Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/galaxyxml/tool/__init__.py @ 38:a30536c100bf draft

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author fubar
date Wed, 12 Aug 2020 01:43:46 -0400
parents ce2b1f8ea68d
children
comparison
equal deleted inserted replaced
37:099047ee7094 38:a30536c100bf
1 import copy 1 import copy
2 import logging 2 import logging
3
4 from galaxyxml import GalaxyXML, Util
5 from galaxyxml.tool.parameters import XMLParam
6
3 from lxml import etree 7 from lxml import etree
4 from galaxyxml import Util, GalaxyXML
5 from galaxyxml.tool.parameters import XMLParam
6 8
7 VALID_TOOL_TYPES = ("data_source", "data_source_async") 9 VALID_TOOL_TYPES = ("data_source", "data_source_async")
8 VALID_URL_METHODS = ("get", "post") 10 VALID_URL_METHODS = ("get", "post")
9 11
10 logging.basicConfig(level=logging.INFO) 12 logging.basicConfig(level=logging.INFO)
11 logger = logging.getLogger(__name__) 13 logger = logging.getLogger(__name__)
12 14
13 15
14 class Tool(GalaxyXML): 16 class Tool(GalaxyXML):
17
15 def __init__( 18 def __init__(
16 self, 19 self,
17 name, 20 name,
18 id, 21 id,
19 version, 22 version,
49 kwargs = Util.coerce(kwargs) 52 kwargs = Util.coerce(kwargs)
50 self.root = etree.Element("tool", **kwargs) 53 self.root = etree.Element("tool", **kwargs)
51 54
52 if tool_type is not None: 55 if tool_type is not None:
53 if tool_type not in VALID_TOOL_TYPES: 56 if tool_type not in VALID_TOOL_TYPES:
54 raise Exception( 57 raise Exception("Tool type must be one of %s" % ",".join(VALID_TOOL_TYPES))
55 "Tool type must be one of %s" % ",".join(VALID_TOOL_TYPES)
56 )
57 else: 58 else:
58 kwargs["tool_type"] = tool_type 59 kwargs["tool_type"] = tool_type
59 60
60 if URL_method is not None: 61 if URL_method is not None:
61 if URL_method in VALID_URL_METHODS: 62 if URL_method in VALID_URL_METHODS:
62 kwargs["URL_method"] = URL_method 63 kwargs["URL_method"] = URL_method
63 else: 64 else:
64 raise Exception( 65 raise Exception("URL_method must be one of %s" % ",".join(VALID_URL_METHODS))
65 "URL_method must be one of %s" % ",".join(VALID_URL_METHODS)
66 )
67 66
68 description_node = etree.SubElement(self.root, "description") 67 description_node = etree.SubElement(self.root, "description")
69 description_node.text = description 68 description_node.text = description
70 69
71 def add_comment(self, comment_txt): 70 def add_comment(self, comment_txt):
148 147
149 if keep_old_command: 148 if keep_old_command:
150 if getattr(self, "command", None): 149 if getattr(self, "command", None):
151 command_node.text = etree.CDATA(export_xml.command) 150 command_node.text = etree.CDATA(export_xml.command)
152 else: 151 else:
153 logger.warning( 152 logger.warning("The tool does not have any old command stored. " + "Only the command line is written.")
154 "The tool does not have any old command stored. "
155 + "Only the command line is written."
156 )
157 command_node.text = export_xml.executable 153 command_node.text = export_xml.executable
158 else: 154 else:
159 actual_cli = "%s %s" % ( 155 actual_cli = "%s %s" % (export_xml.executable, export_xml.clean_command_string(command_line))
160 export_xml.executable,
161 export_xml.clean_command_string(command_line),
162 )
163 command_node.text = etree.CDATA(actual_cli.strip()) 156 command_node.text = etree.CDATA(actual_cli.strip())
164 157
165 try: 158 try:
166 export_xml.append(export_xml.inputs) 159 export_xml.append(export_xml.inputs)
167 except Exception: 160 except Exception: