gfdnavi 1.3.0.0

data/db/create_derived_spatial_attributes.sql

@@ -0,0 +1,12 @@
+create view derived_spatial_attributes 
+as 
+select s2.id,s.variable_id,s2.directory_id,s2.longitude_lb,s2.latitude_lb,
+       s2.longitude_rt,s2.latitude_rt,s2.lon_ax_name,s2.lat_ax_name 
+from spatial_attributes s, spatial_attributes s2, variables v, directories d  
+where s.longitude_lb=0 and s.latitude_lb=0 and s.longitude_rt=0 and s.latitude_rt=0 
+      and v.id = s.variable_id and v.directory_id = d.id and d.id = s2.directory_id 
+union 
+select * 
+from spatial_attributes 
+where not(longitude_lb=0 and latitude_lb=0 and longitude_rt=0 and latitude_rt=0) 
+and not(variable_id IS NULL);

data/db/draw_methods/line.yml

@@ -0,0 +1,6 @@
+:name: line
+:description: line plot
+:ndims: 1
+:nvars: 1
+:vizshot_method: line
+:attributes: []

data/db/draw_methods/scatter.yml

@@ -0,0 +1,38 @@
+:name: scatter
+:description: scatter plot
+:ndims: 1
+:nvars: 2
+:vizshot_method: scatter
+:attributes: []
+:script: |
+  newfrm = opt.delete(:newfrm)
+  GGraph::scatter(gphys, gphys1, newfrm, opt)
+
+:ggraph: |
+  gropn_1_if_not_yet
+  unless defined?(@@scater_options)
+    @@scater_options = Misc::KeywordOptAutoHelp.new(
+      ['title', nil, 'Title of the figure'],
+      ['annotate', true, 'if false, do not put texts on the right margin even when newframe==true'],
+      ['index', 1, 'mark index'],
+      ['type', 2, 'mark type'],
+      ['size', 0.01, 'marks size']
+    )
+  end
+  opts = @@scater_options.interpret(options)
+  gphys = gphys.first1D.copy
+  gphys1 = gphys1.first1D.copy
+  len = gphys.length
+  unless len == gphys1.length
+    raise ArgumentError, "length of gphys and gphys1 do not agree with each other"
+  end
+  x = gphys.data
+  y = gphys1.data
+  if newframe
+    fig(x,y)
+    axes(x,y)
+    title( opts['title'] )
+    annotate(gphys.lost_axes) if opts['annotate']
+  end
+  DCL::uumrkz(x.val, y.val, opts['type'], opts['index'], opts['size'])
+

data/db/draw_methods/tone.yml

@@ -0,0 +1,64 @@
+:name: tone
+:description: tone and contour plot
+:ndims: 2
+:nvars: 1
+:vizshot_method: tone_cont
+:setting_html: |
+  <div>
+    <%= check_box("analysis", "tone_tone") %>
+    <label for="analysis_tone">Draw tone</label>
+    <%= check_box("analysis", "tone_contour") %>
+    <label for="analysis_contour">Draw contour</label>
+    <br/>
+    <label for="analysis_min">minimum tone level</label>
+    <%= text_field("analysis", "tone_min", :size => 4, :maxlength => 12) %>
+    <br/>
+    <label for="analysis_max">maximum tone level</label>
+    <%= text_field("analysis", "tone_max", :size => 4, :maxlength => 12) %>
+    <br/>
+    <label for="analysis_nlev">num of tone levels</label>
+    <%= text_field("analysis", "tone_nlev", :size => 2, :maxlength => 2) %>
+    <br/>
+    <%= check_box("analysis", "tone_log") %>
+    <label for="Color bar">Logarithmic levels</label>
+    <br/>
+    <label for="analysis_levels">comma-separated tone levels:</label>
+    <%= text_field("analysis", "tone_levels", :size => 30, :maxlength => 200) %>
+    <br/>
+    <%= check_box("analysis", "tone_color_bar") %>
+    <label for="Color bar">Color bar</label>
+  </div>
+
+:attributes:
+- :name: tone
+  :default: true
+  :type: boolean
+  :parser: vizshot
+- :name: contour
+  :default: true
+  :type: boolean
+  :parser: vizshot
+- :name: min
+  :type: float
+  :optional: true
+  :parser: ggraph
+- :name: max
+  :type: float
+  :optional: true
+  :parser: ggraph
+- :name: nlev
+  :type: int
+  :optional: true
+  :parser: ggraph
+- :name: levels
+  :type: array_float
+  :optional: true
+  :parser: ggraph
+- :name: color_bar
+  :default: true
+  :type: boolean
+  :parser: vizshot
+- :name: log
+  :default: false
+  :type: boolean
+  :parser: ggraph

data/db/draw_methods/vector.yml

@@ -0,0 +1,19 @@
+:name: vector
+:description: vector plot
+:ndims: 2
+:nvars: 2
+:vizshot_method: vector
+:attributes: []
+:setting_html: |
+  <%
+  @order_type = "vector"
+  @order_names = %w(X Y)
+  @num_for_each = 2
+  @group_name = "diagram"
+  @order = @analysis.draw_variables_order
+  %>
+  <div>
+    X-Y component
+    <%= render(:partial => "variables_order") %>
+  </div>
+

data/db/dump_db.rb

@@ -0,0 +1,43 @@
+#!/usr/bin/env ruby
+
+require File.join(File.dirname(__FILE__), "..", "config", "environment")
+
+tables = %w( functions function_outputs value_types function_arguments 
+             diagram_caches diagram_cache_data diagram_cache_sessions
+           )
+
+hash = Hash.new
+
+exist_tables = ActiveRecord::Base.connection.tables
+tables.each do |table_name|
+
+  model_name = table_name.classify
+  model_name += "e" if table_name == "diagram_caches"
+  if exist_tables.include?(table_name)
+    ar = ActiveRecord.class_eval(model_name)
+    ary = Array.new
+    ar.find(:all).each{|row|
+      ary.push row.attributes
+    }
+    hash[ar.table_name] = ary if ary.length > 0
+  end
+
+end
+
+if hash.length == 0
+  exit
+end
+
+dt = DateTime.now
+fname = File.join(File.dirname(__FILE__),
+                  "database_save-#{dt.year}#{"%02i"%dt.month}#{"%02i"%dt.day}#{"%02i"%dt.hour}#{"%02i"%dt.min}#{"%02i"%dt.sec}")
+
+if File.exist?(fname)
+  abort "file already exists: #{File.basename(fname)}"
+end
+
+File.open(fname, "w"){|file|
+  file.write hash.to_yaml
+}
+
+print "sucessed to dump database data to #{fname}\n"

data/db/functions/additions.yml

@@ -0,0 +1,10 @@
+:name: addition
+:description: add two data
+:nvars: 2
+:script: |
+  [gphys0 + gphys1]
+
+:outputs:
+- :name: sum
+  :subscript: sum
+  :description: sum of two data

data/db/functions/cut.yml

@@ -0,0 +1,10 @@
+:name: cut
+:description: cut out a subset of data
+:nvars: 1
+:script: |
+  [gphys0.copy]
+
+:outputs:
+- :name: subset
+  :subscript: sub
+  :description: a subset 

data/db/functions/division.yml

@@ -0,0 +1,10 @@
+:name: division
+:description: division a data by the other
+:nvars: 2
+:script: |
+  [gphys0 / gphys1]
+
+:outputs:
+- :name: quotient
+  :subscript: quot
+  :description: quotient of two data

data/db/functions/mean.yml

@@ -0,0 +1,28 @@
+:name: mean
+:description: averaging on the specific dimensions
+:nvars: 1
+:script: |
+  [gphys0.mean(*arg0)]
+
+:setting_html: |
+  <label for="analysis[function_arguments][0]">
+    the dimensions for mean
+  </label>
+  <select id="analysis[function_arguments][0]" name="analysis[function_arguments][0][]" multiple>
+  <%
+  @analysis.dimensions.each{|dim|
+    dname = dim[:name]
+  %>
+    <option <%=@analysis.function_arguments[0]==dname ? "selected" : ""%>><%=h(dname)%></option>
+  <% } %>
+  </select>
+
+:arguments:
+- :description: the dimension for mean
+  :value_type: array_string
+  :default: []
+  :position: 0
+:outputs:
+- :name: mean
+  :subscript: mean
+  :description: mean

data/db/functions/multiplication.yml

@@ -0,0 +1,10 @@
+:name: multiplication
+:description: multiplication of two data
+:nvars: 2
+:script: |
+  [gphys0 * gphys1]
+
+:outputs:
+- :name: product
+  :subscript: prod
+  :description: product of two data

data/db/functions/stddev.yml

@@ -0,0 +1,28 @@
+:name: stddev
+:description: the first dimensional standard deviation
+:nvars: 1
+:script: |
+  [gphys0.stddev(*arg0)]
+
+:setting_html: |
+  <label for="analysis[function_arguments][0]">
+    the dimensions for stddev
+  </label>
+  <select id="analysis[function_arguments][0]" name="analysis[function_arguments][0][]" multiple>
+  <%
+  @analysis.dimensions.each{|dim|
+    dname = dim[:name]
+  %>
+    <option <%=@analysis.function_arguments[0]==dname ? "selected" : ""%>><%=h(dname)%></option>
+  <% } %>
+  </select>
+
+:arguments:
+- :description: the dimension for standard deviation 
+  :value_type: array_string
+  :default: []
+  :position: 0
+:outputs:
+- :name: stddev
+  :subscript: stddev
+  :description: standard deviation

data/db/functions/subtraction.yml

@@ -0,0 +1,10 @@
+:name: subtraction
+:description: subtraction a data from the other
+:nvars: 2
+:script: |
+  [gphys0 - gphys1]
+
+:outputs:
+- :name: difference
+  :subscript: diff
+  :description: difference of two data

data/db/migrate/001_initial_scheme.rb

@@ -0,0 +1,289 @@
+class InitialScheme < ActiveRecord::Migration
+
+  def self.up
+    create_table "nodes", :force => true do |t|
+      t.column "parent_id", :integer
+      t.column "name", :string, :null => false
+      t.column "path", :string, :null => false
+      t.column "node_type", :integer, :null => false
+               # 0: directory
+               # 1: variable, 2: image
+               # 3: knowledge, 4: function, 5: draw_method
+      t.column "mtime", :datetime, :null => false
+      t.column "owner_id", :integer, :null => false
+      t.column "other_mode", :integer, :default => 4, :null => false
+      t.column "rgroups", :integer, :length => 12, :default => 0  # 64bit
+      t.column "wgroups", :integer, :length => 12, :default => 0  # 64bit
+      t.column "size", :integer, :length => 12                    # 64bit
+      t.column "guest_owner_id", :integer
+      t.column "file", :string
+      t.column "other_readable", :boolean, :null => false
+      t.column "groups_readable", :integer, :length=>12, :null=>false #64bit
+      t.string "title", :null => true
+      t.text   "description", :null => true
+      t.timestamps
+    end
+    add_index :nodes, :path, :unique => true
+
+    create_table "guest_owners", :force => true do |t|
+      t.column "name", :string, :null => false
+      t.column "email", :string
+      t.column "identifier", :string, :null => false
+    end
+
+    create_table "directories", :force => true do |t|
+      t.column "node_id", :integer, :null => false
+      t.column "plain_file", :boolean, :default => false, :null => false
+      t.column "downloadable", :boolean, :default => true, :null => false
+    end
+
+    create_table "actual_files", :force => true do |t|
+      t.column "variable_id", :integer, :null => false
+      t.column "path", :string, :null => false
+    end
+
+    create_table "variables", :force => true do |t|
+      t.column "node_id", :integer, :null => false
+    end
+
+    create_table "images", :force => true do |t|
+      t.column "node_id", :integer, :null => false
+      t.column "vizshot", :text
+    end
+
+    create_table "knowledges", :force => true do |t|
+      t.column "node_id", :integer, :null => false
+      t.column "category", :string, :null => false
+#      t.column "title", :string, :null => false
+      t.column "creator", :string
+      t.column "textbody", :text, :null => false
+      t.column "description", :text
+      t.column "default_layout", :integer, :null => false
+      t.column "horizontal_figures", :integer, :null => false
+      t.column "figures_size_status", :integer, :null => false
+      # �w�肵���}�̑傫���̒P�ʂƁA�c�����A0�`3�̐����l�ŕ\��
+      #    | height | width
+      # %  |     00 |    01
+      # px |     10 |    11
+      t.column "figures_size_number", :integer, :null => false
+      t.column "comment_on", :integer # �R�����g���ɂȂ���Knowledge��node_id���i�[
+      t.column "comment_number", :integer # ���Ԗڂ̃R�����g��
+    end
+
+    create_table "knowledge_figures", :force => true do |t|
+      t.column "knowledge_id", :integer
+      t.column "image_id", :integer
+      t.column "caption", :text, :null => false
+    end
+
+    create_table "knowledge_backups", :force => true do |t|
+      t.column "title", :string, :null => false
+      t.column "creator", :string
+      t.column "textbody", :text, :null => false
+      t.column "description", :text
+      t.column "default_layout", :integer, :null => false
+      t.column "horizontal_figures", :integer, :null => false
+      t.column "figures_size_status", :integer, :null => false
+      t.column "figures_size_number", :integer, :null => false
+      t.column "comment_on", :integer
+      t.column "comment_number", :integer
+      t.column "mtime", :datetime, :null => false
+      t.column "backup_on", :string, :null => false
+      t.column "version_number", :integer, :null => false
+      t.column "temporary", :boolean, :null => false
+      t.column "owner_id", :integer, :null => false
+      t.column "rgroups", :integer, :length => 12, :default => 0  # 64bit
+      t.column "other_mode", :integer, :default => 4, :null => false
+    end
+        
+    create_table "knowledge_figure_backups", :force => true do |t|
+      t.column "knowledge_backup_id", :integer, :null => false
+      t.column "image_id", :integer
+      t.column "caption", :text, :null => false
+    end
+
+    create_table "node_relations", :force => true do |t|
+      t.column "name", :text, :null => false
+      t.column "reference", :integer, :null => false
+      t.column "referenced_by", :integer, :null => false
+    end
+    add_index :node_relations, :reference
+    add_index :node_relations, :referenced_by
+
+    create_table "keyword_attributes", :force => true do |t|
+      t.column "node_id", :integer, :null => false
+      t.column "name", :string, :null => false
+      t.column "value", :text
+      t.column "num_value", :binary
+      t.column "lang", :string
+    end
+
+    create_table "spatial_and_time_attributes", :force => true do |t|
+      t.column "node_id", :integer, :null => false
+      t.column "longitude_lb", :float, :default => nil 
+      t.column "latitude_lb", :float, :default => nil
+      t.column "longitude_rt", :float, :default => nil
+      t.column "latitude_rt", :float, :default => nil
+      t.column "starttime", :datetime, :default => nil
+      t.column "endtime", :datetime, :default => nil
+    end
+
+    create_table "value_types", :force => true do |t|
+      t.column "name", :string, :null => false
+    end
+
+    create_table "functions", :force => true do |t|
+      t.column "node_id", :integer, :null => false
+      t.column "description", :text
+      t.column "nvars", :integer, :null => false
+      t.column "script", :text, :null => false
+      t.column "setting_html", :text
+      t.column "default", :boolean, :default => false
+    end
+
+    create_table "function_outputs", :force => true do |t|
+      t.column "function_id", :integer, :null => false
+      t.column "name", :string, :null => false
+      t.column "description", :text
+      t.column "subscript", :string, :null => false
+      t.column "position", :integer
+    end
+
+    create_table "function_arguments", :force => true do |t|
+      t.column "function_id", :integer, :null => false
+      t.column "description", :text
+      t.column "value_type_id", :integer, :null => false
+      t.column "default", :string
+      t.column "position", :integer
+    end
+
+    create_table "draw_methods", :force => true do |t|
+      t.column "node_id", :integer, :null => false
+      t.column "description", :text
+      t.column "ndims", :integer, :null => false
+      t.column "nvars", :integer, :null => false
+      t.column "vizshot_method", :string, :null => false
+      t.column "script", :text
+      t.column "ggraph", :text
+      t.column "setting_html", :text
+      t.column "default", :boolean, :default => false
+    end
+
+    create_table "draw_method_attributes", :force => true do |t|
+      t.column "draw_method_id", :integer, :null => false
+      t.column "name", :string, :null => false
+      t.column "value_type_id", :integer, :null => false
+      t.column "default", :string
+      t.column "optional", :boolean, :default => false, :null => false
+      t.column "parser", :string
+    end
+
+    create_table "users", :force => true do |t|
+      t.column "login", :string, :null => false
+      t.column "password", :string, :null => false
+      t.column "full_name", :string, :null => false
+      t.column "email_address", :string, :null => false
+      t.column "affiliation", :string, :null => false
+      t.column "super_user", :boolean, :default => false, :null => false
+      t.column "groups", :integer, :length => 12, :default => 0
+#      t.column "openid", :boolean
+      t.column "internal_user", :boolean, :default => false, :null => false
+    end
+
+    create_table "sign_up_users", :force => true do |t|
+      t.column "login", :string, :null => false
+      t.column "password", :string, :null => false
+      t.column "full_name", :string, :null => false
+      t.column "email_address", :string, :null => false
+      t.column "affiliation", :string, :null => false
+#      t.column "openid", :boolean
+    end
+
+    create_table "groups", :force => true do |t|
+      t.column "name", :string, :null => false
+      t.column "owner_id", :integer, :null => false
+      t.column "description", :string, :null => true
+    end
+
+##    create_table "group_members", :force => true do |t|
+##      t.column "group_id", :integer, :null => false
+##      t.column "user_id", :integer, :null => false
+##    end
+
+    create_table "diagram_caches", :force => true do |t|
+      t.column "vizshot", :text, :null => false
+      t.column "path", :string, :null => false
+      t.column "label", :string, :null => false
+    end
+
+    create_table "diagram_cache_data", :force => true do |t|
+      t.column "diagram_cache_id", :integer, :null => false
+      t.column "variable_id", :integer, :null => false
+    end
+
+    create_table "diagram_cache_sessions", :force => true do |t|
+      t.column "diagram_cache_id", :integer, :null => false
+      t.column "session", :string, :null => false
+      t.column "share", :boolean, :default => true, :null => false
+    end
+
+    create_table "draw_parameters", :force => true do |t|
+      t.column "node_id", :integer, :null => false
+      t.column "name", :string, :null => false
+      t.column "value", :string, :null => false
+    end
+
+    create_table "query_histories", :force => true do |t|
+      t.column "args",         :string
+      t.column "querytype",    :string
+      t.column "user_id",      :integer
+      t.column "time",         :datetime
+      t.column "description",  :string
+      t.column "queryset_id",  :int
+      t.column "conditions",  :text
+      t.column "count",        :integer
+      t.column "session_id",		:string
+    end
+
+    create_table "node_lineages", :force => true do |t|
+      t.column "ancestor",	:integer, :null=>false
+      t.column "descendant", :integer, :null=>false
+      t.column "rel_depth",	:integer, :default=>1, :null=>false
+    end
+    add_index :node_lineages, :ancestor
+    add_index :node_lineages, :descendant
+
+  end
+
+  def self.down
+
+    drop_table(:nodes) rescue nil
+    drop_table(:guest_owners) rescue nil
+    drop_table(:directories) rescue nil
+    drop_table(:actual_files) rescue nil
+    drop_table(:variables) rescue nil
+    drop_table(:images) rescue nil
+    drop_table(:knowledges) rescue nil
+    drop_table(:knowledge_figures) rescue nil
+    drop_table(:node_relations) rescue nil
+    drop_table(:keyword_attributes) rescue nil
+    drop_table(:spatial_and_time_attributes) rescue nil
+    drop_table(:draw_method_attributes) rescue nil
+    drop_table(:draw_methods) rescue nil
+    drop_table(:function_outputs) rescue nil
+    drop_table(:function_arguments) rescue nil
+    drop_table(:functions) rescue nil
+    drop_table(:value_types) rescue nil
+    drop_table(:users) rescue nil
+    drop_table(:sign_up_users) rescue nil
+    drop_table(:groups) rescue nil
+##    drop_table(:group_members) rescue nil
+    drop_table(:diagram_caches) rescue nil
+    drop_table(:diagram_cache_data) rescue nil
+    drop_table(:diagram_cache_sessions) rescue nil
+    drop_table(:draw_parameters) rescue nil
+    drop_table(:query_histories) rescue nil
+    drop_table(:node_lineages) rescue nil
+
+  end
+end