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87 lines
3 KiB
Python
87 lines
3 KiB
Python
#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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import csv
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import argparse
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import uuid
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import json
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(description='CSV to Galaxy')
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parser.add_argument("-c", "--csv", required=True, help="input csv")
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parser.add_argument("-v", "--value", type=int, required=True, help="number of the column with the value")
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parser.add_argument("-e", "--value_description", type=int, nargs='+', help="number of the column with description, if not defined, all other data wil be concataned")
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parser.add_argument("-w", "--version", type=int, help="version of the galaxy")
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parser.add_argument("-d", "--description", help="description of the galaxy")
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parser.add_argument("-a", "--authors", nargs='+', help="author of the galaxy")
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parser.add_argument("-s", "--source", help="source of the galaxy")
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parser.add_argument("-t", "--type", help="type of galaxy, also the name of the generated json")
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parser.add_argument("-n", "--name", help="name of the galaxy")
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parser.add_argument("-u", "--title", action='store_true', help="set it if the first line contains the name of the columns")
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args = parser.parse_args()
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values = []
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if args.title is None:
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args.title = False
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with open(args.csv, newline='') as csvfile:
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csvreader = csv.reader(csvfile, delimiter=',', quotechar='"')
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for data in csvreader:
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if args.title:
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args.title = False
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continue
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temp = {}
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temp["value"] = data[args.value]
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temp["description"] = ""
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if args.value_description is not None:
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for i in args.value_description:
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if data[i] != "":
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temp["description"] = temp["description"] + data[i].replace('\n', ' ') + "; "
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else:
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for i in range(len(data)):
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if i != args.value and data[i] != "":
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temp["description"] = temp["description"] + data[i] + "; "
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values.append(temp)
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galaxy = {}
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galaxy["values"] = values
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if args.version is not None:
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galaxy["version"] = args.version
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else:
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galaxy["version"] = 1
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galaxy["uuid"] = str(uuid.uuid4())
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if args.description is not None:
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galaxy["description"] = args.description
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else:
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galaxy["description"] = "automagically generated galaxy"
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if args.authors is not None:
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galaxy["authors"] = []
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for author in args.authors:
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galaxy["authors"].append(author)
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else:
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galaxy["authors"] = ["Various"]
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if args.source is not None:
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galaxy["source"] = args.source
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else:
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galaxy["source"] = "source"
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if args.type is not None:
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galaxy["type"] = args.type
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else:
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galaxy["type"] = "type"
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if args.name is not None:
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galaxy["name"] = args.name
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else:
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galaxy["name"] = "name"
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print (galaxy)
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with open(args.type+'.json', 'w') as outfile:
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json.dump(galaxy, outfile)
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