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Commit b5500b7a authored by Anze Vavpetic's avatar Anze Vavpetic
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fixed package structures for the following packages: nlp, decision support,... 

fixed package structures for the following packages: nlp, decision support, subgroup discovery, bioinformatics.
parent eace9f79
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Showing with 123 additions and 172 deletions
mothra/settings.py
View file @ b5500b7a
......@@ -171,6 +171,10 @@ if USE_CONCURRENCY:
'south',
'workflows',
'workflows.latino',
'workflows.decision_support',
'workflows.bioinformatics',
'workflows.subgroup_discovery',
'workflows.nlp',
'website',
'signuplogin',
'django_extensions',
......@@ -190,6 +194,7 @@ else:
'south',
'workflows',
'workflows.latino',
'workflows.decision_support',
'website',
'signuplogin',
'django_extensions',
......
workflows/bioinformatics/settings.py 0 → 100644
View file @ b5500b7a
import os
package_name = 'bioinformatics'
package_root = os.path.dirname(__file__)
package_statics = os.path.join(os.path.dirname(__file__), 'static', package_name)
package_bin = os.path.join(package_root, 'bin')
auto_update_db = True
create_backups = True
workflows/decision_support/settings.py 0 → 100644
View file @ b5500b7a
import os
package_name = 'decision_support'
package_root = os.path.dirname(__file__)
package_statics = os.path.join(os.path.dirname(__file__), 'static', package_name)
package_bin = os.path.join(package_root, 'bin')
auto_update_db = True
create_backups = True
workflows/interaction_views.py
View file @ b5500b7a
import sys
from django.shortcuts import render
from decision_support.interaction import *
from subgroup_discovery.interaction import *
from workflows import packageLibImporter
def setattr_local(name, value, package):
......
workflows/library.py
View file @ b5500b7a
from workflows.security import safeOpen
import nlp
import cPickle
import json
import sys
from decision_support.library import *
from subgroup_discovery.library import *
from workflows import packageLibImporter
def setattr_local(name, value, package):
......@@ -808,47 +805,6 @@ def odt_to_arff(input_dict):
output_dict['arff'] = f.getvalue()
return output_dict
# NLP tools
def merge_sentences(input_dict):
"""
Merges the input sentences in XML according to the specified method.
"""
method = input_dict['method']
merged_sen, id_to_sent = set(), {}
ids_list = []
for sentsXML in input_dict['sentences']:
sents = nlp.parse_def_sentences(sentsXML)
ids = set(map(lambda x: x['id'], sents))
ids_list.append(ids)
# Save the map from id to sentence
for sent in sents:
id_to_sent[sent['id']] = sent
if len(merged_sen) == 0:
merged_sen = ids
if method == 'union':
merged_sen = merged_sen | ids
elif method == 'intersection':
merged_sen = merged_sen & ids
elif method == 'intersection_two':
for ids_alt in ids_list:
merged_sen = merged_sen | (ids_alt & ids)
return {'merged_sentences' : nlp.sentences_to_xml([id_to_sent[sid] for sid in merged_sen])}
def load_corpus(input_dict):
'''
Parses an input file and encodes it in base 64.
'''
import os.path
import base64
f = safeOpen(input_dict['file'])
fname = os.path.basename(input_dict['file'])
data = base64.b64encode(f.read())
from services.webservice import WebService
ws = WebService('http://bodysnatcher.ijs.si:8092/totale?wsdl', 600)
response = ws.client.parseFile(fileName=fname, inFile=data)
return {'corpus' : response['parsedFile']}
def string_to_file(input_dict):
return {}
......
workflows/nlp/library.py 0 → 100644
View file @ b5500b7a
import nlp
import os.path
import base64
from services.webservice import WebService
def merge_sentences(input_dict):
"""
Merges the input sentences in XML according to the specified method.
"""
method = input_dict['method']
merged_sen, id_to_sent = set(), {}
ids_list = []
for sentsXML in input_dict['sentences']:
sents = nlp.parse_def_sentences(sentsXML)
ids = set(map(lambda x: x['id'], sents))
ids_list.append(ids)
# Save the map from id to sentence
for sent in sents:
id_to_sent[sent['id']] = sent
if len(merged_sen) == 0:
merged_sen = ids
if method == 'union':
merged_sen = merged_sen | ids
elif method == 'intersection':
merged_sen = merged_sen & ids
elif method == 'intersection_two':
for ids_alt in ids_list:
merged_sen = merged_sen | (ids_alt & ids)
return {'merged_sentences' : nlp.sentences_to_xml([id_to_sent[sid] for sid in merged_sen])}
def load_corpus(input_dict):
'''
Parses an input file and encodes it in base 64.
'''
f = safeOpen(input_dict['file'])
fname = os.path.basename(input_dict['file'])
data = base64.b64encode(f.read())
ws = WebService('http://bodysnatcher.ijs.si:8092/totale?wsdl', 600)
response = ws.client.parseFile(fileName=fname, inFile=data)
return {'corpus' : response['parsedFile']}
workflows/nlp/settings.py 0 → 100644
View file @ b5500b7a
import os
package_name = 'nlp'
package_root = os.path.dirname(__file__)
package_statics = os.path.join(os.path.dirname(__file__), 'static', package_name)
package_bin = os.path.join(package_root, 'bin')
auto_update_db = True
create_backups = True
workflows/nlp/visualization_views.py 0 → 100644
View file @ b5500b7a
import nlp
def definition_sentences_viewer(request, input_dict, output_dict, widget):
"""
Parses the input XML and displays the definition sentences given as input.
@author: Anze Vavpetic, 2012
"""
sentences = nlp.parse_def_sentences(input_dict['candidates'])
return render(request, 'visualizations/def_sentences.html',{'widget' : widget, 'sentences' : sentences})
def term_candidate_viewer(request, input_dict, output_dict, widget):
"""
Parses the input and displays the term candidates.
@author: Anze Vavpetic, 2012
"""
terms = []
for line in input_dict['candidates'].split('\n'):
try:
score, cand, lemma = line.split('\t')
except:
continue
terms.append({'score' : score,
'cand' : cand.replace('[', '').replace(']',''),
#'lemma' : lemma.replace('<<', '').replace('>>','')
})
terms = sorted(terms, key = lambda x: x['score'], reverse=True)
return render(request, 'visualizations/terms.html', {'widget' : widget, 'terms' : terms})
workflows/subgroup_discovery/library.py
View file @ b5500b7a
......@@ -3,14 +3,14 @@ Subgroup discovery library functions.
@author: Anze Vavpetic <anze.vavpetic@ijs.si>
'''
import json
import logging
try:
import json
from SubgroupDiscovery.SD_learner_classifier import SD_learner
from SubgroupDiscovery.SDRule import SDRules
import Orange
except:
pass
print logging.warning('Could not import subgroup discovery orange package.')
class SubgroupDiscovery:
# Available algorithms and their parameters
......
workflows/subgroup_discovery/settings.py 0 → 100644
View file @ b5500b7a
import os
package_name = 'subgroup_discovery'
package_root = os.path.dirname(__file__)
package_statics = os.path.join(os.path.dirname(__file__), 'static', package_name)
package_bin = os.path.join(package_root, 'bin')
auto_update_db = True
create_backups = True
workflows/templates/interactions/insilico_search.html deleted 100755 → 0
View file @ eace9f79
<div id="widgetinteract-{{widget.pk}}" rel="{{widget.pk}}" class="widgetinteractdialog" title="{{widget.name}} interaction" width="700" height="600">
<div>
Use the sliders to adjust the weights.<br><br>
<form>
<table cellpadding="0" cellspacing="0" border="0" class="display" id="weightSel{{widget.pk}}">
<thead>
<tr>
<th>Attribute</th>
<th>Smaller attribute values are better</th>
<th>Weight</th>
<th>Weight (numeric)</th>
</tr>
</thead>
<tbody>
{% for att in attributes %}
<tr>
<td>
{{att}}
</td>
<td>
<input id="smallerIsBetter{{widget.pk}}{{att}}" name="smallerIsBetter{{widget.pk}}{{att}}" type="checkbox" value="true" style="display:inline;" />
</td>
<td>
<div style="width:200px;" id="slider{{widget.pk}}{{att}}"></div>
<script type="text/javascript">
// Slider code.
$("#slider{{widget.pk}}{{att}}").slider({
value:0,
min:0,
max:100,
slide: function( event, ui ) {
$( "#weight{{widget.pk}}{{att}}").val( $("#slider{{widget.pk}}{{att}}").slider("value") );
},
stop: function ( event, ui ) {
$( "#weight{{widget.pk}}{{att}}").val( $("#slider{{widget.pk}}{{att}}").slider("value") );
}
});
// Change the slider position when manually editing the weight.
$("#weight{{widget.pk}}{{att}}").change(function() {
$("#slider{{widget.pk}}{{att}}").slider("value", $("#weight{{widget.pk}}{{att}}").val());
});
</script>
</td>
<td>
<input type="number" style="width:30px; display:inline;" name="weight{{widget.pk}}{{att}}" id="weight{{widget.pk}}{{att}}" value="0"/>
</td>
</tr>
{% endfor %}
</tbody>
</table>
<input type="hidden" name="widget_id" value="{{widget.pk}}"/>
</form>
<br/>
<button id="normalizeButton{{widget.pk}}">Normalize weights!</button>
<button id="resetButton{{widget.pk}}">Reset!</button>
<script type="text/javascript">
// Data table code.
$('#weightSel{{widget.pk}}').dataTable( {
"bJQueryUI": true,
"bPaginate" : false,
"bSort" : false,
"bFilter" : false
});
// Normalization code.
$("#normalizeButton{{widget.pk}}").button().click(function() {
var weight_elements = $('[id^="weight{{widget.pk}}"]');
var weight_sum = 0;
weight_elements.each(function(index) {
weight_sum += parseFloat($(this).val());
});
if (weight_sum > 0) {
weight_elements.each(function(index) {
//round(100 * parseFloat($(this).val()) / weight_sum)
$(this).val(Math.round(100 * parseFloat($(this).val()) / weight_sum));
$(this).change();
});
}
});
// Reset button code.
$("#resetButton{{widget.pk}}").button().click(function() {
$('[id^="weight{{widget.pk}}"]').each(function() {
$(this).val(0);
$(this).change();
});
});
</script>
</div>
</div>
\ No newline at end of file
workflows/visualization_views.py
View file @ b5500b7a
import sys
from django.shortcuts import render
from django.http import Http404, HttpResponse
import nlp
from decision_support.visualization import *
from subgroup_discovery.visualization import *
from workflows import packageLibImporter
def setattr_local(name, value, package):
......@@ -194,34 +191,3 @@ def sdmsegs_viewer(request,input_dict,output_dict,widget):
}
output_dict = {'json_output':output}
return render(request, 'visualizations/sdmsegs_viewer.html',{'widget':widget,'input_dict':input_dict,'output_dict':output_dict})
def definition_sentences_viewer(request, input_dict, output_dict, widget):
"""
Parses the input XML and displays the definition sentences given as input.
@author: Anze Vavpetic, 2012
"""
sentences = nlp.parse_def_sentences(input_dict['candidates'])
return render(request, 'visualizations/def_sentences.html',{'widget' : widget, 'sentences' : sentences})
def term_candidate_viewer(request, input_dict, output_dict, widget):
"""
Parses the input and displays the term candidates.
@author: Anze Vavpeltic, 2012
"""
terms = []
for line in input_dict['candidates'].split('\n'):
try:
score, cand, lemma = line.split('\t')
except:
continue
terms.append({'score' : score,
'cand' : cand.replace('[', '').replace(']',''),
#'lemma' : lemma.replace('<<', '').replace('>>','')
})
terms = sorted(terms, key = lambda x: x['score'], reverse=True)
return render(request, 'visualizations/terms.html', {'widget' : widget, 'terms' : terms})
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