
"pid"
value=
"
{
$pid
}
"
/>
<div
class=
"
control
-group"
>
<label
class=
"control-label"
>
Last name
</label>
<div
class=
"co
ntrols
"
>
<input
type=
"text"
id=
"last_name_val"
class=
"
typeahead
"
name=
"last_name_val"
placeholder=
"Last name"
/>
<div
class=
"
form
-group"
>
<label
class=
"
col-sm-2
control-label"
>
Last name
</label>
<div
class=
"co
l-sm-10
"
>
<input
type=
"text"
id=
"last_name_val"
class=
"
form-control
"
name=
"last_name_val"
placeholder=
"Last name"
/>
</div>
</div>
<div
class=
"
control
-group"
>
<label
class=
"control-label"
>
First name
</label>
<div
class=
"co
ntrols
"
>
<input
type=
"text"
id=
"first_name_val"
class=
"
typeahead
"
name=
"first_name_val"
placeholder=
"First name"
/>
<div
class=
"
form
-group"
>
<label
class=
"
col-sm-2
control-label"
>
First name
</label>
<div
class=
"co
l-sm-10
"
>
<input
type=
"text"
id=
"first_name_val"
class=
"
form-control
"
name=
"first_name_val"
placeholder=
"First name"
/>
</div>
</div>
<div
class=
"
control
-group"
>
<label
class=
"control-label"
>
Login
</label>
<div
class=
"co
ntrols
"
>
<input
type=
"text"
id=
"username_val"
class=
"
typeahead
"
name=
"username_val"
placeholder=
"Login"
/>
<div
class=
"
form
-group"
>
<label
class=
"
col-sm-2
control-label"
>
Login
</label>
<div
class=
"co
l-sm-10
"
>
<input
type=
"text"
id=
"username_val"
class=
"
form-control
"
name=
"username_val"
placeholder=
"Login"
/>
</div>
</div>
<div
class=
"
control
-group"
>
<label
class=
"control-label"
>
Password
</label>
<div
class=
"co
ntrols
"
>
<div
class=
"
form
-group"
>
<label
class=
"
col-sm-2
control-label"
>
Password
</label>
<div
class=
"co
l-sm-10
"
>
<div
class=
"input-append"
>
<input
class=
"
text
"
type=
"password"
id=
"user_password_pwd_val"
name=
"user_password_pwd_val"
placeholder=
"Password"
/>
<input
class=
"
form-control
"
type=
"password"
id=
"user_password_pwd_val"
name=
"user_password_pwd_val"
placeholder=
"Password"
/>
</div>
</div>
</div>
<div
class=
"
control
-group"
>
<label
class=
"control-label"
>
Retype password
</label>
<div
class=
"co
ntrols
"
>
<div
class=
"
form
-group"
>
<label
class=
"
col-sm-2
control-label"
>
Retype password
</label>
<div
class=
"co
l-sm-10
"
>
<div
class=
"input-append"
>
<input
class=
"
text
"
type=
"password"
id=
"user_password_pwd2_val"
name=
"user_password_pwd2_val"
placeholder=
"Password"
/>
<input
class=
"
form-control
"
type=
"password"
id=
"user_password_pwd2_val"
name=
"user_password_pwd2_val"
placeholder=
"Password"
/>
</div>
</div>
</div>
<div
class=
"
control
-group"
>
<label
class=
"control-label"
>
Email
</label>
<div
class=
"co
ntrols
"
>
<input
type=
"text"
id=
"email_val"
class=
"
typeahead
"
name=
"email_val"
placeholder=
"Email"
/>
<div
class=
"
form
-group"
>
<label
class=
"
col-sm-2
control-label"
>
Email
</label>
<div
class=
"co
l-sm-10
"
>
<input
type=
"text"
id=
"email_val"
class=
"
form-control
"
name=
"email_val"
placeholder=
"Email"
/>
</div>
</div>
<div
class=
"
control
-group"
>
<label
class=
"control-label"
>
Laboratory
</label>
<div
class=
"co
ntrols
"
>
<input
type=
"text"
id=
"title_val"
class=
"
group_typeahead
"
name=
"title_val"
placeholder=
"Laboratory"
/>
<div
class=
"
form
-group"
>
<label
class=
"
col-sm-2
control-label"
>
Laboratory
</label>
<div
class=
"co
l-sm-10
"
>
<input
type=
"text"
id=
"title_val"
class=
"
form-control
"
name=
"title_val"
placeholder=
"Laboratory"
/>
</div>
</div>
<div
class=
"
control
-group"
>
<label
class=
"control-label"
>
Organism
</label>
<div
class=
"co
ntrols
"
>
<input
type=
"text"
id=
"organism_val"
class=
"
group_typeahead
"
name=
"organism_val"
placeholder=
"Organism"
/>
<div
class=
"
form
-group"
>
<label
class=
"
col-sm-2
control-label"
>
Organism
</label>
<div
class=
"co
l-sm-10
"
>
<input
type=
"text"
id=
"organism_val"
class=
"
form-control
"
name=
"organism_val"
placeholder=
"Organism"
/>
</div>
</div>
<div
class=
"
control
-group"
>
<label
class=
"control-label"
>
Location
</label>
<div
class=
"co
ntrols
"
>
<input
type=
"text"
id=
"location_val"
class=
"
group_typeahead
"
name=
"location_val"
placeholder=
"Location"
/>
<div
class=
"
form
-group"
>
<label
class=
"
col-sm-2
control-label"
>
Location
</label>
<div
class=
"co
l-sm-10
"
>
<input
type=
"text"
id=
"location_val"
class=
"
form-control
"
name=
"location_val"
placeholder=
"Location"
/>
</div>
</div>
</form>
<div
style=
"float:right;margin-top:10px"
>
<button
class=
"btn"
id=
"raz_form_install"
><i
class=
"icon-repeat"
></i>
Clear form
</button>