
---------------------------------------------------------------------------------------------------------------------------
eq1(SourceFile) - What source files SF were YW annotations extracted from?
---------------------------------------------------------------------------------------------------------------------------
eq1(../simulate_data_collection.py)

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eq2(ProgramName) - What are the names N of all program blocks?
---------------------------------------------------------------------------------------------------------------------------
eq2(log_rejected_sample)
eq2(load_screening_results)
eq2(calculate_strategy)
eq2(collect_next_image)
eq2(transform_images)
eq2(simulate_data_collection)
eq2(log_average_image_intensity)
eq2(transform_image)
eq2(initialize_run)
eq2(collect_data_set)

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eq3(PortName) - What out ports are qualified with URIs?
---------------------------------------------------------------------------------------------------------------------------
eq3(collection_log)
eq3(corrected_image_file)
eq3(raw_image_file)
eq3(rejection_log)
eq3(run_log)

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mq1(SourceFile,StartLine,EndLine) - Where is the definition of block simulate_data_collection.collect_data_set?
---------------------------------------------------------------------------------------------------------------------------
mq1(../simulate_data_collection.py,86,103)

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mq2(WorkflowName,Description) - What is the name and description of the top-level workflow?
---------------------------------------------------------------------------------------------------------------------------
mq2(simulate_data_collection,Workflow for collecting diffraction data from high quality crystals in a cassette.)

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mq3(FunctionName) - What are the names of any top-level functions?
---------------------------------------------------------------------------------------------------------------------------
mq3(transform_image)
mq3(collect_next_image)
mq3(calculate_strategy)

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mq4(ProgramName) -  What are the names of the programs comprising the top-level workflow?
---------------------------------------------------------------------------------------------------------------------------
mq4(log_average_image_intensity)
mq4(transform_images)
mq4(collect_data_set)
mq4(log_rejected_sample)
mq4(calculate_strategy)
mq4(load_screening_results)
mq4(initialize_run)

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mq5(DataName) - What are the names and descriptions of the inputs to the top-level workflow?
---------------------------------------------------------------------------------------------------------------------------
mq5(calibration_image_file,File used to correct raw diffraction images.)
mq5(sample_spreadsheet,CSV file giving quality score for each crystal.)
mq5(data_redundancy,The desired redundancy of the data sets collected.)
mq5(sample_score_cutoff,The minimum quality score required of crystals.)
mq5(cassette_id,The unique ID of the cassette containing the crystals.)

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mq6(DataName,Description) - What data is output by program block simulate_data_collection.collect_data_set?
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mq6(raw_image,Path of file storing the raw diffraction image.)
mq6(frame_number,Index of diffraction image within data set.)
mq6(energy,Energy (in eV) at which the diffraction image was collected.)
mq6(sample_id,The crystal that the diffraction image was collected from.)

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mq7(ProgramName) - What program blocks provide input directly to simulate_data_collection.collect_data_set?
---------------------------------------------------------------------------------------------------------------------------
mq7(simulate_data_collection.calculate_strategy)

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mq8(ProgramName) - What programs have input ports that receive data simulate_data_collection[cassette_id]
---------------------------------------------------------------------------------------------------------------------------
mq8(simulate_data_collection.log_average_image_intensity)
mq8(simulate_data_collection.collect_data_set)
mq8(simulate_data_collection.log_rejected_sample)
mq8(simulate_data_collection.load_screening_results)
mq8(simulate_data_collection.initialize_run)

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mq9(PortCount) - How many ports read data simulate_data_collection[frame_number]?
---------------------------------------------------------------------------------------------------------------------------
mq9(2)

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mq10(DataCount) - How many data are read by more than port in workflow simulate_data_collection?
---------------------------------------------------------------------------------------------------------------------------
mq10(6)

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mq11(ProgramName) - What program blocks are immediately downstream of calculate_strategy?
---------------------------------------------------------------------------------------------------------------------------
mq11(collect_data_set)
mq11(log_rejected_sample)

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mq12(UpstreamProgramName) - What program blocks are immediately upstream of transform_images?
---------------------------------------------------------------------------------------------------------------------------
mq12(collect_data_set)

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mq13(UpstreamProgramName) - What program blocks are upstream of transform_images?
---------------------------------------------------------------------------------------------------------------------------
mq13(collect_data_set)
mq13(calculate_strategy)
mq13(load_screening_results)

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mq14(DownstreamProgramName) - What program blocks are anywhere downstream of calculate_strategy?
---------------------------------------------------------------------------------------------------------------------------
mq14(log_average_image_intensity)
mq14(transform_images)
mq14(collect_data_set)
mq14(log_rejected_sample)

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mq15(DownstreamDataName) - What data is immediately downstream of raw_image?
---------------------------------------------------------------------------------------------------------------------------
mq15(pixel_count)
mq15(total_intensity)
mq15(run_log)
mq15(corrected_image)

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mq16(UpstreamDataName) - What data is immediately upstream of raw_image?
---------------------------------------------------------------------------------------------------------------------------
mq16(energies)
mq16(num_images)
mq16(accepted_sample)
mq16(cassette_id)

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mq17(DownstreamDataName) - What data is downstream of accepted_sample?
---------------------------------------------------------------------------------------------------------------------------
mq17(run_log)
mq17(sample_id)
mq17(frame_number)
mq17(raw_image)
mq17(total_intensity)
mq17(pixel_count)
mq17(energy)
mq17(collection_log)
mq17(corrected_image)

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mq18(UpstreamDataName) - What data is upstream of raw_image?
---------------------------------------------------------------------------------------------------------------------------
mq18(energies)
mq18(sample_score_cutoff)
mq18(sample_name)
mq18(sample_spreadsheet)
mq18(accepted_sample)
mq18(num_images)
mq18(sample_quality)
mq18(cassette_id)
mq18(data_redundancy)

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mq19(UriVariableName) - What URI variables are associated with writes of data simulate_data_collection[corrected_image]?
---------------------------------------------------------------------------------------------------------------------------
mq19(frame_number)
mq19(energy)
mq19(sample_id)

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mq20(UpStreamDataName) - What URI variables do data written to raw_image and corrected_image have in common?
---------------------------------------------------------------------------------------------------------------------------
mq20(sample_id)
mq20(energy)
mq20(frame_number)

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rq0(VarName, VarValue) - What URI variable values are associated with resource run/data/DRT322/DRT322_11000eV_028.img?
---------------------------------------------------------------------------------------------------------------------------
rq0(sample_id,DRT322)
rq0(energy,11000)
rq0(frame_number,028)

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rq1(Sample) - What samples did the run of the script collect images from?
---------------------------------------------------------------------------------------------------------------------------
rq1(DRT322)
rq1(DRT240)

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rq2(Energy) - What energies were used during collection of images from sample DRT322?
---------------------------------------------------------------------------------------------------------------------------
rq2(11000)
rq2(10000)

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rq3(RawImageFile) - Where is the raw image from which corrected image run/data/DRT322/DRT322_11000eV_028.img is derived?
---------------------------------------------------------------------------------------------------------------------------
rq3(run/raw/q55/DRT322/e11000/image_028.raw)

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rq4(RawImageFile) - Are there any raw images for which there are no corresponding corrected images?
---------------------------------------------------------------------------------------------------------------------------
rq4(run/raw/q55/DRT240/e12000/image_002.raw)

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rq5(Cassette) - What cassette held the sample from which run/data/DRT240/DRT240_10000eV_010.img was derived?
---------------------------------------------------------------------------------------------------------------------------
rq5(q55)
