version 2.04.05

README.md

@@ -1,5 +1,10 @@
 # Genboree
 
-Main Genboree installation is available online at http://genboree.org. This package contains sources of base components from this installation. This version of Genboree<sup>TM</sup> Server includes Genboree Workbench, GenboreeKB and Redmine with several plugins. This version can be installed on a computer with a 64-bit Linux operating system (access to root account is required). 
+The main Genboree installation is available online at http://genboree.org. This package contains sources of base components from this installation. 
+This version of Genboree<sup>TM</sup> Server includes Genboree Workbench, GenboreeKB and Redmine with several plugins. 
+This version can be installed on a computer with a 64-bit Linux operating system (access to root account is required). 
 
-GitHub repository contains all sources and scripts from Genboree. However Genboree requires dozens of dependencies that are not included in this repository. The best way to install Genboree is to use the installation package that can be downloaded from ftp://genboree.org/software/genboree/genboree-2.05.01.tar. There is an installation instruction in the docs directory.
+This GitHub repository contains all sources and scripts from Genboree. 
+However Genboree requires dozens of dependencies that are not included in this repository. 
+The best way to install Genboree is to use the installation package that can be downloaded from [Releases page](https://github.com/BRL-BCM/genboree/releases).
+There is an installation instruction in the docs directory.

scripts/build_all.sh

@@ -23,9 +23,6 @@ cp ../src/license.txt  ../src/agpl-3.0.txt  ${DIR_TARGET}
 ./build_data.sh  "$@"
 ./build_final.sh "$@"
 ./build_redmine.sh "$@"
-# ---- remove .svn directories
-find ${DIR_TARGET} -type d -name .svn -exec rm -rf {} \;  || true
-find ${DIR_DATA}   -type d -name .svn -exec rm -rf {} \;  || true
 # ---- Make a final package
 mv ${DIR_TARGET} ./local
 mv ${DIR_DATA}   ./data

scripts/conf_runtime.sh

@@ -17,8 +17,6 @@ export TMPDIR=${DIR_TARGET}/tmp
 
 # svn://histidine.brl.bcmd.bcm.edu/brl-repo/PATCH_NOTES/genboree/2014-11-12.contentGen
 export OMIM_API_KEY=VKGiMHRGQwe3m18OEED1Yw
-# API key for bioPortal
-export BIOPORTAL_API_KEY=e750aaca-98af-49fa-8349-82caf2ce4f5b
 
 # svn://histidine.brl.bcmd.bcm.edu/brl-repo/PATCH_NOTES/genboree/2015-08-13.snifferMove
 export SNIFFER_CONF_FILE=${DIR_TARGET}/conf/snifferFormatInfo.json

src/conf/genboree.config.properties

@@ -341,4 +341,4 @@ gbApiExtConfsDir=/usr/local/brl/local/conf/apiExtensions
 FTPsmRNAPipelineReadCountCategories=/usr/local/brl/local/conf/FTPsmRNAPipeline/FTPsmRNAPipelineReadCountCategories.conf
 
 # required by Pathogenicity Calculator 2.6
-gridConfV2_6Header=/usr/local/brl/local/apache/htdocs/clingenInference/V2.6/includes/header.incl
+calcBaseDir=/usr/local/brl/local/apache/htdocs/

src/etc/nginx.conf

@@ -332,26 +332,6 @@ http {
             break ;
         }
 
-        # Redmine - Upload Request - KbDocs File Upload
-        location = /redmine/genboree_kbs/collection/uploaddocs {
-            client_body_buffer_size     8m ;
-            client_body_temp_path       /usr/local/brl/local/tmp/nginx/client_file_upload   1   2   3 ; # use 3 levels to organize temp files
-            client_body_in_file_only    on ;
-            client_max_body_size        100000m ; # 100gb file upload max, for example
-            proxy_pass_request_headers  on ;
-            include /usr/local/brl/local/etc/nginx/proxy_set_headers.conf ;
-            proxy_set_header        X-GB-Uploaded-File    $request_body_file ;
-            proxy_set_header        X-GB-Uploaded-Content-Type  $content_type ;
-            proxy_set_header        X-GB-Saved-Uploaded   true ;
-            proxy_set_header        Content-Type text/plain ;
-            proxy_set_header        Connection close;
-            proxy_hide_header       Etag ;
-            proxy_set_body          "${request_body_file} ; ${content_type}" ;
-            proxy_pass              http://thin_redmine ;
-            proxy_redirect          off ;
-            break ;
-        }
-
         # Redmine - Upload Request - DB File Upload
         location = /redmine/genboree_kbs/doc/uploadfile {
             client_body_buffer_size         8m ;

src/etc/nginx/proxy_set_headers.conf

@@ -2,7 +2,6 @@
  # - Can use this include to reset the standard ones.
  proxy_set_header        Host              $host ;
  proxy_set_header        X-Real-IP         $remote_addr ;
- proxy_set_header        X-Coming-From-IP  $remote_addr ;
  proxy_set_header        X-Forwarded-For   $proxy_add_x_forwarded_for ;
  proxy_set_header        X-Proxy-Host      $proxy_host ;
  proxy_set_header        X-Proxy-Port      $proxy_port ;

src/home/lib/genboreeTools.rb

@@ -237,11 +237,6 @@ def genboree_add_kb(group, kb, description = nil)
   api_put(kbUri, payload)
 end
 
-def genboree_delete_kb(group, kb)
-  kbUri = '/REST/v1/grp/' + CGI::escape(group) + '/kb/' + CGI::escape(kb)
-  api_delete(kbUri)
-end
-
 # check if kb exists
 def genboree_kb_exists(group, kb)
   return api_object_exists('/REST/v1/grp/' + CGI::escape(group) + '/kb/' + CGI::escape(kb))
@@ -255,33 +250,20 @@ def genboree_set_kb_public(group, kb)
   # Construct unlock record for the KB we want to unlock
   unlockRec = { "url" => kbUrl, "public" => true }
   # Sent PUT request
-  api_put("/REST/v1/grp/#{CGI::escape(group)}/unlockedResources", [unlockRec].to_json)
+  api_put("/REST/v1/grp/#{group}/unlockedResources", [unlockRec].to_json)
 end
 
 # assign user to group (change role, if user already assigned)
 def genboree_assign_user_to_group_as_subscriber(user, group)
-  api_put("/REST/v1/grp/#{CGI::escape(group)}/usr/#{CGI::escape(user)}/role", {"role"=>"subscriber", "permissionBits"=>""})
+  api_put("/REST/v1/grp/#{group}/usr/#{user}/role", {"role"=>"subscriber", "permissionBits"=>""})
 end
 def genboree_assign_user_to_group_as_author(user, group)
-  api_put("/REST/v1/grp/#{CGI::escape(group)}/usr/#{CGI::escape(user)}/role", {"role"=>"author", "permissionBits"=>""})
-end
-
-def genboree_kb_add_collection(group, kb, collection, model)
-  uri = "/REST/v1/grp/#{CGI::escape(group)}/kb/#{CGI::escape(kb)}/coll/#{CGI::escape(collection)}/model"
-  model = model.to_json if model.is_a?(Hash)
-  api_put(uri, model)
-end
-
-def genboree_kb_add_transform(group, kb, transformDefinition)
-  transformDefinition = JSON.parse(transformDefinition) if transformDefinition.is_a?(String)
-  name = transformDefinition['Transformation']['value']
-  uri = "/REST/v1/grp/#{CGI::escape(group)}/kb/#{CGI::escape(kb)}/transform/#{CGI::escape(name)}"
-  api_put(uri, transformDefinition.to_json)
+  api_put("/REST/v1/grp/#{group}/usr/#{user}/role", {"role"=>"author", "permissionBits"=>""})
 end
 
 # load documents to KB collections
 def genboree_kb_add_documents(group, kb, collection, documents, autoAdjustId=true, substitutions=Hash.new, chunk_size=128)
-  uri = "/REST/v1/grp/#{CGI::escape(group)}/kb/#{CGI::escape(kb)}/coll/#{CGI::escape(collection)}/docs"
+  uri = "/REST/v1/grp/#{group}/kb/#{kb}/coll/#{collection}/docs"
   uri += "?autoAdjust=true" if autoAdjustId
   while documents.size > 0
     payload = { "data" => documents.shift(chunk_size) }
@@ -294,7 +276,7 @@ def genboree_kb_add_documents(group, kb, collection, documents, autoAdjustId=tru
 end
 
 def genboree_kb_add_documents_from_file(group, kb, collection, filename, autoAdjustId=true, substitutions=Hash.new, chunk_size=128)
-  uri = "/REST/v1/grp/#{CGI::escape(group)}/kb/#{CGI::escape(kb)}/coll/#{CGI::escape(collection)}/docs"
+  uri = "/REST/v1/grp/#{group}/kb/#{kb}/coll/#{collection}/docs"
   uri += "?autoAdjust=true" if autoAdjustId
   api_put_from_file_in_chunks(uri, filename, substitutions, chunk_size)
 end
@@ -333,28 +315,6 @@ def redmine_assign_user_to_project(user_login, project_identifier, roles_names)
   redmine_api_post("/projects/#{project_identifier}/memberships.json", '{"membership":{"user_id":' + "#{user_id}" + ',"role_ids":' + roles_ids.to_json + '}}')
 end
 
-# set configuration of genboree_kb project
-def redmine_configure_project_genboree_kb(project_identifier, genboree_group, kb_name)
-  # find project id
-  resp = redmine_api_get("/projects/#{project_identifier}.json")
-  id = resp["project"]["id"]
-  raise "Cannot find project with identifier: #{project_identifier}" if id.nil?
-  # set record's fields
-  fields = Hash.new
-  fields['project_id'] = id
-  fields['name'] = "#{kb_name}"
-  fields['gbGroup'] = "#{genboree_group}"
-  fields['gbHost'] = 'localhost'
-  # check if the record exists and rub insert or update
-  sql = "SELECT COUNT(1) AS count FROM genboree_kbs WHERE project_id=#{id}"
-  if runSqlStatement_redmine(sql).first['count'].to_i == 0
-    sql = sql_insert('genboree_kbs', fields)
-  else
-    sql = sql_update('genboree_kbs', fields) + " WHERE project_id=#{id}"
-  end
-  runSqlStatement_redmine(sql)
-end
-
 # set configuration of genboree_ac project
 def redmine_configure_project_genboree_ac(project_identifier, ac_genboree_group, ac_kb_name, orphanet_kb_name, 
                                           release_kb_name = nil, header_include_file = nil, footer_include_file = nil)
@@ -387,55 +347,6 @@ def redmine_configure_project_genboree_ac(project_identifier, ac_genboree_group,
   runSqlStatement_redmine(sql)
 end
 
-# set configuration of genboree_exrna_at project
-def redmine_configure_project_genboree_exrna_at(project_identifier, genboree_group, kb_name, home_page = "/redmine/projects/#{project_identifier}/exat")
-  # find project id
-  resp = redmine_api_get("/projects/#{project_identifier}.json")
-  id = resp["project"]["id"]
-  raise "Cannot find project with identifier: #{project_identifier}" if id.nil?
-  # set record's fields
-  fields = Hash.new
-  fields['project_id'] = id
-  fields['gbHost'] = 'localhost'
-  fields['gbGroup'] = genboree_group
-  fields['gbKb'] = kb_name
-  fields['appLabel'] = nil
-  fields['useRedmineLayout'] = 1
-  fields['headerIncludeFileLocation'] = nil
-  fields['footerIncludeFileLocation'] = nil
-  fields['analysesColl'] = 'Analyses'
-  fields['biosamplesColl'] = 'Biosamples'
-  fields['donorsColl'] = 'Donors'
-  fields['experimentsColl'] = 'Experiments'
-  fields['jobsColl'] = 'Jobs'
-  fields['resultFilesColl'] = 'Result Files'
-  fields['runsColl'] = 'Runs'
-  fields['studiesColl'] = 'Studies'
-  fields['submissionsColl'] = 'Submissions'
-  fields['updateData'] = 0
-  fields['newsFile'] = ''
-  fields['contactTo'] = ''
-  fields['contactBccs'] = ''
-  fields['jobHost'] = 'localhost'
-  fields['toolUsageHost'] = ''
-  fields['toolUsageGrp'] = ''
-  fields['toolUsageKb'] = ''
-  fields['toolUsageColl'] = ''
-  fields['toolUsageView'] = ''
-  fields['privateSubmitters'] = ''
-  fields['homePageUrl'] = home_page
-  fields['infoFlashHtml'] = ''
-  fields['prevVersions'] = ''
-  # check if the record exists and rub insert or update
-  sql = "SELECT COUNT(1) AS count FROM genboree_exrna_ats WHERE project_id=#{id}"
-  if runSqlStatement_redmine(sql).first['count'].to_i == 0
-    sql = sql_insert('genboree_exrna_ats', fields)
-  else
-    sql = sql_update('genboree_exrna_ats', fields) + " WHERE project_id=#{id}"
-  end
-  runSqlStatement_redmine(sql)
-end
-
 =begin
 
 class KbCollection

src/redmine/plugins/genboree_generic/app/helpers/generic_helpers/before_filters_helper.rb

@@ -7,14 +7,6 @@ module BeforeFiltersHelper
     # BEFORE_FILTERS - useful before_filter methods for your controller
     # ----------------------------------------------------------------
 
-    # Popular the @urlMount variable with this Redmine's mount point (first dir in path)
-    def getKbMount()
-      @redmineMount = @kbMount = @urlMount = RedmineApp::Application.routes.default_scope[:path].to_s.gsub(/'/, "\\\\'").gsub(/\n/, ' ') ;
-      $stderr.debugPuts(__FILE__, __method__, 'DEBUG', "generic getKbMount has set @redmineMount, @kbMount, @urlMount to #{@redmineMount.inspect}")
-    end
-    alias_method(:redmineMount, :getKbMount)
-    alias_method(:getUrlMount, :getUrlMount)
-
     # Authorize the user for the requested action. In addition to regular checks, allow if project is public.
     #   Always allow members through
     def authorize_with_public_project(ctrl = params[:controller], action = params[:action], global = false)

src/redmine/plugins/genboree_generic/app/helpers/plugin_helpers/before_filters_helper.rb

@@ -8,22 +8,13 @@ module BeforeFiltersHelper
 
     # Retrieve the project-specific plugin settings record.
     # @note Assume the Controller defines PLUGIN_SETTINGS_MODEL_CLASS.
-    # @param [Project] project Optional. Defaults to @project when used within controller. To support settings
-    #   must hand in Project object. 
-    # @param [Class] settingsClass Optional. Not needed in controller, since will use PLUGIN_SETTINGS_MODEL_CLASS defined in your controller.
-    #    To support settings  must hand in settings class/model.
     # @return [Object] An instance of the plugin model settings for the current project
     #   with access to any project-specific settings for this plugin.
-    def plugin_proj_settings(project=@project, settingsClass=nil)
-      if(settingsClass.nil?) # then within controller _instance_ and can get class from controller
-        settingsClass = ( defined?(self.class::PLUGIN_SETTINGS_MODEL_CLASS) ? self.class::PLUGIN_SETTINGS_MODEL_CLASS : nil )
-      end
+    def plugin_proj_settings()
       @pluginProjSettings = nil
-      if(settingsClass)
+      if(defined?(self.class::PLUGIN_SETTINGS_MODEL_CLASS))
         #$stderr.debugPuts(__FILE__, __method__, '++++++ DEBUG', "Have model class: #{self.class::PLUGIN_SETTINGS_MODEL_CLASS.inspect}")
-        @pluginProjSettings = settingsClass.find_by_project_id(project) # rescue nil
-      else
-        $stderr.debugPuts(__FILE__, __method__, 'WARNING', "Either this *plugin* controller (#{self.class.inspect}) does not define PLUGIN_SETTINGS_MODEL_CLASS or we're not in a controller / instance context (e.g. project-settings) and the appropriate settings class was not passed in.")
+        @pluginProjSettings = self.class::PLUGIN_SETTINGS_MODEL_CLASS.find_by_project_id(@project) # rescue nil
       end
       @pluginProjSettings
     end

src/redmine/plugins/genboree_generic/lib/gb_api/sync_api_requester.rb

@@ -19,12 +19,7 @@ def apiPut(rsrcPath, payload, fieldMap={})
       retVal = { :respObj => '', :status => 500}
       # Add standard field info to fieldMap IFF not provided
       gbAuthHelper = GbApi::GbAuthHelper.new()
-      if(@redmineProject.nil?)
-       login, pass = gbAuthHelper.authPairForUserAndHost(@reqHost, @redmineUser)
-        #$stderr.debugPuts(__FILE__, __method__, "DEBUG", "Login Pass from authPairForUserAndHost")
-      else
-        login, pass = gbAuthHelper.authPairForUserAndHostInProjContext(@redmineProject, @reqHost, @redmineUser)
-      end
+      login, pass = gbAuthHelper.authPairForUserAndHostInProjContext(@redmineProject, @reqHost, @redmineUser)
       if(login and pass)
         apiCaller = BRL::REST::ApiCaller.new(@reqHost, rsrcPath, login, pass)
         apiCaller.put( fieldMap, payload )

src/redmine/plugins/genboree_generic/lib/gb_tools/gb_tool_submitter.rb

@@ -1,11 +1,9 @@
 module GbTools
  # a simple class to submit Genboree tool jobs
   class GbToolSubmitter 
-    def initialize(env, jobHost, redminePrj)
-      raise ArgumentError, "HOST_ERROR: The rack environment - cannot be #{env.class} (nil or empty)" if(env.nil? or env.empty?) 
-      raise ArgumentError, "HOST_ERROR: The jobhost - #{jobHost.inspect} cannot be #{jobHost.class} (nil or empty)" if(jobHost.nil? or jobHost.empty?) 
-
-      @apiReq = GbApi::JsonAsyncApiRequester.new(env, jobHost, redminePrj)   
+    def initialize(jobHost, rmProject)
+      @jobHost = jobHost
+      @redminePrj = rmProject
     end
 
     # submits the tool to the tool job rest resource path
@@ -15,19 +13,11 @@ def initialize(env, jobHost, redminePrj)
     # @todo apiPut to be replaced by the async request 
     def submit(toolIdStr, jobConf)
       submitResp = {:respObj => nil, :status => nil}
-      rsrcPath = "/REST/v1/genboree/tool/{toolIdStr}/job"
-      fieldMap  = {:toolIdStr => toolIdStr}
-      @apiReq.bodyFinish {
-        headers = @apiReq.respHeaders
-        status = @apiReq.respStatus
-        headers['Content-Type'] = "text/plain"
-      $stderr.debugPuts(__FILE__, __method__, 'DEBUG',  "@apiReq ------- #{@apiReq.respBody.inspect}")
-        @apiReq.sendToClient(status, headers, JSON.generate(@apiReq.respBody))
-      }
-      $stderr.debugPuts(__FILE__, __method__, 'DEBUG',  "rsrcPath ------- #{rsrcPath.inspect}")
-      $stderr.debugPuts(__FILE__, __method__, 'DEBUG',  "fieldMap------- #{fieldMap.inspect}")
-      @apiReq.put(rsrcPath, fieldMap, jobConf.to_json)
-
+        rsrcPath = "/REST/v1/genboree/tool/{toolIdStr}/job"
+        fieldMap  = {:toolIdStr => toolIdStr}
+        syncReq = GbApi::SyncApiRequester.new(@jobHost, @redminePrj)
+        submitResp = syncReq.apiPut(rsrcPath, JSON.generate(jobConf), fieldMap)
+      return submitResp
     end
 
 

src/redmine/plugins/genboree_kbs/app/controllers/genboree_kb_collection_controller.rb

@@ -38,9 +38,7 @@ def index()
     @showModelVersionsGrid = ( params['showModelVersionsGrid'] and params['showModelVersionsGrid'] == 'true' ) ? true : false
     @createNewDoc = ( params['createNewDoc'] and params['createNewDoc'] == 'true' ) ? true : false
     @createNewDocWithTemplate = ( params['createNewDocWithTemplate'] and params['createNewDocWithTemplate'] == 'true' ) ? true : false
-    @createNewDocWithQuestionnaire = ( params['createNewDocWithQuestionnaire'] and params['createNewDocWithQuestionnaire'] == 'true' ) ? true : false
     @templateId = params['templateId'] || ''
-    @questionnaireId = params['questionnaireId'] || ''
     @kbMount = RedmineApp::Application.routes.default_scope[:path]
     # If the page is being accessed without logging in, redirect user to login page
     # If the original URL was pointing to a particular document and/or collection,
@@ -67,6 +65,7 @@ def index()
   end
 
 
+
   def getCollList()
     apiResult = apiGet( "/REST/v1/grp/{grp}/kb/{kb}" )
     unless(apiResult[:respObj] and apiResult[:respObj]['data'])
@@ -172,9 +171,7 @@ def constructBackUrl(projectId)
     backUrl << "&showViewGrid=true" if(@showViewGrid)
     backUrl << "&createNewDoc=true" if(@createNewDoc)
     backUrl << "&createNewDocWithTemplate=true" if(@createNewDocWithTemplate)
-    backUrl << "&createNewDocWithQuestionnaire=true" if(@createNewDocWithQuestionnaire)
     backUrl << "&templateId=#{CGI.escape(@templateId)}" if(@templateId != "")
-    backUrl << "&questionnaireId=#{CGI.escape(@questionnaireId)}" if(@questionnaireId != "")
     return backUrl
   end
 

src/redmine/plugins/genboree_kbs/app/controllers/genboree_kb_controller.rb

@@ -21,7 +21,6 @@ def create
 
   def update
     kb = GenboreeKb.find_by_project_id(params['project_id'])
-    @genboreeKb = kb
     kb.name = params['name']
     kb.description = params['description']
     kb.gbGroup = params['gbGroup']