From 7460910673db9fb8adc1586b3db14d3a84dcf243 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?D=C3=A9borah=20Servili?=
 <Delta-Sierra@users.noreply.github.com>
Date: Fri, 27 Jan 2017 16:28:06 +0100
Subject: [PATCH] add csv to galaxy converter

---
 tools/csv_to_galaxy.py | 83 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 83 insertions(+)
 create mode 100644 tools/csv_to_galaxy.py

diff --git a/tools/csv_to_galaxy.py b/tools/csv_to_galaxy.py
new file mode 100644
index 00000000..8f3e99c2
--- /dev/null
+++ b/tools/csv_to_galaxy.py
@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import csv
+import argparse
+import uuid
+import json
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='CSV to Galaxy')
+    parser.add_argument("-c", "--csv", required=True, help="input csv")
+    parser.add_argument("-v", "--value", type=int, required=True, help="number of the column with the value")
+    parser.add_argument("-e", "--value_description", type=int, help="number of the column with description, if not defined, all other data wil be concataned")
+    parser.add_argument("-w", "--version", type=int, help="version of the galaxy")
+    parser.add_argument("-d", "--description", help="description of the galaxy")
+    parser.add_argument("-a", "--author", help="author of the galaxy")
+    parser.add_argument("-s", "--source", help="source of the galaxy")
+    parser.add_argument("-t", "--type", help="type of galaxy, also the name of the generated json")
+    parser.add_argument("-n", "--name", help="name of the galaxy")
+    parser.add_argument("-u", "--title", action='store_true', help="set it if the first line contains the name of the columns")
+
+    args = parser.parse_args()
+
+    values = []
+    if args.title is None:
+        args.title = False
+
+    with open(args.csv, newline='') as csvfile:
+        csvreader = csv.reader(csvfile, delimiter=',', quotechar='"')
+        for data in csvreader:
+            if args.title:
+                args.title = False
+                continue
+            temp = {}
+            temp["value"] = data[args.value]
+            if args.value_description is not None:
+                temp["description"] = data[args.value_description]
+            else:
+                temp["description"] = ""
+                for i in range(len(data)):
+                    if i != args.value and data[i] != "":
+                        temp["description"] = temp["description"] + data[i] + "; "
+            values.append(temp)
+
+    galaxy = {}
+    galaxy["values"] = values
+
+    if args.version is not None:
+        galaxy["version"] = args.version
+    else:
+        galaxy["version"] = 1
+
+    galaxy["uuid"] = str(uuid.uuid4())
+
+    if args.description is not None:
+        galaxy["description"] = args.description
+    else:
+        galaxy["description"] = "automagically generated galaxy"
+
+    if args.author is not None:
+        galaxy["authors"] = [args.author]
+    else:
+        galaxy["authors"] = ["authorname"]
+
+    if args.source is not None:
+        galaxy["source"] = args.source
+    else:
+        galaxy["source"] = "source"
+
+    if args.type is not None:
+        galaxy["type"] = args.type
+    else:
+        galaxy["type"] = "type"
+
+    if args.name is not None:
+        galaxy["name"] = args.name
+    else:
+        galaxy["name"] = "name"
+
+    print (galaxy)
+
+    with open(args.type+'.json', 'w') as outfile:
+            json.dump(galaxy, outfile)