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vidjil
vidjil
Commits
1e8a3869
Commit
1e8a3869
authored
Nov 21, 2018
by
Ryan Herbert
Committed by
Mathieu Giraud
Nov 21, 2018
Browse files
remove unused views and routes
See
#3076
parent
6ff00141
Pipeline
#50782
failed with stages
in 7 minutes and 20 seconds
Changes
4
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
server/web2py/applications/vidjil/views/patient/confirm.html
deleted
100644 → 0
View file @
6ff00141
{{extend 'db_layout.html'}}
{{import vidjil_utils}}
{{('message' in globals())}}
{{if 'message' in globals():}}
{{
data_count = 0
patient_name = vidjil_utils.anon_ids(request.vars["id"])
sequence_count = db( (db.sequence_file.id == db.sample_set_membership.sequence_file_id)
&
(db.sample_set_membership.sample_set_id == db.patient.sample_set_id)
&
(db.patient.id == request.vars["id"])).count()
data_count = db( (db.sequence_file.id == db.sample_set_membership.sequence_file_id)
&
(db.sample_set_membership.sample_set_id == db.patient.sample_set_id)
&
(db.patient.id == request.vars["id"])
&
(db.results_file.sequence_file_id == db.sequence_file.id)).count()
}}
<div>
<h3>
{{=message}}: {{=patient_name}}
</h3>
Are you sure you want to delete the patient {{=patient_name}} ?
</br>
This will delete {{=sequence_count}} sequence file(s) and {{=data_count}} result files.
</br>
This action cannot be undone.
<div
class=
"center"
>
<button
onclick=
"db.call('patient/delete', {'id' :'{{=request.vars["
id
"]}}'}
)"
>
delete
</button>
<button
onclick=
"db.call('patient/index')"
>
cancel
</button>
</div>
</div>
{{elif 'content' in globals():}}
{{=content}}
{{else:}}
{{=BEAUTIFY(response._vars)}}
{{pass}}
server/web2py/applications/vidjil/views/patient/index.html
deleted
100644 → 0
View file @
6ff00141
{{extend 'db_layout.html'}}
{{import vidjil_utils}}
{{total_file_count = 0 ; total_size = 0}}
<h3></h3>
<div
class=
"db_block"
>
<div
class=
"db_block_left"
>
search
<input
id=
"db_filter_input"
type=
"text"
value=
"{{=request.vars["
filter
"]}}"
onchange=
"db.call('patient/index', {'filter' : this.value} )"
>
</div>
</div>
<div
id=
"db_table_container"
>
<table
class=
"db_table"
id=
"table"
>
<thead>
<tr><td
class=
"column_200 pointer"
onclick=
"db.call('patient/index', {'sort' :'last_name', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="last_name"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
name
</td>
<td
class=
"column_100 pointer"
onclick=
"db.call('patient/index', {'sort' :'birth', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="birth"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
birth
</td>
<td
class=
"pointer"
onclick=
"db.call('patient/index', {'sort' :'info', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="info"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
info
</td>
<td
class=
"pointer"
class=
"column_100"
onclick=
"db.call('patient/index', {'sort' :'configs', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="configs"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
results
</td>
{{if isAdmin:}}
<td
class=
"column_100 pointer"
onclick=
"db.call('patient/index', {'sort' :'groups', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="groups"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
groups
</td>
{{pass}}
{{if isAdmin:}}
<td
class=
"column_100 pointer"
onclick=
"db.call('patient/index', {'sort' :'creator', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="creator"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
creator
</td>
{{pass}}
<td
class=
"column_100 pointer"
onclick=
"db.call('patient/index', {'sort' :'files', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="files"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
files
</td>
<td
class=
"column5"
>
</td>
<td
class=
"column5"
>
</td>
<td
class=
"column5"
>
</td>
</tr>
</thead>
{{for row in query :}}
<tr
class=
"pointer"
onclick=
"db.call('sample_set/index', {'id' :'{{=row['sample_set_id']}}' , 'config_id' : {{=row['most_used_conf']}} } )"
>
<td>
{{ patient_name = vidjil_utils.anon_names(row['sample_set_id'], row['first_name'], row['last_name'], row['anon_allowed'])}}
{{= patient_name}}
</td>
<td>
{{ if row['birth'] is not None: }} {{=row['birth'] }} {{ pass }}
</td>
<td>
{{=row['info'] }}
</td>
<td>
{{ configs = [] }}
{{for conf in row['conf_list'] :}}
{{filename = patient_name + " (" + conf['name'] + ")"}}
{{if conf['fused_file'] is not None :}}
{{ configs.append(str(A(conf['name'], _href="index.html?patient=" + str(row['id']) + "
&
config=" + str(conf['id']), _type="text/html",
_onclick="event.preventDefault();event.stopPropagation();if( event.which == 2 ) { window.open(this.href); } else { myUrl.loadURL(db, { 'patient' : '" + str(row['id']) + "' , 'config' : " + str(conf['id']) + " }, '" + filename + "' ); }"))) }}
{{else:}}
{{ configs.append(conf['name']) }}
{{pass}}
{{pass}}
{{= XML(", ".join(configs)) }}
</td>
{{if isAdmin:}}
<td>
{{=row['groups']}}
</td>
{{pass}}
{{if isAdmin:}}
<td>
{{=row['creator']}}
</td>
{{pass}}
<td>
{{=row['file_count']}} ({{=vidjil_utils.format_size(row['size'])}})
</td>
{{ total_file_count += row['file_count'] ; total_size += row['size'] }}
{{if isAdmin:}}
<td
onclick=
"db.call('patient/permission', {'id' :'{{=row['id']}}'} )"
>
<i
class=
"icon-key"
title=
"set permissions"
></i>
</td>
{{else:}}
<td></td>
{{pass}}
{{if row['has_permission']:}}
<td
onclick=
"db.call('patient/edit', {'id' :'{{=row['id']}}'} )"
>
<i
class=
"icon-pencil-2"
title=
"edit patient information"
></i>
</td>
<td
onclick=
"db.call('patient/confirm', {'id' :'{{=row['id']}}'} )"
>
<i
class=
"icon-erase"
title=
"delete patient"
></i>
</td>
{{else:}}
<td></td><td></td>
{{pass}}
</tr>
{{pass}}
</table>
<table
class=
"db_table"
id=
"db_fixed_header"
></table>
</div>
<div
class=
"db_block"
>
<div
class=
"db_block_left"
>
{{if auth.can_create_patient():}}
<span
class=
"button2"
onclick=
"db.call('patient/add')"
>
+ new patients
</span>
<span
class=
"button2"
onclick=
"db.call('sample_set/custom', {'filter': '{{=request.vars['filter']}}' })"
>
compare samples/patients
</span>
{{else:}}
<!-- <span class="button2 inactive" onclick="db.call('patient/add')" title="you don't have permission to create new patient"> add patient </span> -->
{{pass}}
</div>
<div
class=
"db_block_right"
>
<br
/>
{{ =len(query) }} patients, {{ =total_file_count }} files ({{ =vidjil_utils.format_size(total_size) }})
</div>
</div>
server/web2py/applications/vidjil/views/run/confirm.html
deleted
100644 → 0
View file @
6ff00141
{{extend 'db_layout.html'}}
{{import vidjil_utils}}
{{('message' in globals())}}
{{if 'message' in globals():}}
{{
data_count = 0
run_name = db.run[request.vars["id"]].name
}}
<div>
<h3>
{{=message}}: {{=run_name}}
</h3>
Are you sure you want to delete the run {{=run_name}} ?
</br>
This action cannot be undone.
<div
class=
"center"
>
<button
onclick=
"db.call('run/delete', {'id' :'{{=request.vars["
id
"]}}'}
)"
>
delete
</button>
<button
onclick=
"db.call('run/index')"
>
cancel
</button>
</div>
</div>
{{elif 'content' in globals():}}
{{=content}}
{{else:}}
{{=BEAUTIFY(response._vars)}}
{{pass}}
server/web2py/applications/vidjil/views/run/index.html
deleted
100644 → 0
View file @
6ff00141
{{extend 'db_layout.html'}}
{{import vidjil_utils}}
{{total_file_count = 0 ; total_size = 0}}
<h3></h3>
<div
class=
"db_block"
>
<div
class=
"db_block_left"
>
search
<input
id=
"db_filter_input"
type=
"text"
value=
"{{=request.vars["
filter
"]}}"
onchange=
"db.call('patient/index', {'filter' : this.value} )"
>
</div>
</div>
<div
id=
"db_table_container"
>
<table
class=
"db_table"
id=
"table"
>
<thead>
<tr><td
class=
"column_200 pointer"
onclick=
"db.call('run/index', {'sort' :'name', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="name"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
name
</td>
<td
class=
"column_100 pointer"
onclick=
"db.call('run/index', {'sort' :'run_date', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="run_date"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
date
</td>
<td
class=
"pointer"
onclick=
"db.call('run/index', {'sort' :'info', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="info"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
info
</td>
<td
class=
"pointer"
class=
"column_100"
onclick=
"db.call('run/index', {'sort' :'configs', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="configs"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
configs
</td>
{{if isAdmin:}}
<td
class=
"column_100 pointer"
onclick=
"db.call('run/index', {'sort' :'groups', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="groups"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
groups
</td>
{{pass}}
{{if isAdmin:}}
<td
class=
"column_100 pointer"
onclick=
"db.call('run/index', {'sort' :'creator', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="creator"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
creator
</td>
{{pass}}
<td
class=
"column_100 pointer"
onclick=
"db.call('run/index', {'sort' :'files', 'filter' : '{{=request.vars["
filter
"]}}'
{{
if
not
reverse
and
request.vars
["
sort
"
]=
="files"
:
}}
,
'
reverse
'
:
true
{{
pass
}}
})"
>
files
</td>
<td
class=
"column5"
>
</td>
<td
class=
"column5"
>
</td>
<td
class=
"column5"
>
</td>
</tr>
</thead>
{{for row in query :}}
<tr
class=
"pointer"
onclick=
"db.call('sample_set/index', {'id' :'{{=row['sample_set_id']}}' , 'config_id' : {{=row['most_used_conf']}} } )"
>
<td>
{{=row['name']}}
</td>
<td>
{{ if row['run_date'] is not None: }} {{=row['run_date'] }} {{ pass }}
</td>
<td>
{{=row['info']}}
</td>
<td>
{{ configs = [] }}
{{for conf in row['conf_list'] :}}
{{filename = row['name'] + " (" + conf['name'] + ")"}}
{{if conf['fused_file'] is not None :}}
{{ configs.append(str(A(conf['name'], _href="index.html?sample_set=" + str(row['sample_set_id']) + "
&
config=" + str(conf['id']), _type="text/html",
_onclick="event.preventDefault();event.stopPropagation();if( event.which == 2 ) { window.open(this.href); } else { myUrl.loadUrl(db, { 'sample_set_id' : '" + str(row['sample_set_id']) + "' , 'config' : " + str(conf['id']) + " }, '" + filename + "' ); }"))) }}
{{else:}}
{{ configs.append(conf['name']) }}
{{pass}}
{{pass}}
{{= XML(", ".join(configs)) }}
</td>
{{if isAdmin:}}
<td>
{{=row['groups']}}
</td>
{{pass}}
{{if isAdmin:}}
<td>
{{=row['creator']}}
</td>
{{pass}}
<td>
{{=row['file_count']}} ({{=vidjil_utils.format_size(row['size'])}})
</td>
{{ total_file_count += row['file_count'] ; total_size += row['size'] }}
{{if isAdmin:}}
<td
onclick=
"db.call('run/permission', {'id' :'{{=row['id']}}'} )"
>
<i
class=
"icon-key"
title=
"set permissions"
></i>
</td>
{{else:}}
<td></td>
{{pass}}
{{if row['has_admin_permission']:}}
<td
onclick=
"db.call('run/edit', {'id' :'{{=row['id']}}'} )"
>
<i
class=
"icon-pencil-2"
title=
"edit run information"
></i>
</td>
<td
onclick=
"db.call('run/confirm', {'id' :'{{=row['id']}}'} )"
>
<i
class=
"icon-erase"
title=
"delete run"
></i>
</td>
{{else:}}
<td></td><td></td>
{{pass}}
</tr>
{{pass}}
</table>
<table
class=
"db_table"
id=
"db_fixed_header"
></table>
</div>
<div
class=
"db_block"
>
<div
class=
"db_block_left"
>
{{if auth.can_create_patient():}}
<span
class=
"button2"
onclick=
"db.call('run/add')"
>
+ new runs
</span>
<span
class=
"button2"
onclick=
"db.call('sample_set/custom', {'filter': '{{=request.vars['filter']}}' })"
>
compare samples/runs
</span>
{{else:}}
<!-- <span class="button2 inactive" onclick="db.call('patient/add')" title="you don't have permission to create new patient"> add patient </span> -->
{{pass}}
</div>
<div
class=
"db_block_right"
>
<br
/>
{{ =len(query) }} runs, {{ =total_file_count }} files ({{ =vidjil_utils.format_size(total_size) }})
</div>
</div>
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