Replaced csv.writer line ending setting of os.linesep with '\n'.

yesworkflow-org · Jul 17, 2016 · 81de894 · 81de894
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diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,17 @@
+# Auto detect text files and perform LF normalization
+* text=auto
+
+# Custom for Visual Studio
+*.cs     diff=csharp
+
+# Standard to msysgit
+*.doc	 diff=astextplain
+*.DOC	 diff=astextplain
+*.docx diff=astextplain
+*.DOCX diff=astextplain
+*.dot  diff=astextplain
+*.DOT  diff=astextplain
+*.pdf  diff=astextplain
+*.PDF	 diff=astextplain
+*.rtf	 diff=astextplain
+*.RTF	 diff=astextplain
diff --git a/examples/simulate_data_collection/query_outputs.txt b/examples/simulate_data_collection/query_outputs.txt
@@ -1,110 +1,110 @@
-
-
----------------------------------------------------------------------------------------------------
-EQ1 : What source files were YW annotations extracted from?
-
-eq1(SourceFile)
-...................................................................................................
-eq1('simulate_data_collection.py').
-
-
----------------------------------------------------------------------------------------------------
-EQ2 : What are the names N of all program blocks?
-
-eq2(ProgramName)
-...................................................................................................
-eq2(log_rejected_sample).
-eq2(initialize_run).
-eq2(transform_images).
-eq2(load_screening_results).
-eq2(collect_next_image).
-eq2(calculate_strategy).
-eq2(log_average_image_intensity).
-eq2(simulate_data_collection).
-eq2(collect_data_set).
-eq2(transform_image).
-
-
----------------------------------------------------------------------------------------------------
-EQ3 : What out ports are qualified with URIs
-
-eq3(PortName)
-...................................................................................................
-eq3(collection_log).
-eq3(corrected_image_file).
-eq3(raw_image_file).
-eq3(rejection_log).
-eq3(run_log).
-
-
----------------------------------------------------------------------------------------------------
-YW_Q1 : What is the name and description of the workflow implemented by the script?
-
-yw_q1(WorkflowName, Description)
-...................................................................................................
-yw_q1(simulate_data_collection,'Workflow for collecting diffraction data from high quality crystals in a cassette.').
-
-
----------------------------------------------------------------------------------------------------
-YW_Q2 : What workflow steps comprise the top-level workflow?
-
-yw_q2(StepName, Description)
-...................................................................................................
-yw_q2(log_average_image_intensity,'Record statistics about each diffraction image.').
-yw_q2(transform_images,'Correct raw image using the detector calibration image.').
-yw_q2(collect_data_set,'Collect data set using the given data collection parameters.').
-yw_q2(log_rejected_sample,'Record which samples were rejected.').
-yw_q2(calculate_strategy,'Reject unsuitable crystals and compute 
- best data sets to collect for accepted crystals.').
-yw_q2(load_screening_results,'Load sample information from spreadsheet.').
-yw_q2(initialize_run,'Create run directory and initialize log files.').
-
-
----------------------------------------------------------------------------------------------------
-YW_Q3 : Where is the definition of workflow step emphasize_greeting?
-
-yw_q3(SourceFile, StartLine, EndLine)
-...................................................................................................
-
-
----------------------------------------------------------------------------------------------------
-YW_Q4 : What are the names and descriptions of any outputs of the workflow?
-
-yw_q4(OutputName, Description)
-...................................................................................................
-yw_q4(corrected_image,'The corrected diffraction images collected on all crystals.').
-
-
----------------------------------------------------------------------------------------------------
-YW_Q5 : What data flows from the emphasize_greeting workflow step to the print_greeting step?
-
-yw_q5(DataName)
-...................................................................................................
-
-
----------------------------------------------------------------------------------------------------
-NW_Q1 : What functions are called from the top level of the script?
-
-nw_q1(FunctionName)
-...................................................................................................
-
-
----------------------------------------------------------------------------------------------------
-NW_Q2 : What variable values are passed to greet_user() from the top of the script?
-
-nw_q2(Variable, Value)
-...................................................................................................
-
-
----------------------------------------------------------------------------------------------------
-NW_Q3 : What literal values are passed to the greeting argument of greet_user() from the top of the script?
-
-nw_q3(Literal)
-...................................................................................................
-
-
----------------------------------------------------------------------------------------------------
-YW_NW_Q1 : What Python variables carries values of emphasized_greeting into the print_greeting workflow step?
-
-yw_nw_q1(VariableId, VariableName, VariableValue)
-...................................................................................................
+
+
+---------------------------------------------------------------------------------------------------
+EQ1 : What source files were YW annotations extracted from?
+
+eq1(SourceFile)
+...................................................................................................
+eq1('simulate_data_collection.py').
+
+
+---------------------------------------------------------------------------------------------------
+EQ2 : What are the names N of all program blocks?
+
+eq2(ProgramName)
+...................................................................................................
+eq2(transform_image).
+eq2(load_screening_results).
+eq2(initialize_run).
+eq2(collect_next_image).
+eq2(calculate_strategy).
+eq2(transform_images).
+eq2(log_rejected_sample).
+eq2(simulate_data_collection).
+eq2(collect_data_set).
+eq2(log_average_image_intensity).
+
+
+---------------------------------------------------------------------------------------------------
+EQ3 : What out ports are qualified with URIs
+
+eq3(PortName)
+...................................................................................................
+eq3(collection_log).
+eq3(corrected_image_file).
+eq3(raw_image_file).
+eq3(rejection_log).
+eq3(run_log).
+
+
+---------------------------------------------------------------------------------------------------
+YW_Q1 : What is the name and description of the workflow implemented by the script?
+
+yw_q1(WorkflowName, Description)
+...................................................................................................
+yw_q1(simulate_data_collection,'Workflow for collecting diffraction data from high quality crystals in a cassette.').
+
+
+---------------------------------------------------------------------------------------------------
+YW_Q2 : What workflow steps comprise the top-level workflow?
+
+yw_q2(StepName, Description)
+...................................................................................................
+yw_q2(log_average_image_intensity,'Record statistics about each diffraction image.').
+yw_q2(transform_images,'Correct raw image using the detector calibration image.').
+yw_q2(collect_data_set,'Collect data set using the given data collection parameters.').
+yw_q2(log_rejected_sample,'Record which samples were rejected.').
+yw_q2(calculate_strategy,'Reject unsuitable crystals and compute 
+ best data sets to collect for accepted crystals.').
+yw_q2(load_screening_results,'Load sample information from spreadsheet.').
+yw_q2(initialize_run,'Create run directory and initialize log files.').
+
+
+---------------------------------------------------------------------------------------------------
+YW_Q3 : Where is the definition of workflow step emphasize_greeting?
+
+yw_q3(SourceFile, StartLine, EndLine)
+...................................................................................................
+
+
+---------------------------------------------------------------------------------------------------
+YW_Q4 : What are the names and descriptions of any outputs of the workflow?
+
+yw_q4(OutputName, Description)
+...................................................................................................
+yw_q4(corrected_image,'The corrected diffraction images collected on all crystals.').
+
+
+---------------------------------------------------------------------------------------------------
+YW_Q5 : What data flows from the emphasize_greeting workflow step to the print_greeting step?
+
+yw_q5(DataName)
+...................................................................................................
+
+
+---------------------------------------------------------------------------------------------------
+NW_Q1 : What functions are called from the top level of the script?
+
+nw_q1(FunctionName)
+...................................................................................................
+
+
+---------------------------------------------------------------------------------------------------
+NW_Q2 : What variable values are passed to greet_user() from the top of the script?
+
+nw_q2(Variable, Value)
+...................................................................................................
+
+
+---------------------------------------------------------------------------------------------------
+NW_Q3 : What literal values are passed to the greeting argument of greet_user() from the top of the script?
+
+nw_q3(Literal)
+...................................................................................................
+
+
+---------------------------------------------------------------------------------------------------
+YW_NW_Q1 : What Python variables carries values of emphasized_greeting into the print_greeting workflow step?
+
+yw_nw_q1(VariableId, VariableName, VariableValue)
+...................................................................................................