Mercurial > repos > siwaa > gama_desc

annotate desc.py @ 0:23b15c0eabff draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
author siwaa
date Mon, 18 Nov 2024 13:57:51 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
1 #!/usr/bin/env python
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
2 # coding: utf-8
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
3
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
4 #-----------------------------------------------------------------
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
5 __author__ = "Nathalie Rousse (nathalie.rousse@inrae.fr)"
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
6 __copyright__ = "Copyright (C) 2024, Inrae (https://www.inrae.fr)"
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
7 __license__ = "MIT"
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
8 #-----------------------------------------------------------------
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
9
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
10 import json
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
11
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
12 # Produces a description JSON data from a GAML model file
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
13
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
14 ###############################################################################
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
15
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
16 def make_json_experiments_by_types(gaml_file_path):
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
17
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
18 # experiments contains lists of experiment names, by type
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
19 experiments = { "gui": [], "batch": [], "test": [], "memorize": [] }
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
20
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
21 with open(gaml_file_path, 'r') as f:
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
22 lines = f.readlines()
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
23
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
24 for line in lines:
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
25 experiment_name, type = None, None # default
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
26 line_kept = True # default
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
27 if "experiment" not in line : line_kept = False
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
28 if ("type " not in line and "type:" not in line) : line_kept = False
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
29
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
30 if line_kept :
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
31 words = line.split()
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
32 if words[0] == 'experiment' :
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
33 experiment_name = words[1]
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
34 else:
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
35 line_kept = False
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
36
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
37 if line_kept :
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
38 while " :" in line:
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
39 line = line.replace(" :", ":")
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
40 line = line.replace(":", ": ")
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
41 words = line.split()
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
42 for i,word in enumerate(words) :
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
43 if word == "type:" :
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
44 if words[i+1] in ("gui", "batch", "test", "memorize"):
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
45 type = words[i+1]
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
46 if line_kept and (experiment_name is not None) and (type is not None):
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
47 experiments[type].append(experiment_name)
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
48
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
49 return experiments
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
50
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
51 ###############################################################################
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
52
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
53 GAML_FILE_PATH = "model.gaml"
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
54 DESC_JSON_FILE_PATH = "desc.json"
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
55
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
56 try :
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
57 desc = dict()
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
58 experiments = make_json_experiments_by_types(gaml_file_path=GAML_FILE_PATH)
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
59 desc['experiments_by_types'] = experiments
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
60 print(desc)
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
61 with open(DESC_JSON_FILE_PATH, "w") as json_file:
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
62 json_file.write(json.dumps(desc))
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
63
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
64 except Exception as e :
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
65 errortype = type(e).__name__
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
66 errordetails = e.args
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
67 print("ERROR:", errortype, errordetails)
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
68
23b15c0eabff planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
siwaa
parents:
diff changeset
69 ###############################################################################