From d0006c50909a7f134df4e246f747831e3a5547ed Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Tue, 24 May 2011 15:11:12 +0200 Subject: Fixing regression detection --- lib/parser.rb | 66 +++++++++++++++++++++++++++++++++++++++++++++-------------- 1 file changed, 51 insertions(+), 15 deletions(-) (limited to 'lib') diff --git a/lib/parser.rb b/lib/parser.rb index 7bdee95..5f847c3 100644 --- a/lib/parser.rb +++ b/lib/parser.rb @@ -277,7 +277,16 @@ module OpenTox def load_spreadsheet(book) book.default_sheet = 0 add_features book.row(1) - 2.upto(book.last_row) { |i| add_values book.row(i) } + + # AM: fix mixed read in + regression_features=false + 2.upto(book.last_row) { |i| + row = book.row(i) + regression_features = detect_regression_features row + break if regression_features==true + } + + 2.upto(book.last_row) { |i| add_values book.row(i),regression_features } warnings @dataset end @@ -289,11 +298,21 @@ module OpenTox row = 0 input = csv.split("\n") add_features split_row(input.shift) - input.each { |row| add_values split_row(row) } + + + # AM: fix mixed read in + regression_features=false + input.each { |row| + row = split_row(row) + regression_features = detect_regression_features row + break if regression_features==true + } + input.each { |row| add_values split_row(row),regression_features } warnings @dataset end + private def warnings @@ -335,7 +354,20 @@ module OpenTox end end - def add_values(row) + def detect_regression_features row + row.shift + regression_features=false + row.each_index do |i| + value = row[i] + type = feature_type(value) + if type == OT.NumericFeature + regression_features=true + end + end + regression_features + end + + def add_values(row, regression_features=false) smiles = row.shift compound = Compound.from_smiles(smiles) @@ -353,19 +385,23 @@ module OpenTox @feature_types[feature] << type - case type - when OT.NominalFeature - case value.to_s - when TRUE_REGEXP - val = true - when FALSE_REGEXP - val = false - end - when OT.NumericFeature + if (regression_features) val = value.to_f - when OT.StringFeature - val = value.to_s - @activity_errors << smiles+", "+row.join(", ") + else + case type + when OT.NominalFeature + case value.to_s + when TRUE_REGEXP + val = true + when FALSE_REGEXP + val = false + end + when OT.NumericFeature + val = value.to_f + when OT.StringFeature + val = value.to_s + @activity_errors << smiles+", "+row.join(", ") + end end if val!=nil @dataset.add(compound.uri, feature, val) -- cgit v1.2.3 From baca9424a84b6a21363cac891cdef72f44c116b1 Mon Sep 17 00:00:00 2001 From: mguetlein Date: Wed, 25 May 2011 10:08:04 +0200 Subject: remove duplicate debug msg --- lib/rest_client_wrapper.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'lib') diff --git a/lib/rest_client_wrapper.rb b/lib/rest_client_wrapper.rb index 747a353..53887a2 100644 --- a/lib/rest_client_wrapper.rb +++ b/lib/rest_client_wrapper.rb @@ -131,7 +131,7 @@ module OpenTox raise "unknown content-type for task : '"+res.content_type.to_s+"'"+" base-uri: "+base_uri.to_s+" content: "+res[0..200].to_s end - LOGGER.debug "result is a task '"+task.uri.to_s+"', wait for completion" + #LOGGER.debug "result is a task '"+task.uri.to_s+"', wait for completion" task.wait_for_completion waiting_task unless task.completed? # maybe task was cancelled / error if task.errorReport -- cgit v1.2.3 From 52e73a3da8e99da9a0a973b6ef9934297bc6511e Mon Sep 17 00:00:00 2001 From: mguetlein Date: Wed, 25 May 2011 11:55:41 +0200 Subject: remove check for task status when code is 201 (after discussion with nina and fabian) --- lib/task.rb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'lib') diff --git a/lib/task.rb b/lib/task.rb index 42d3d17..146a756 100644 --- a/lib/task.rb +++ b/lib/task.rb @@ -288,7 +288,8 @@ module OpenTox if @http_code == 202 raise "#{@uri}: illegal task state, code is 202, but hasStatus is not Running: '"+@metadata[OT.hasStatus]+"'" unless running? elsif @http_code == 201 - raise "#{@uri}: illegal task state, code is 201, but hasStatus is not Completed: '"+@metadata[OT.hasStatus]+"'" unless completed? + # ignore hasStatus + # raise "#{@uri}: illegal task state, code is 201, but hasStatus is not Completed: '"+@metadata[OT.hasStatus]+"'" unless completed? raise "#{@uri}: illegal task state, code is 201, resultURI is no task-URI: '"+@metadata[OT.resultURI].to_s+ "'" unless @metadata[OT.resultURI] and @metadata[OT.resultURI].to_s.uri? end -- cgit v1.2.3 From 153c740268c1bf6255f14f80550f690179a72fd9 Mon Sep 17 00:00:00 2001 From: mr Date: Wed, 25 May 2011 13:35:42 +0200 Subject: fix if subjectid is nil --- lib/helper.rb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'lib') diff --git a/lib/helper.rb b/lib/helper.rb index 3a6126a..995f3e9 100644 --- a/lib/helper.rb +++ b/lib/helper.rb @@ -44,8 +44,9 @@ helpers do def uri_available?(urlStr) url = URI.parse(urlStr) + subjectidstr = @subjectid ? "?subjectid=#{CGI.escape @subjectid}" : "" Net::HTTP.start(url.host, url.port) do |http| - return http.head("#{url.request_uri}?subjectid=#{CGI.escape @subjectid}").code == "200" + return http.head("#{url.request_uri}#{subjectidstr}").code == "200" end end -- cgit v1.2.3