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LTS5/connectomeviewer
d9c452626446779dd48a627886e48404a4bd776e
Add split fibers script to scratch
diff --git a/scratch/split_fibers.py b/scratch/split_fibers.py new file mode 100755 index 0000000..0253685 --- /dev/null +++ b/scratch/split_fibers.py @@ -0,0 +1,88 @@ +# check if fibers touch other grey matter labeled regions + +import numpy as np +import cfflib as cf + +# load data +a=cf.load('DATAALE/control01_tp1_r...
LTS5/connectomeviewer
cf3a9a83b75c123356ba3b73b136b1336d223a0e
Add cortico-cortico CTrack Code Oracle
diff --git a/cviewer/plugins/codeoracle/actions.py b/cviewer/plugins/codeoracle/actions.py index 9d12a75..21bde65 100644 --- a/cviewer/plugins/codeoracle/actions.py +++ b/cviewer/plugins/codeoracle/actions.py @@ -1,321 +1,341 @@ import logging from enthought.io.api import File from enthought.pyface.api import File...
LTS5/connectomeviewer
b0e532267ad2d2ee8e3fb5176b9d2a87840b770b
Fix bug with None View. Thanks to Christian Haselgrove for reporting
diff --git a/cviewer/app.py b/cviewer/app.py index 35582d2..d71df52 100644 --- a/cviewer/app.py +++ b/cviewer/app.py @@ -1,340 +1,340 @@ """ The Connectome Viewer Envisage application with Plugins """ # Copyright (C) 2009-2010, Ecole Polytechnique Federale de Lausanne (EPFL) and # University Hospital Center and...
LTS5/connectomeviewer
86d883a3f0ba048b624f054dc7ec3d55b5064f33
Removed obsolete folder in setup.py
diff --git a/cviewer/setup.py b/cviewer/setup.py index c7465bf..c239d11 100644 --- a/cviewer/setup.py +++ b/cviewer/setup.py @@ -1,26 +1,25 @@ import ConfigParser import os ################################################################################ def configuration(parent_package='',top_path=None): fro...
LTS5/connectomeviewer
58815a607efcab07e8f231949a4c8435ca9af4ec
Fix setup.py import
diff --git a/cviewer/plugins/setup.py b/cviewer/plugins/setup.py index 93aa534..f96a82a 100644 --- a/cviewer/plugins/setup.py +++ b/cviewer/plugins/setup.py @@ -1,23 +1,20 @@ def configuration(parent_package='',top_path=None): from numpy.distutils.misc_util import Configuration config = Configuration('plug...
LTS5/connectomeviewer
d83f1fe0e5eeaff1ad69917e921eb77a1613eb94
Fix of no edge value network
diff --git a/cviewer/plugins/codeoracle/cnetwork_action.py b/cviewer/plugins/codeoracle/cnetwork_action.py index f2bd088..d43a2fe 100644 --- a/cviewer/plugins/codeoracle/cnetwork_action.py +++ b/cviewer/plugins/codeoracle/cnetwork_action.py @@ -1,163 +1,164 @@ from enthought.traits.api import Code, Button, Int, on_t...
LTS5/connectomeviewer
6862e30f09ce2d5c1cd19734d4b7d627a6f5d075
Fix for no edges network in code oracle
diff --git a/cviewer/plugins/codeoracle/cnetwork_action.py b/cviewer/plugins/codeoracle/cnetwork_action.py index 7253cab..f2bd088 100644 --- a/cviewer/plugins/codeoracle/cnetwork_action.py +++ b/cviewer/plugins/codeoracle/cnetwork_action.py @@ -1,163 +1,163 @@ from enthought.traits.api import Code, Button, Int, on_t...
LTS5/connectomeviewer
4a08fcbf61173d755502ee0b8bb648db510fdc1c
Adding a button to run the script
diff --git a/cviewer/plugins/text_editor/editor/text_editor.py b/cviewer/plugins/text_editor/editor/text_editor.py index 692c494..eff59aa 100644 --- a/cviewer/plugins/text_editor/editor/text_editor.py +++ b/cviewer/plugins/text_editor/editor/text_editor.py @@ -1,234 +1,243 @@ """ A text editor. """ # Standard lib...
LTS5/connectomeviewer
2f46aae7e943676b44fe6916e18cc5b37153b9e1
Fix copyright
diff --git a/COPYRIGHT b/COPYRIGHT index 8a27dd7..e83ef1f 100644 --- a/COPYRIGHT +++ b/COPYRIGHT @@ -1,34 +1,27 @@ Copyright (C) 2009-2011, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland All rights reserved. Redistribution and use in sourc...
LTS5/connectomeviewer
472e0b0cf3ae82f68885a6bb0a51518db40ab09c
Cleanup
diff --git a/cviewer/cviewer_workbench_application.py b/cviewer/cviewer_workbench_application.py index ff52c67..5595622 100755 --- a/cviewer/cviewer_workbench_application.py +++ b/cviewer/cviewer_workbench_application.py @@ -1,127 +1,128 @@ """ The Connectome Viewer Envisage Workbench Application class """ # Copyr...
LTS5/connectomeviewer
8744663c9405776461b65e87a86a4625aee7924d
fixing up executable permissions
diff --git a/.gitignore b/.gitignore old mode 100755 new mode 100644 diff --git a/COPYRIGHT b/COPYRIGHT old mode 100755 new mode 100644 diff --git a/MANIFEST.in b/MANIFEST.in old mode 100755 new mode 100644 diff --git a/README.rst b/README.rst old mode 100755 new mode 100644 diff --git a/build_helpers.py b/build_helper...
LTS5/connectomeviewer
e9560139dce73508e4dbc83b2a1374fbd6d8cb2d
Adding another CNetwork viz script
diff --git a/cviewer/plugins/codeoracle/actions.py b/cviewer/plugins/codeoracle/actions.py index c03426e..9d12a75 100644 --- a/cviewer/plugins/codeoracle/actions.py +++ b/cviewer/plugins/codeoracle/actions.py @@ -1,302 +1,321 @@ import logging from enthought.io.api import File from enthought.pyface.api import File...
LTS5/connectomeviewer
23174828ffc3a32c54427eff673897b9e31cac63
Release Candidate 2.0
diff --git a/cviewer/info.py b/cviewer/info.py index 6a9b73e..1b1d204 100644 --- a/cviewer/info.py +++ b/cviewer/info.py @@ -1,83 +1,83 @@ ''' Release data for ConnectomeViewer This script should do no imports. It only defines variables. ''' -version = '2.0.0-RC1' +version = '2.0.0-RC2' is_release = False lon...
LTS5/connectomeviewer
d3a8d3ea618acce4375f49ca89349590688ccf65
Updating cfflib XNAT API in Code Oracle
diff --git a/cviewer/plugins/codeoracle/scripts.py b/cviewer/plugins/codeoracle/scripts.py index a4e8c8a..410e91a 100644 --- a/cviewer/plugins/codeoracle/scripts.py +++ b/cviewer/plugins/codeoracle/scripts.py @@ -1,599 +1,602 @@ nipypebet = """ # Prerequisite: # 1. You need to have Nipype installed on your system....
LTS5/connectomeviewer
b60ec097e54064315835bcdff34930cb8a5827d1
Adding network report to Code Oracle
diff --git a/cviewer/plugins/codeoracle/actions.py b/cviewer/plugins/codeoracle/actions.py index 94e9265..c03426e 100644 --- a/cviewer/plugins/codeoracle/actions.py +++ b/cviewer/plugins/codeoracle/actions.py @@ -1,281 +1,302 @@ import logging from enthought.io.api import File from enthought.pyface.api import File...
LTS5/connectomeviewer
b1950e43e2fb13760b5d131709aa2db2f2335b5e
Add missing *.so files
diff --git a/.gitignore b/.gitignore index 52d5509..6451635 100755 --- a/.gitignore +++ b/.gitignore @@ -1,17 +1,13 @@ *.bin *.log *.pyc -*.so *.c doc/_build/ doc/build/ doc/manual build/ dist/ -ConnectomeViewer.egg-info/ -libs-queue/ MANIFEST .project -.pydevproject .settings/ .idea/ diff --git a/cviewer/...
LTS5/connectomeviewer
919504d30b578104dcb674431c0e1c7e04c1e5d1
Importing nibabel intent_codes from the correct location for nibabel>=1.1.0
diff --git a/cviewer/plugins/cff2/csurface_darray.py b/cviewer/plugins/cff2/csurface_darray.py index 7707391..60a0e08 100644 --- a/cviewer/plugins/cff2/csurface_darray.py +++ b/cviewer/plugins/cff2/csurface_darray.py @@ -1,58 +1,61 @@ """ The ConnectomeViewer wrapper for a cfflib object """ # Copyright (C) 2009-2010,...
LTS5/connectomeviewer
5599a512cffb20945f3e75cc0de45fbd0035e63e
Raise exception when no edges to visualize
diff --git a/cviewer/plugins/codeoracle/cnetwork_action.py b/cviewer/plugins/codeoracle/cnetwork_action.py index 691b8ef..7253cab 100644 --- a/cviewer/plugins/codeoracle/cnetwork_action.py +++ b/cviewer/plugins/codeoracle/cnetwork_action.py @@ -1,160 +1,163 @@ from enthought.traits.api import Code, Button, Int, on_t...
LTS5/connectomeviewer
76de7360484e158ff9a8bedf14344b812c06e0d3
Adding the Connectome Mapper as a widget
diff --git a/cviewer/app.py b/cviewer/app.py index 8f7f7a5..a346274 100755 --- a/cviewer/app.py +++ b/cviewer/app.py @@ -1,345 +1,355 @@ """ The ConnectomeViewer Envisage application with Plugins """ # Copyright (C) 2009-2010, Ecole Polytechnique Federale de Lausanne (EPFL) and # University Hospital Center and ...
LTS5/connectomeviewer
c0ac6c2e8ea8e90ae6d4ca80fd598d53e68e9b9b
Patch docs not to show source
diff --git a/doc/conf.py b/doc/conf.py index 9bd8b06..23767c9 100755 --- a/doc/conf.py +++ b/doc/conf.py @@ -1,214 +1,214 @@ # -*- coding: utf-8 -*- # # sampledoc documentation build configuration file, created by # sphinx-quickstart on Tue Jun 3 12:40:24 2008. # # This file is execfile()d with the current direc...
LTS5/connectomeviewer
ddce07ed764353237b4f10173ff0e315f3367ec9
Adding cfflib to install instructions
diff --git a/doc/users/installation.rst b/doc/users/installation.rst index 6174880..7ab4382 100755 --- a/doc/users/installation.rst +++ b/doc/users/installation.rst @@ -1,58 +1,62 @@ .. _installation: ========================== Download and Installation ========================== .. warning:: This content is s...
LTS5/connectomeviewer
38340935d21541f94ae00ca49f560e887dcb9b54
Release candiate 2.0.0-RC1. Updated docu
diff --git a/COPYRIGHT b/COPYRIGHT index 02f90dc..8a27dd7 100755 --- a/COPYRIGHT +++ b/COPYRIGHT @@ -1,34 +1,34 @@ Copyright (C) 2009-2011, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland All rights reserved. Redistribution and use in sourc...
LTS5/connectomeviewer
3d912ab517ada563f58efd10fe64660ba48035af
Adding hint to XNAT code oracle
diff --git a/cviewer/plugins/codeoracle/scripts.py b/cviewer/plugins/codeoracle/scripts.py index ffd5842..7a4521c 100644 --- a/cviewer/plugins/codeoracle/scripts.py +++ b/cviewer/plugins/codeoracle/scripts.py @@ -1,570 +1,575 @@ nipypebet = """ # Prerequisite: # 1. You need to have Nipype installed on your system....
LTS5/connectomeviewer
94520584dc67513cae2e84c9467881602fb1841b
Fix bug when display surfaces
diff --git a/cviewer/plugins/codeoracle/actions.py b/cviewer/plugins/codeoracle/actions.py index 3450652..7ac7068 100644 --- a/cviewer/plugins/codeoracle/actions.py +++ b/cviewer/plugins/codeoracle/actions.py @@ -1,273 +1,273 @@ import logging from enthought.io.api import File from enthought.pyface.api import File...
LTS5/connectomeviewer
d7ef02d5b2087ca7e6bfbddd0b79342aae274f94
Fixes in the Code Oracle
diff --git a/cviewer/plugins/codeoracle/scripts.py b/cviewer/plugins/codeoracle/scripts.py index d9af8bf..d88f861 100644 --- a/cviewer/plugins/codeoracle/scripts.py +++ b/cviewer/plugins/codeoracle/scripts.py @@ -1,636 +1,638 @@ nipypebet = """ # Prerequisite: # 1. You need to have Nipype installed on your system....
LTS5/connectomeviewer
005c35cc9502d19a6456150dba869f5380df6630
Adding nipype bet script
diff --git a/cviewer/plugins/codeoracle/actions.py b/cviewer/plugins/codeoracle/actions.py index 823d08e..3450652 100644 --- a/cviewer/plugins/codeoracle/actions.py +++ b/cviewer/plugins/codeoracle/actions.py @@ -1,251 +1,273 @@ import logging from enthought.io.api import File from enthought.pyface.api import File...
LTS5/connectomeviewer
6d23112d4cc3e4f29e27347d16a2cb630740d081
Added XNAT Push Pull Code Oracle
diff --git a/cviewer/plugins/codeoracle/actions.py b/cviewer/plugins/codeoracle/actions.py index a7391b6..823d08e 100644 --- a/cviewer/plugins/codeoracle/actions.py +++ b/cviewer/plugins/codeoracle/actions.py @@ -1,235 +1,251 @@ import logging from enthought.io.api import File from enthought.pyface.api import File...
LTS5/connectomeviewer
20256768c09b26b1363f6b56cc9c24deff8503b3
Fixes to get installation working
diff --git a/cviewer/libs/setup.py b/cviewer/libs/setup.py index 11e96fe..53f1288 100644 --- a/cviewer/libs/setup.py +++ b/cviewer/libs/setup.py @@ -1,33 +1,33 @@ import ConfigParser import os ################################################################################ def configuration(parent_package='',top_...
LTS5/connectomeviewer
9abfeab978a6d2b0c35d757bcb76093a8f37ee5a
Fix in Chaco connection matrix viewer
diff --git a/cviewer/visualization/matrix/con_matrix_viewer.py b/cviewer/visualization/matrix/con_matrix_viewer.py index 7a8c30e..5f257b7 100644 --- a/cviewer/visualization/matrix/con_matrix_viewer.py +++ b/cviewer/visualization/matrix/con_matrix_viewer.py @@ -1,195 +1,199 @@ """ Matrix Viewer Extension * Left-drag p...
Anber/django-schedule-field
3428732570eba342457b9e4551c9e9f33333cda5
.button > .schedule-menu-item
diff --git a/media/widgets/schedule/schedule.js b/media/widgets/schedule/schedule.js index 23a5177..ccbfc4a 100644 --- a/media/widgets/schedule/schedule.js +++ b/media/widgets/schedule/schedule.js @@ -1,221 +1,221 @@ if (!Array.prototype.map) { Array.prototype.map = function(fun /*, thisp*/) { var len = this.l...
Anber/django-schedule-field
1f30ee7eef45b9991627eb578ce9d0fcf1e8c924
Remove <script> from widget
diff --git a/media/widgets/schedule/schedule.js b/media/widgets/schedule/schedule.js index 9032a30..23a5177 100644 --- a/media/widgets/schedule/schedule.js +++ b/media/widgets/schedule/schedule.js @@ -1,215 +1,221 @@ if (!Array.prototype.map) { Array.prototype.map = function(fun /*, thisp*/) { var len = this.l...
seouri/medvane3
c4d615e4087e62c44f38f3d803642177abc4d113
be consitent on displaying bibliome age
diff --git a/app/views/bibliomes/index.html.erb b/app/views/bibliomes/index.html.erb index e03e199..5f83cda 100644 --- a/app/views/bibliomes/index.html.erb +++ b/app/views/bibliomes/index.html.erb @@ -1,8 +1,8 @@ <% page_title(@prefix + "Bibliomes") %> <%= page_entries_info @bibliomes %> <ul> <% for item in @bibl...
seouri/medvane3
c64baa1984719a4412e565ed4b4268bdb03063b3
added In Process Bibliomes page
diff --git a/app/controllers/bibliomes_controller.rb b/app/controllers/bibliomes_controller.rb index 713a703..2114e7d 100644 --- a/app/controllers/bibliomes_controller.rb +++ b/app/controllers/bibliomes_controller.rb @@ -1,114 +1,122 @@ class BibliomesController < ApplicationController def index @bibliomes = B...
seouri/medvane3
0c7c67a59279291a63acff637d50f5be1ae9012b
fixed postgresql type cast problem and incorrect column name
diff --git a/app/models/bibliome.rb b/app/models/bibliome.rb index 8ee05f0..7758398 100644 --- a/app/models/bibliome.rb +++ b/app/models/bibliome.rb @@ -1,54 +1,54 @@ class Bibliome < ActiveRecord::Base has_many :bibliome_articles has_many :articles, :through => :bibliome_articles, :order => "#{BibliomeArticle.t...
seouri/medvane3
e1a270fe6b4f911751bf219a6b0b6c01d476fecc
fixed bug never showing recent/poplular medvanes
diff --git a/app/views/pages/home.html.erb b/app/views/pages/home.html.erb index b79b815..f347c74 100644 --- a/app/views/pages/home.html.erb +++ b/app/views/pages/home.html.erb @@ -1,34 +1,34 @@ <% page_title("Biomedical Research at a Glance") -%> <h2>Build Your Own Bibliome</h2> <% form_tag new_bibliome_path, :...
seouri/medvane3
a4502c3c2115475dc62995ecb8fccd264824016c
migrate down only if migrated up
diff --git a/db/schema.rb b/db/schema.rb index eee3d47..4fbec66 100644 --- a/db/schema.rb +++ b/db/schema.rb @@ -1,332 +1,332 @@ # This file is auto-generated from the current state of the database. Instead of editing this file, # please use the migrations feature of Active Record to incrementally modify your databa...
seouri/medvane3
b7342e638b3ef49554ac68af8d4e9dd332be914f
changed postgresql ruby gem to 'pg'
diff --git a/config/database.yml.postgresql b/config/database.yml.postgresql index f735584..198c96d 100644 --- a/config/database.yml.postgresql +++ b/config/database.yml.postgresql @@ -1,51 +1,51 @@ # PostgreSQL. Versions 7.4 and 8.x are supported. # # Install the ruby-postgres driver: -# gem install ruby-postgres...
seouri/medvane3
843655c1870de2b906663653f3b03cb5840834dc
show period tab as button
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index 7ef037e..bd63768 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -1,106 +1,105 @@ # Methods added to this helper will be available to all templates in the application. module ApplicationH...
seouri/medvane3
fec31a80a3acca42477dd3505e4421105f706f7b
refactored Medvane setup tasks so that they can be run as background job as well
diff --git a/db/migrate/20100127150217_create_published_genes.rb b/db/migrate/20100127150217_create_published_genes.rb index b9861ac..6458771 100644 --- a/db/migrate/20100127150217_create_published_genes.rb +++ b/db/migrate/20100127150217_create_published_genes.rb @@ -1,13 +1,12 @@ class CreatePublishedGenes < ActiveR...
seouri/medvane3
9aa853b0aa247e01e2db4bb116b5013a279c0ef5
fix lib name for libxml
diff --git a/config/environment.rb b/config/environment.rb index 1c04cf2..96b84c8 100644 --- a/config/environment.rb +++ b/config/environment.rb @@ -1,46 +1,46 @@ # Be sure to restart your server when you modify this file # Specifies gem version of Rails to use when vendor/rails is not present RAILS_GEM_VERSION = ...
seouri/medvane3
60aad9e7a047b1271cc797b10c129f41f7232069
added libxml-ruby gem v1.1.3
diff --git a/config/environment.rb b/config/environment.rb index 8ffcf08..1c04cf2 100644 --- a/config/environment.rb +++ b/config/environment.rb @@ -1,45 +1,46 @@ # Be sure to restart your server when you modify this file # Specifies gem version of Rails to use when vendor/rails is not present RAILS_GEM_VERSION = ...
seouri/medvane3
df69f894f5d53ffc08927144b3bc226c3bfacb24
added libxml-ruby gems for Heroku
diff --git a/.gems b/.gems index dd94229..033c57a 100644 --- a/.gems +++ b/.gems @@ -1,4 +1,5 @@ googlecharts --version 1.4.0 --source gemcutter.org will_paginate --version 2.3.12 --source gemcutter.org bio --version 1.3.1 --source gemcutter.org delayed_job --version 1.8.4 --source gemcutter.org +libxml-ruby --vers...
seouri/medvane3
b76de6d3661e5571a231b36d4746c926b74f6b33
added postgresql db config example
diff --git a/config/database.yml.sample b/config/database.yml.mysql similarity index 100% rename from config/database.yml.sample rename to config/database.yml.mysql diff --git a/config/database.yml.postgresql b/config/database.yml.postgresql new file mode 100644 index 0000000..f735584 --- /dev/null +++ b/config/databas...
seouri/medvane3
bc907b507d88fb0fb281733fa035202d3bb825f2
added Gene, PublishedGene, Taxonomy
diff --git a/app/controllers/genes_controller.rb b/app/controllers/genes_controller.rb new file mode 100644 index 0000000..12118ec --- /dev/null +++ b/app/controllers/genes_controller.rb @@ -0,0 +1,85 @@ +class GenesController < ApplicationController + # GET /genes + # GET /genes.xml + def index + @genes = Gene.a...
seouri/medvane3
dfdc88c7f5799adc606716531150b3275af9d470
show executed time for rake db:seed
diff --git a/db/seeds.rb b/db/seeds.rb index 752384a..bc77800 100644 --- a/db/seeds.rb +++ b/db/seeds.rb @@ -1,32 +1,35 @@ descriptor_file = File.join(File.dirname(__FILE__), 'desc.2010.txt') if File.stat(descriptor_file).size > 0 + puts "[#{Time.now.to_s}] load Subject" File.foreach(descriptor_file) do |record| ...
seouri/medvane3
40d226b9acbf06c4d32fbf8d3ab6cb6b7ee60cd5
added mdvn:journals task to Heroku cron job
diff --git a/lib/tasks/cron.rake b/lib/tasks/cron.rake index 1c2d9a7..3e6234c 100644 --- a/lib/tasks/cron.rake +++ b/lib/tasks/cron.rake @@ -1,2 +1,5 @@ task :cron => :environment do + if Time.now.hour == 4 + Rake::Task['mdvn:journals'].execute + end end \ No newline at end of file
seouri/medvane3
c0477b50e809b75662a8230cd2f663afec7f8efe
show journal update information
diff --git a/lib/tasks/medvane.rake b/lib/tasks/medvane.rake index fe053b9..b247cef 100644 --- a/lib/tasks/medvane.rake +++ b/lib/tasks/medvane.rake @@ -1,20 +1,29 @@ namespace :mdvn do desc "Updates Journal from PubMed" task :journals => :environment do journal_ids = Journal.all(:select => :id).map {|j| j....
seouri/medvane3
153b215f4421299014f19260fb583af0e2fe51c9
don't need to include again
diff --git a/lib/tasks/medvane.rake b/lib/tasks/medvane.rake index 7653e81..fe053b9 100644 --- a/lib/tasks/medvane.rake +++ b/lib/tasks/medvane.rake @@ -1,21 +1,20 @@ namespace :mdvn do desc "Updates Journal from PubMed" task :journals => :environment do - require 'pubmed_journal' journal_ids = Journal.a...
seouri/medvane3
edd761f03993a41b78a18b00573114202a6e9554
remove debugging code
diff --git a/lib/tasks/medvane.rake b/lib/tasks/medvane.rake index 1aad190..7653e81 100644 --- a/lib/tasks/medvane.rake +++ b/lib/tasks/medvane.rake @@ -1,22 +1,21 @@ namespace :mdvn do desc "Updates Journal from PubMed" task :journals => :environment do require 'pubmed_journal' - require 'pp' journ...
seouri/medvane3
51848926d66a15f638fc2df624e7656dc6c2518c
prepare for rake mdvn:genes
diff --git a/lib/tasks/medvane.rake b/lib/tasks/medvane.rake index 09e37e5..1aad190 100644 --- a/lib/tasks/medvane.rake +++ b/lib/tasks/medvane.rake @@ -1,16 +1,22 @@ namespace :mdvn do desc "Updates Journal from PubMed" task :journals => :environment do require 'pubmed_journal' require 'pp' journ...
seouri/medvane3
ea3062b7a7004710fa58eb1f592b5b40e64a5c74
use journal title with ellipsis if the length is longer than 236 characters
diff --git a/lib/medline.rb b/lib/medline.rb index 3379ced..1d07e67 100644 --- a/lib/medline.rb +++ b/lib/medline.rb @@ -1,99 +1,107 @@ module Bio class MEDLINE < NCBIDB MONTH = { "Jan" => 1, "Feb" => 2, "Mar" => 3, "Apr" => 4, "May" => 5, "Jun" => 6, "Jul" => 7...
seouri/medvane3
65f6a9a5f7d70467da87b70b7cb0c45a0cf471e2
added PubMed journal update rake task
diff --git a/lib/pubmed_journal.rb b/lib/pubmed_journal.rb new file mode 100644 index 0000000..4131cab --- /dev/null +++ b/lib/pubmed_journal.rb @@ -0,0 +1,71 @@ +require 'open-uri' +require 'libxml' + +module PubmedJournal + class JournalCallback + include LibXML::XML::SaxParser::Callbacks + + CONTENT_KEY = '...
seouri/medvane3
415157b7037bc991508270f468a8592e9c81b4d8
number with delimiter for bibliome import status
diff --git a/app/helpers/bibliomes_helper.rb b/app/helpers/bibliomes_helper.rb index d608b0f..8dd48d0 100644 --- a/app/helpers/bibliomes_helper.rb +++ b/app/helpers/bibliomes_helper.rb @@ -1,46 +1,46 @@ module BibliomesHelper def status(bibliome) unless bibliome.built? - status = "#{bibliome.total_article...
seouri/medvane3
f324390fc15e710a303f13471ecc7c0ef1475952
number with delimiter for bibliome import status
diff --git a/app/helpers/bibliomes_helper.rb b/app/helpers/bibliomes_helper.rb index 2d5807b..d608b0f 100644 --- a/app/helpers/bibliomes_helper.rb +++ b/app/helpers/bibliomes_helper.rb @@ -1,46 +1,46 @@ module BibliomesHelper def status(bibliome) unless bibliome.built? status = "#{bibliome.total_article...
seouri/medvane3
bedf1954b0b08e8688b8eaeff90f8006f0a9a361
ensure that there is any result from eutils efetch
diff --git a/lib/pubmed_import.rb b/lib/pubmed_import.rb index 0f57626..89eefc5 100644 --- a/lib/pubmed_import.rb +++ b/lib/pubmed_import.rb @@ -1,222 +1,222 @@ require 'cgi' require 'net/http' require 'uri' require 'medline' # 1. get 5000 PMIDs for a given search # 2. select PMIDs not in Article # 3. fetch arti...
seouri/medvane3
b8b1ba676d2741231d8e1b3535dd5c077f8c6468
refactored period parameter in the links
diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb index 25a99ab..afa765b 100644 --- a/app/controllers/application_controller.rb +++ b/app/controllers/application_controller.rb @@ -1,32 +1,33 @@ # Filters added to this controller apply to all controllers in the applicati...
seouri/medvane3
32bd085f52396d1e4d8ef9bada406ef409cafb85
cosmetic change
diff --git a/public/stylesheets/screen.css b/public/stylesheets/screen.css index c7dbe01..5d63b73 100644 --- a/public/stylesheets/screen.css +++ b/public/stylesheets/screen.css @@ -1,160 +1,161 @@ /* red: #913 yellow: #ea1 */ body { margin: 0; padding: 0; } a, a:visited { color: #913; } a:hover ...
seouri/medvane3
5993ca6fac772e34d70675dc403570a0aab0642b
cosmetic change
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index 2263930..fe983c1 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -1,109 +1,109 @@ # Methods added to this helper will be available to all templates in the application. module ApplicationH...
seouri/medvane3
5dd5e363eab35846f55b7925f987aea4c8507680
added 'see also' for author
diff --git a/app/helpers/authors_helper.rb b/app/helpers/authors_helper.rb index f22e1f9..7028266 100644 --- a/app/helpers/authors_helper.rb +++ b/app/helpers/authors_helper.rb @@ -1,2 +1,12 @@ module AuthorsHelper + def see_also(author) + return if author.see_also.size == 0 + period = @period == "all" ? nil : ...
seouri/medvane3
2002adef6e1aac8d46072a9360437df704e63e1a
upgraded will_paginate to v2.3.12
diff --git a/config/environment.rb b/config/environment.rb index 2c7ac63..8ffcf08 100644 --- a/config/environment.rb +++ b/config/environment.rb @@ -1,45 +1,45 @@ # Be sure to restart your server when you modify this file # Specifies gem version of Rails to use when vendor/rails is not present RAILS_GEM_VERSION = ...
seouri/medvane3
c7bceb0958b2128515f83a613c2f9bb3f17ed07c
PostgreSQL does binary search. Convert JOURNAL ARTICLE to Journal Article. Need to fix other object types, too.
diff --git a/lib/pubmed_import.rb b/lib/pubmed_import.rb index c1d5eca..0f57626 100644 --- a/lib/pubmed_import.rb +++ b/lib/pubmed_import.rb @@ -1,222 +1,222 @@ require 'cgi' require 'net/http' require 'uri' require 'medline' # 1. get 5000 PMIDs for a given search # 2. select PMIDs not in Article # 3. fetch arti...
seouri/medvane3
5b8a26ddd258d1cdf9ee9391527b4c8b82357de9
create new pubtype if not found
diff --git a/lib/pubmed_import.rb b/lib/pubmed_import.rb index 95bfe53..c1d5eca 100644 --- a/lib/pubmed_import.rb +++ b/lib/pubmed_import.rb @@ -1,222 +1,222 @@ require 'cgi' require 'net/http' require 'uri' require 'medline' # 1. get 5000 PMIDs for a given search # 2. select PMIDs not in Article # 3. fetch arti...
seouri/medvane3
1d48aee9e528d8dc4eefe12529d3213ea82ba0f4
check if there is a bibliome
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index 02c7eed..2263930 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -1,109 +1,109 @@ # Methods added to this helper will be available to all templates in the application. module ApplicationH...
seouri/medvane3
c4f01ff086a303b1dcf776e62dc025ec3522f37d
show bibliome nav only for built bibliome
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index 41f167f..02c7eed 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -1,109 +1,109 @@ # Methods added to this helper will be available to all templates in the application. module ApplicationH...
seouri/medvane3
d8e48ac58ebfbfb94c725495c62823bf5b790e6f
set the right parameter for delayed_job
diff --git a/config/initializers/delayed_job.rb b/config/initializers/delayed_job.rb index ff88833..de85f51 100644 --- a/config/initializers/delayed_job.rb +++ b/config/initializers/delayed_job.rb @@ -1 +1 @@ -Delayed::Worker.destroy_failed_jobs = false \ No newline at end of file +Delayed::Job.destroy_failed_jobs = fa...
seouri/medvane3
e0e893538c3ffd2fc8eb620367c29b12ff992be7
keep failed jobs in the table & give lower priority for later jobs in the same import
diff --git a/app/controllers/bibliomes_controller.rb b/app/controllers/bibliomes_controller.rb index d7c084b..713a703 100644 --- a/app/controllers/bibliomes_controller.rb +++ b/app/controllers/bibliomes_controller.rb @@ -1,113 +1,114 @@ class BibliomesController < ApplicationController def index @bibliomes = B...
seouri/medvane3
0195250fc34458b10802a113041fb3a1af0561a0
added sparkline for publication history
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index 903a829..41f167f 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -1,98 +1,109 @@ # Methods added to this helper will be available to all templates in the application. module ApplicationHe...
seouri/medvane3
faceb98e819620ce21a565a718030fb22b5244b0
removed notes
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index 2c47ce1..903a829 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -1,105 +1,98 @@ # Methods added to this helper will be available to all templates in the application. module ApplicationHe...
seouri/medvane3
8fc85d7788ee59f8ed32cc3b10b7f4b385b92d68
number with delimiter
diff --git a/app/views/authors/index.html.erb b/app/views/authors/index.html.erb index 65a0c7d..04279db 100644 --- a/app/views/authors/index.html.erb +++ b/app/views/authors/index.html.erb @@ -1,9 +1,9 @@ <% page_title("Authors", @bibliome.query)%> <h2>Authors</h2> <%= page_entries_info @authors %> <ol> <% @author...
seouri/medvane3
c627718893d97303817c0ad7feef58f741cc799a
remove period param for 'all'
diff --git a/app/helpers/bibliomes_helper.rb b/app/helpers/bibliomes_helper.rb index 16fbc2a..d3d947c 100644 --- a/app/helpers/bibliomes_helper.rb +++ b/app/helpers/bibliomes_helper.rb @@ -1,46 +1,47 @@ module BibliomesHelper def status(bibliome) unless bibliome.built? status = "#{bibliome.total_article...
seouri/medvane3
91d0df74f4d40ed0f17e0c5c9b9c88fee0b8804b
added bibliome nav
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index 32b1336..2c47ce1 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -1,94 +1,105 @@ # Methods added to this helper will be available to all templates in the application. module ApplicationHe...
seouri/medvane3
c85dee3593e2b363a3acf8862458c897023664c8
don't append period parameter for 'all'
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index 0d7beef..32b1336 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -1,93 +1,94 @@ # Methods added to this helper will be available to all templates in the application. module ApplicationHel...
seouri/medvane3
57e42309b94a8cbac71678fb74404e536e1b9b79
show subjects for each article
diff --git a/app/controllers/articles_controller.rb b/app/controllers/articles_controller.rb index 6700212..88e9b97 100644 --- a/app/controllers/articles_controller.rb +++ b/app/controllers/articles_controller.rb @@ -1,85 +1,85 @@ class ArticlesController < ApplicationController # GET /articles # GET /articles.x...
seouri/medvane3
6ae8eca1d1c4390ae0f40469a4bc4d9470ddfc1f
refactored html title to be consitent
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index 39a9afa..0d7beef 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -1,93 +1,93 @@ # Methods added to this helper will be available to all templates in the application. module ApplicationHel...
seouri/medvane3
88f102f6f427955e1b381ea3c659851649a53a8e
use counter in the bibliome for total entries in pagination
diff --git a/app/controllers/articles_controller.rb b/app/controllers/articles_controller.rb index 19ca901..6700212 100644 --- a/app/controllers/articles_controller.rb +++ b/app/controllers/articles_controller.rb @@ -1,85 +1,85 @@ class ArticlesController < ApplicationController # GET /articles # GET /articles.x...
seouri/medvane3
a3203e969f96f655ec78fe73d47455b42b3e6044
added publication history graph
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index 9ffc1d8..39a9afa 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -1,60 +1,93 @@ # Methods added to this helper will be available to all templates in the application. module ApplicationHel...
seouri/medvane3
938bb0726d7f74afd275e9bf59e9cd4c5515c2f8
smaller period links for iPhone
diff --git a/public/stylesheets/screen.css b/public/stylesheets/screen.css index 62f46c2..e806e85 100644 --- a/public/stylesheets/screen.css +++ b/public/stylesheets/screen.css @@ -1,126 +1,127 @@ /* red: #913 yellow: #ea1 */ body { margin: 0; padding: 0; } a, a:visited { color: #913; } a:hover ...
seouri/medvane3
0345f630cceb6142cb3b6dad43383e43c4d62ed3
period tab working
diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb index 351490c..25a99ab 100644 --- a/app/controllers/application_controller.rb +++ b/app/controllers/application_controller.rb @@ -1,32 +1,32 @@ # Filters added to this controller apply to all controllers in the applicati...
seouri/medvane3
57c06d38447afb5a2ec803366e26c9ee2aee67cb
added period parameter
diff --git a/app/controllers/authors_controller.rb b/app/controllers/authors_controller.rb index 97bf65b..b5123a1 100644 --- a/app/controllers/authors_controller.rb +++ b/app/controllers/authors_controller.rb @@ -1,89 +1,89 @@ class AuthorsController < ApplicationController # GET /authors # GET /authors.xml d...
seouri/medvane3
c48727ae04948fb6504ff177876732ae45e29981
check if there is a line to change
diff --git a/lib/medline.rb b/lib/medline.rb index 9d7c81f..3379ced 100644 --- a/lib/medline.rb +++ b/lib/medline.rb @@ -1,97 +1,99 @@ module Bio class MEDLINE < NCBIDB MONTH = { "Jan" => 1, "Feb" => 2, "Mar" => 3, "Apr" => 4, "May" => 5, "Jun" => 6, "Jul" => 7,...
seouri/medvane3
37ddcc23d9548093311ba35fcfa12aee3a7c7082
added indices
diff --git a/app/controllers/articles_controller.rb b/app/controllers/articles_controller.rb index e8c229c..19ca901 100644 --- a/app/controllers/articles_controller.rb +++ b/app/controllers/articles_controller.rb @@ -1,85 +1,85 @@ class ArticlesController < ApplicationController # GET /articles # GET /articles.x...
seouri/medvane3
a6294ca3c954b43e07a8ea82323ea83e67edef0c
eagerload bibliome
diff --git a/app/controllers/authors_controller.rb b/app/controllers/authors_controller.rb index 6128367..74c64fa 100644 --- a/app/controllers/authors_controller.rb +++ b/app/controllers/authors_controller.rb @@ -1,89 +1,89 @@ class AuthorsController < ApplicationController # GET /authors # GET /authors.xml d...
seouri/medvane3
bf6393db1e90ee1fc0801eeac38f70efc6f9451b
make link only when there are more items to show
diff --git a/app/views/pages/home.html.erb b/app/views/pages/home.html.erb index 976db0e..fedebd1 100644 --- a/app/views/pages/home.html.erb +++ b/app/views/pages/home.html.erb @@ -1,34 +1,34 @@ <% page_title("Biomedical Research at a Glance") -%> <h2>Build Your Own Bibliome</h2> <% form_tag new_bibliome_path, :...
seouri/medvane3
be0ac4d938964d5aa02cc869445ccaf47012606d
too long autogenerated index name
diff --git a/db/schema.rb b/db/schema.rb index c57b03e..98d2534 100644 --- a/db/schema.rb +++ b/db/schema.rb @@ -1,304 +1,304 @@ # This file is auto-generated from the current state of the database. Instead of editing this file, # please use the migrations feature of Active Record to incrementally modify your databa...
seouri/medvane3
afbf46c6b0a26682b5e8753a5bab9882744624c2
too long autogenerated index name
diff --git a/db/migrate/20091215164444_create_authors.rb b/db/migrate/20091215164444_create_authors.rb index 44bc97b..ac556ad 100644 --- a/db/migrate/20091215164444_create_authors.rb +++ b/db/migrate/20091215164444_create_authors.rb @@ -1,16 +1,16 @@ class CreateAuthors < ActiveRecord::Migration def self.up cr...
seouri/medvane3
08480d8c21a89d3ee69366aa940b3cbf09140dc9
too long autogenerated index name
diff --git a/db/migrate/20091221211045_create_journal_subjects.rb b/db/migrate/20091221211045_create_journal_subjects.rb index 7aab8bd..63a0e09 100644 --- a/db/migrate/20091221211045_create_journal_subjects.rb +++ b/db/migrate/20091221211045_create_journal_subjects.rb @@ -1,19 +1,19 @@ class CreateJournalSubjects < Ac...
seouri/medvane3
ec0ad47c0885eed510c26a2be6589eb96325074c
set period
diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb index b59cec3..351490c 100644 --- a/app/controllers/application_controller.rb +++ b/app/controllers/application_controller.rb @@ -1,24 +1,32 @@ # Filters added to this controller apply to all controllers in the applicati...
seouri/medvane3
251812edcc7b5e81b934ea50684e11af16ac4428
process 500 articles per job
diff --git a/lib/pubmed_import.rb b/lib/pubmed_import.rb index 506d6ce..faf610d 100644 --- a/lib/pubmed_import.rb +++ b/lib/pubmed_import.rb @@ -1,221 +1,221 @@ require 'cgi' require 'net/http' require 'uri' require 'medline' # 1. get 5000 PMIDs for a given search # 2. select PMIDs not in Article # 3. fetch arti...
seouri/medvane3
d055f5b0a69aa9ec5297fc33d9ade7b820e96550
make compatible with postgresql
diff --git a/app/models/bibliome_author.rb b/app/models/bibliome_author.rb index 2c56023..eef2c58 100644 --- a/app/models/bibliome_author.rb +++ b/app/models/bibliome_author.rb @@ -1,10 +1,10 @@ class BibliomeAuthor < ActiveRecord::Base belongs_to :bibliome belongs_to :author validates_uniqueness_of :author...
seouri/medvane3
ac19e12df19d52b798ee889a5b6f35b0a6aed96a
the current bibliome object is not up-to-date with articles_count. recalculate first, then compare with total_articles
diff --git a/lib/pubmed_import.rb b/lib/pubmed_import.rb index 05ab8c3..506d6ce 100644 --- a/lib/pubmed_import.rb +++ b/lib/pubmed_import.rb @@ -1,220 +1,221 @@ require 'cgi' require 'net/http' require 'uri' require 'medline' # 1. get 5000 PMIDs for a given search # 2. select PMIDs not in Article # 3. fetch arti...
elvisphilipn/RealTimeCygWin
f40277e3baea30f1aeeb85bb01a95454c6ef06dc
Uploaded final code
diff --git a/SEG4145_Assignment4.c b/SEG4145_Assignment4.c index c94a265..de37073 100644 --- a/SEG4145_Assignment4.c +++ b/SEG4145_Assignment4.c @@ -1,169 +1,428 @@ +/* + * Ahmed Ben Messaoud - 4291509 + * Elvis-Philip Niyonkuru - 3441001 + */ + /* ******************************************************************...
elvisphilipn/RealTimeCygWin
e157a26a100f87cea64215e8f382e5c4dbd29874
Added Eclipse project files so that it can build properly in Eclipse
diff --git a/.cproject b/.cproject new file mode 100644 index 0000000..5af0820 --- /dev/null +++ b/.cproject @@ -0,0 +1,673 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<?fileVersion 4.0.0?> + +<cproject storage_type_id="org.eclipse.cdt.core.XmlProjectDescriptionStorage"> +<storageModule moduleId="org.ec...
elvisphilipn/RealTimeCygWin
2d39a4aedad451f54d0e628d7c1196cb08485e7a
Oups forgot to add ignore file
diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..57f3029 --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ +*.exe +*.o +*.a \ No newline at end of file
jjk/XamhainII
f5f48839236031aff2af7f3aaa36d328ba992c56
Don't "internet enable" the generated disk image.
diff --git a/Info.plist b/Info.plist index b97c63d..d44cc6c 100644 --- a/Info.plist +++ b/Info.plist @@ -1,28 +1,30 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"> <plist version="1.0"> <dict> <key>CFBundleDevelopment...
jjk/XamhainII
7a347cfad3c313def802d995009b18de3d0c3ced
Provide custom icon for mounting the disk image.
diff --git a/misc/DiskImage.icns b/misc/DiskImage.icns new file mode 100644 index 0000000..d3b918d Binary files /dev/null and b/misc/DiskImage.icns differ diff --git a/misc/DiskImage.png b/misc/DiskImage.png new file mode 100644 index 0000000..c4a6f27 Binary files /dev/null and b/misc/DiskImage.png differ diff --git a/...
jjk/XamhainII
3ba2c234d32c1509e531a18d23180962fbf85e30
Use proper language name and make UI localizable.
diff --git a/Info.plist b/Info.plist index 2888dc2..b97c63d 100644 --- a/Info.plist +++ b/Info.plist @@ -1,28 +1,28 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"> <plist version="1.0"> <dict> <key>CFBundleDevelopment...
jjk/XamhainII
07ffffda4003caa06b7f75aa01b7124ac5f70362
Build a nice installable package.
diff --git a/XamhainII.xcodeproj/project.pbxproj b/XamhainII.xcodeproj/project.pbxproj index 9e73d03..2dd1bb3 100644 --- a/XamhainII.xcodeproj/project.pbxproj +++ b/XamhainII.xcodeproj/project.pbxproj @@ -7,737 +7,738 @@ objects = { /* Begin PBXAggregateTarget section */ 000D03D61089C45F003F010E /* XamhainII.dm...
jjk/XamhainII
2caa1165fbbd468e677b07b3ccba92f301adf53c
Touch up the UI a bit.
diff --git a/XamhainConfigureSheet.xib b/XamhainConfigureSheet.xib index 6a28435..abd3e8b 100644 --- a/XamhainConfigureSheet.xib +++ b/XamhainConfigureSheet.xib @@ -1,2740 +1,2863 @@ <?xml version="1.0" encoding="UTF-8"?> <archive type="com.apple.InterfaceBuilder3.Cocoa.XIB" version="7.10"> <data> <int key="IBDo...
jjk/XamhainII
af7038e02a2178d5dcda3078214efebcc8e78d9e
Improve configuration UI.
diff --git a/XamhainConfigureSheet.xib b/XamhainConfigureSheet.xib index 04de8b9..6a28435 100644 --- a/XamhainConfigureSheet.xib +++ b/XamhainConfigureSheet.xib @@ -1,981 +1,2757 @@ <?xml version="1.0" encoding="UTF-8"?> <archive type="com.apple.InterfaceBuilder3.Cocoa.XIB" version="7.10"> <data> <int key="IBDoc...
jjk/XamhainII
3f84aab601738242423d6752037100e868e446aa
Some small improvements.
diff --git a/defaults.plist b/defaults.plist index 611595f..d323ee5 100644 --- a/defaults.plist +++ b/defaults.plist @@ -1,56 +1,56 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"> <plist version="1.0"> <dict> <key>Bro...