From b5500b7afa7ba99d8bded1e7f6df5200779355bd Mon Sep 17 00:00:00 2001 From: Anze Vavpetic Date: Mon, 19 Nov 2012 15:22:40 +0100 Subject: [PATCH] fixed package structures for the following packages: nlp, decision support, subgroup discovery, bioinformatics. --- mothra/settings.py | 5 + .../{interaction.py => interaction_views.py} | 0 workflows/bioinformatics/settings.py | 11 +++ ...isualization.py => visualization_views.py} | 0 .../{interaction.py => interaction_views.py} | 0 workflows/decision_support/settings.py | 11 +++ .../templates/interactions/kepner_tregoe.html | 0 .../templates/visualizations/ds_charts.html | 0 .../visualizations/sensitivity_analysis.html | 0 ...isualization.py => visualization_views.py} | 0 workflows/interaction_views.py | 2 - workflows/library.py | 44 --------- workflows/nlp/interaction_views.py | 0 workflows/nlp/library.py | 40 ++++++++ workflows/{ => nlp}/nlp.py | 0 workflows/nlp/settings.py | 11 +++ workflows/nlp/static/icons/treeview/nlp.png | Bin 0 -> 1004 bytes workflows/nlp/static/icons/widget/nlp.png | Bin 0 -> 1004 bytes .../visualizations/def_sentences.html | 0 .../templates/visualizations/terms.html | 0 workflows/nlp/visualization_views.py | 31 ++++++ .../{interaction.py => interaction_views.py} | 0 workflows/subgroup_discovery/library.py | 6 +- workflows/subgroup_discovery/settings.py | 11 +++ .../static/icons/treeview/bar.png | Bin 0 -> 6878 bytes .../static/icons/treeview/builder.png | Bin 0 -> 6533 bytes .../static/icons/treeview/eval.png | Bin 0 -> 6550 bytes .../static/icons/treeview/roc.png | Bin 0 -> 6754 bytes .../static/icons/widget/bar.png | Bin 0 -> 6878 bytes .../static/icons/widget/builder.png | Bin 0 -> 6533 bytes .../static/icons/widget/eval.png | Bin 0 -> 6550 bytes .../static/icons/widget/roc.png | Bin 0 -> 6754 bytes .../interactions/build_subgroups.html | 0 .../interactions/select_subgroups.html | 0 .../interactions/table_from_sets.html | 0 .../subgroup_bar_visualization.html | 0 .../subgroup_roc_visualization.html | 0 ...isualization.py => visualization_views.py} | 0 .../interactions/insilico_search.html | 89 ------------------ workflows/visualization_views.py | 34 ------- 40 files changed, 123 insertions(+), 172 deletions(-) rename workflows/bioinformatics/{interaction.py => interaction_views.py} (100%) create mode 100644 workflows/bioinformatics/settings.py rename workflows/bioinformatics/{visualization.py => visualization_views.py} (100%) rename workflows/decision_support/{interaction.py => interaction_views.py} (100%) create mode 100644 workflows/decision_support/settings.py rename workflows/{ => decision_support}/templates/interactions/kepner_tregoe.html (100%) rename workflows/{ => decision_support}/templates/visualizations/ds_charts.html (100%) rename workflows/{ => decision_support}/templates/visualizations/sensitivity_analysis.html (100%) rename workflows/decision_support/{visualization.py => visualization_views.py} (100%) create mode 100644 workflows/nlp/interaction_views.py create mode 100644 workflows/nlp/library.py rename workflows/{ => nlp}/nlp.py (100%) create mode 100644 workflows/nlp/settings.py create mode 100755 workflows/nlp/static/icons/treeview/nlp.png create mode 100755 workflows/nlp/static/icons/widget/nlp.png rename workflows/{ => nlp}/templates/visualizations/def_sentences.html (100%) rename workflows/{ => nlp}/templates/visualizations/terms.html (100%) create mode 100644 workflows/nlp/visualization_views.py rename workflows/subgroup_discovery/{interaction.py => interaction_views.py} (100%) create mode 100644 workflows/subgroup_discovery/settings.py create mode 100755 workflows/subgroup_discovery/static/icons/treeview/bar.png create mode 100755 workflows/subgroup_discovery/static/icons/treeview/builder.png create mode 100755 workflows/subgroup_discovery/static/icons/treeview/eval.png create mode 100755 workflows/subgroup_discovery/static/icons/treeview/roc.png create mode 100755 workflows/subgroup_discovery/static/icons/widget/bar.png create mode 100755 workflows/subgroup_discovery/static/icons/widget/builder.png create mode 100755 workflows/subgroup_discovery/static/icons/widget/eval.png create mode 100755 workflows/subgroup_discovery/static/icons/widget/roc.png rename workflows/{templates => subgroup_discovery/templates/subgroup_discovery}/interactions/build_subgroups.html (100%) rename workflows/{templates => subgroup_discovery/templates/subgroup_discovery}/interactions/select_subgroups.html (100%) rename workflows/{templates => subgroup_discovery/templates/subgroup_discovery}/interactions/table_from_sets.html (100%) rename workflows/{templates => subgroup_discovery/templates/subgroup_discovery}/visualizations/subgroup_bar_visualization.html (100%) rename workflows/{templates => subgroup_discovery/templates/subgroup_discovery}/visualizations/subgroup_roc_visualization.html (100%) rename workflows/subgroup_discovery/{visualization.py => visualization_views.py} (100%) delete mode 100755 workflows/templates/interactions/insilico_search.html diff --git a/mothra/settings.py b/mothra/settings.py index 98a7a19..979f5a4 100755 --- a/mothra/settings.py +++ b/mothra/settings.py @@ -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', diff --git a/workflows/bioinformatics/interaction.py b/workflows/bioinformatics/interaction_views.py similarity index 100% rename from workflows/bioinformatics/interaction.py rename to workflows/bioinformatics/interaction_views.py diff --git a/workflows/bioinformatics/settings.py b/workflows/bioinformatics/settings.py new file mode 100644 index 0000000..76d5c08 --- /dev/null +++ b/workflows/bioinformatics/settings.py @@ -0,0 +1,11 @@ +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 + diff --git a/workflows/bioinformatics/visualization.py b/workflows/bioinformatics/visualization_views.py similarity index 100% rename from workflows/bioinformatics/visualization.py rename to workflows/bioinformatics/visualization_views.py diff --git a/workflows/decision_support/interaction.py b/workflows/decision_support/interaction_views.py similarity index 100% rename from workflows/decision_support/interaction.py rename to workflows/decision_support/interaction_views.py diff --git a/workflows/decision_support/settings.py b/workflows/decision_support/settings.py new file mode 100644 index 0000000..1569bf1 --- /dev/null +++ b/workflows/decision_support/settings.py @@ -0,0 +1,11 @@ +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 + diff --git a/workflows/templates/interactions/kepner_tregoe.html b/workflows/decision_support/templates/interactions/kepner_tregoe.html similarity index 100% rename from workflows/templates/interactions/kepner_tregoe.html rename to workflows/decision_support/templates/interactions/kepner_tregoe.html diff --git a/workflows/templates/visualizations/ds_charts.html b/workflows/decision_support/templates/visualizations/ds_charts.html similarity index 100% rename from workflows/templates/visualizations/ds_charts.html rename to workflows/decision_support/templates/visualizations/ds_charts.html diff --git a/workflows/templates/visualizations/sensitivity_analysis.html b/workflows/decision_support/templates/visualizations/sensitivity_analysis.html similarity index 100% rename from workflows/templates/visualizations/sensitivity_analysis.html rename to workflows/decision_support/templates/visualizations/sensitivity_analysis.html diff --git a/workflows/decision_support/visualization.py b/workflows/decision_support/visualization_views.py similarity index 100% rename from workflows/decision_support/visualization.py rename to workflows/decision_support/visualization_views.py diff --git a/workflows/interaction_views.py b/workflows/interaction_views.py index 9c17253..0527a1e 100755 --- a/workflows/interaction_views.py +++ b/workflows/interaction_views.py @@ -1,7 +1,5 @@ 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): diff --git a/workflows/library.py b/workflows/library.py index 274674f..b9cb9e9 100755 --- a/workflows/library.py +++ b/workflows/library.py @@ -1,10 +1,7 @@ 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): @@ -807,47 +804,6 @@ def odt_to_arff(input_dict): f = toARFFstring(input_dict['odt']) 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 {} diff --git a/workflows/nlp/interaction_views.py b/workflows/nlp/interaction_views.py new file mode 100644 index 0000000..e69de29 diff --git a/workflows/nlp/library.py b/workflows/nlp/library.py new file mode 100644 index 0000000..a0efae2 --- /dev/null +++ b/workflows/nlp/library.py @@ -0,0 +1,40 @@ +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']} diff --git a/workflows/nlp.py b/workflows/nlp/nlp.py similarity index 100% rename from workflows/nlp.py rename to workflows/nlp/nlp.py diff --git a/workflows/nlp/settings.py b/workflows/nlp/settings.py new file mode 100644 index 0000000..9ce66c4 --- /dev/null +++ b/workflows/nlp/settings.py @@ -0,0 +1,11 @@ +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 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'visualizations/terms.html', {'widget' : widget, 'terms' : terms}) + diff --git a/workflows/subgroup_discovery/interaction.py b/workflows/subgroup_discovery/interaction_views.py similarity index 100% rename from workflows/subgroup_discovery/interaction.py rename to workflows/subgroup_discovery/interaction_views.py diff --git a/workflows/subgroup_discovery/library.py b/workflows/subgroup_discovery/library.py index 950f441..7f3b680 100644 --- a/workflows/subgroup_discovery/library.py +++ b/workflows/subgroup_discovery/library.py @@ -3,14 +3,14 @@ Subgroup discovery library functions. @author: Anze Vavpetic ''' +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 diff --git 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workflows/subgroup_discovery/templates/subgroup_discovery/interactions/select_subgroups.html diff --git a/workflows/templates/interactions/table_from_sets.html b/workflows/subgroup_discovery/templates/subgroup_discovery/interactions/table_from_sets.html similarity index 100% rename from workflows/templates/interactions/table_from_sets.html rename to workflows/subgroup_discovery/templates/subgroup_discovery/interactions/table_from_sets.html diff --git a/workflows/templates/visualizations/subgroup_bar_visualization.html b/workflows/subgroup_discovery/templates/subgroup_discovery/visualizations/subgroup_bar_visualization.html similarity index 100% rename from workflows/templates/visualizations/subgroup_bar_visualization.html rename to workflows/subgroup_discovery/templates/subgroup_discovery/visualizations/subgroup_bar_visualization.html diff --git a/workflows/templates/visualizations/subgroup_roc_visualization.html b/workflows/subgroup_discovery/templates/subgroup_discovery/visualizations/subgroup_roc_visualization.html similarity index 100% rename from workflows/templates/visualizations/subgroup_roc_visualization.html rename to workflows/subgroup_discovery/templates/subgroup_discovery/visualizations/subgroup_roc_visualization.html diff --git a/workflows/subgroup_discovery/visualization.py b/workflows/subgroup_discovery/visualization_views.py similarity index 100% rename from workflows/subgroup_discovery/visualization.py rename to workflows/subgroup_discovery/visualization_views.py diff --git a/workflows/templates/interactions/insilico_search.html b/workflows/templates/interactions/insilico_search.html deleted file mode 100755 index c09b1a1..0000000 --- a/workflows/templates/interactions/insilico_search.html +++ /dev/null @@ -1,89 +0,0 @@ -
-
- Use the sliders to adjust the weights.

-
- - - - - - - - - - - {% for att in attributes %} - - - - - - - {% endfor %} - -
AttributeSmaller attribute values are betterWeightWeight (numeric)
- {{att}} - - - -
- - 		- -
- -
-
- - - -
-
\ No newline at end of file diff --git a/workflows/visualization_views.py b/workflows/visualization_views.py index 9f19d7d..acd9123 100755 --- a/workflows/visualization_views.py +++ b/workflows/visualization_views.py @@ -1,9 +1,6 @@ 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}) - -- GitLab