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synapse add random_numbers.txt --parentId syn1901847 --executed ./generate_random_data.R --used http://mathworld.wolfram.com/NormalDistribution.html
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Python
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# Set provenance for data file generated by the script file
data_file = File(path="random_numbers.txt", parent="syn1901847")
data_file = syn.store(data_file, executed="syn7205215", used="http://mathworld.wolfram.com/NormalDistribution.html")
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R
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# Set provenance for data file generated by the script file
data_file <- File(path="random_numbers.txt", parent="syn1901847")
data_file <- synStore(data_file, executed="syn7205215", used="http://mathworld.wolfram.com/NormalDistribution.html")
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# Add the data file to Synapse
synapse add squares.txt -parentId syn1901847
# Set the provenance for newly created entity syn7209166 using synId
synapse set-provenance -id syn7209166 -executed syn7209078 -used syn7208917
# Set the provenance for newly created entity syn7209166 using local path
synapse set-provenance -id syn7209166 -executed ./square.R -used ./random_numbers.txt
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Python
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# Add the data file to Synapse
squared_file = File(path="squares.txt", parentId="syn1901847")
squared_file = syn.store(squared_file)
# Set provenance for newly created entity syn7209166
squared_file = syn.setProvenance(squared_file, activity = Activity(used = "syn7208917", executed = "syn7209078"))
# Provenance can also be set using local variables instead of looking up synIds
squared_file = syn.setProvenance(squared_file, activity = Activity(used = data_file, executed = "syn7209078"))
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R
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# Add the data file to Synapse
squared_file <- File(path="squares.txt", parentId="syn1901847")
squared_file <- synStore(squared_file)
# Set provenance for newly created entity syn7209166
act <- Activity(name = "Squared numbers", used = "syn7208917", executed = "syn7209078")
synStore(squared_file, activity=act)
# Provenance can also be set using local variables instead of looking up synIds
act <- Activity(name = "Squared numbers", used = data_file, executed = "syn7209078")
squared_file <- synStore(squared_file, activity=act)
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# Delete provenance on entity syn123
delete_provenance = syn.deleteProvenance('syn123')
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R
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# Delete provenance on entity syn123
deleteProvenance = synDeleteProvenance('syn123')
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synapse get-provenance -id syn7209166
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Python
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provenance = syn.getProvenance("syn7209166")
provenance
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R
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provenance <- synGetProvenance("syn7209166")
provenance
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Unfortunately, the web interface does not support assigning the same activity to multiple files. This action must be completed using either the R or the Python client.
Command Line
The command line currently does not support assigning the same activity to multiple files.
Python
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# Code used to generate the file will be syn123456
# Files used to generate the information
expr_file = syn.get("syn246810", download=F)
filter_file = syn.get("syn135791", download=F)
# Activity to assign to multiple files
act = Activity(name="filtering",
used=[expr_file, filter_file],
executed="syn123456")
syn.store(final_file, activity=act)
# Get the activity now associated with an entity
act = syn.getProvenance(final_file)
# Now you can set this activity to as many files as you want (file1, file2, etc are Synapse Files)
file_list = [file_1, file_2, file_3]
file_list = map(lambda x: syn.store(x, activity=act), file_list)
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R
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# Code used to generate the file will be syn123456
# Files used to generate the information
expr_file <- synGet("syn246810", download=F)
filter_file <- synGet("syn135791", download=F)
# Activity to assign to multiple files
act <- Activity(name="filtering",
used=list(expr_file, filter_file),
executed="syn123456")
finalFile <- synStore(finalFile, activity=act)
# Get the activity now associated with an entity
act <- synGetProvenance(finalFile)
# Now you can set this activity to as many files as you want (file1, file2, etc are Synapse Files)
finalList <- c(file1, file2, file3)
finalList <- lapply(finalList, function(x) synStore(x, activity=act))
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