diff toolfactory/galaxyxml/tool/__init__.py @ 35:5d38cb3d9be8 draft

added patched galaxyxml code temporarily until PR accepted

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/galaxyxml/tool/__init__.py	Sat Aug 08 19:55:55 2020 -0400
@@ -0,0 +1,172 @@
+import copy
+import logging
+from lxml import etree
+from galaxyxml import Util, GalaxyXML
+from galaxyxml.tool.parameters import XMLParam
+
+VALID_TOOL_TYPES = ('data_source', 'data_source_async')
+VALID_URL_METHODS = ('get', 'post')
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+class Tool(GalaxyXML):
+
+    def __init__(self, name, id, version, description, executable, hidden=False,
+                 tool_type=None, URL_method=None, workflow_compatible=True,
+                 interpreter=None, version_command='interpreter filename.exe --version',
+                 command_line_override=None):
+
+        self.executable = executable
+        self.interpreter = interpreter
+        self.command_line_override = command_line_override
+        kwargs = {
+            'name': name,
+            'id': id,
+            'version': version,
+            'hidden': hidden,
+            'workflow_compatible': workflow_compatible,
+        }
+        self.version_command = version_command
+
+        # Remove some of the default values to make tools look a bit nicer
+        if not hidden:
+            del kwargs['hidden']
+        if workflow_compatible:
+            del kwargs['workflow_compatible']
+
+        kwargs = Util.coerce(kwargs)
+        self.root = etree.Element('tool', **kwargs)
+
+        if tool_type is not None:
+            if tool_type not in VALID_TOOL_TYPES:
+                raise Exception("Tool type must be one of %s" %
+                                ','.join(VALID_TOOL_TYPES))
+            else:
+                kwargs['tool_type'] = tool_type
+
+                if URL_method is not None:
+                    if URL_method in VALID_URL_METHODS:
+                        kwargs['URL_method'] = URL_method
+                    else:
+                        raise Exception("URL_method must be one of %s" %
+                                        ','.join(VALID_URL_METHODS))
+
+        description_node = etree.SubElement(self.root, 'description')
+        description_node.text = description
+
+    def add_comment(self, comment_txt):
+        comment = etree.Comment(comment_txt)
+        self.root.insert(0, comment)
+
+    def append_version_command(self):
+        version_command = etree.SubElement(self.root, 'version_command')
+        try:
+            version_command.text = etree.CDATA(self.version_command)
+        except Exception:
+            pass
+
+    def append(self, sub_node):
+        if issubclass(type(sub_node), XMLParam):
+            self.root.append(sub_node.node)
+        else:
+            self.root.append(sub_node)
+
+    def clean_command_string(self, command_line):
+        clean = []
+        for x in command_line:
+            if x is not [] and x is not ['']:
+                clean.append(x)
+
+        return '\n'.join(clean)
+
+    def export(self, keep_old_command=False):  # noqa
+
+        export_xml = copy.deepcopy(self)
+
+        try:
+            export_xml.append(export_xml.edam_operations)
+        except Exception:
+            pass
+
+        try:
+            export_xml.append(export_xml.edam_topics)
+        except Exception:
+            pass
+
+        try:
+            export_xml.append(export_xml.requirements)
+        except Exception:
+            pass
+
+        try:
+            export_xml.append(export_xml.configfiles)
+        except Exception:
+            pass
+
+        if self.command_line_override != None:
+            command_line = self.command_line_override
+        else:
+            command_line = []
+            try:
+                command_line.append(export_xml.inputs.cli())
+            except Exception as e:
+                logger.warning(str(e))
+
+            try:
+                command_line.append(export_xml.outputs.cli())
+            except Exception:
+                pass
+
+        # Add stdio section
+        stdio = etree.SubElement(export_xml.root, 'stdio')
+        etree.SubElement(stdio, 'exit_code', range='1:', level='fatal')
+
+        # Append version command
+        export_xml.append_version_command()
+
+        # Steal interpreter from kwargs
+        command_kwargs = {}
+        if export_xml.interpreter is not None:
+            command_kwargs['interpreter'] = export_xml.interpreter
+
+        # Add command section
+        command_node = etree.SubElement(export_xml.root, 'command', **command_kwargs)
+
+        if keep_old_command:
+            if getattr(self, 'command', None):
+                command_node.text = etree.CDATA(export_xml.command)
+            else:
+                logger.warning('The tool does not have any old command stored. ' +
+                               'Only the command line is written.')
+                command_node.text = export_xml.executable
+        else:
+            actual_cli = "%s %s" % (
+                export_xml.executable, export_xml.clean_command_string(command_line))
+            command_node.text = etree.CDATA(actual_cli.strip())
+
+        try:
+            export_xml.append(export_xml.inputs)
+        except Exception:
+            pass
+
+        try:
+            export_xml.append(export_xml.outputs)
+        except Exception:
+            pass
+
+        try:
+            export_xml.append(export_xml.tests)
+        except Exception:
+            pass
+
+        help_element = etree.SubElement(export_xml.root, 'help')
+        help_element.text = etree.CDATA(export_xml.help)
+
+        try:
+            export_xml.append(export_xml.citations)
+        except Exception:
+            pass
+
+        return super(Tool, export_xml).export()