mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-31 01:02:04 +08:00
Dannon Baker
136 lines
5.0 KiB
Python
136 lines
5.0 KiB
Python
import os
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from collections import defaultdict
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from xml.etree import ElementTree as ET
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# Todo: ""
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# execute from galaxy root dir
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tooldict = defaultdict(list)
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def main():
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doc = ET.parse("tool_conf.xml")
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root = doc.getroot()
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# index range 1-1000, current sections/tools divided between 250-750
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sectionindex = 250
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sectionfactor = int(500 / len(root))
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for rootchild in root:
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currentsectionlabel = ""
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if rootchild.tag == "section":
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sectionname = rootchild.attrib["name"]
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# per section tool index range 1-1000, current labels/tools
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# divided between 20 and 750
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toolindex = 250
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toolfactor = int(500 / len(rootchild))
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currentlabel = ""
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for sectionchild in rootchild:
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if sectionchild.tag == "tool":
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addToToolDict(sectionchild, sectionname, sectionindex, toolindex, currentlabel)
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toolindex += toolfactor
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elif sectionchild.tag == "label":
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currentlabel = sectionchild.attrib["text"]
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sectionindex += sectionfactor
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elif rootchild.tag == "tool":
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addToToolDict(rootchild, "", sectionindex, None, currentsectionlabel)
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sectionindex += sectionfactor
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elif rootchild.tag == "label":
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currentsectionlabel = rootchild.attrib["text"]
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sectionindex += sectionfactor
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# scan galaxy root tools dir for tool-specific xmls
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toolconffilelist = getfnl(os.path.join(os.getcwd(), "tools"))
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# foreach tool xml:
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# check if the tags element exists in the tool xml (as child of <tool>)
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# if not, add empty tags element for later use
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# if this tool is in the above tooldict, add the toolboxposition element to the tool xml
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# if not, then nothing.
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for toolconffile in toolconffilelist:
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hastags = False
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hastoolboxpos = False
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# parse tool config file into a document structure as defined by the ElementTree
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tooldoc = ET.parse(toolconffile)
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# get the root element of the toolconfig file
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tooldocroot = tooldoc.getroot()
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# check tags element, set flag
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tagselement = tooldocroot.find("tags")
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if tagselement:
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hastags = True
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# check if toolboxposition element already exists in this tooconfig file
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toolboxposelement = tooldocroot.find("toolboxposition")
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if toolboxposelement:
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hastoolboxpos = True
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if not (hastags and hastoolboxpos):
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original = open(toolconffile)
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contents = original.readlines()
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original.close()
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# the new elements will be added directly below the root tool element
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addelementsatposition = 1
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# but what's on the first line? Root or not?
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if contents[0].startswith("<?"):
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addelementsatposition = 2
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newelements = []
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if not hastoolboxpos:
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if toolconffile in tooldict:
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for attributes in tooldict[toolconffile]:
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# create toolboxposition element
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sectionelement = ET.Element("toolboxposition")
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sectionelement.attrib = attributes
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sectionelement.tail = "\n "
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newelements.append(ET.tostring(sectionelement, "utf-8"))
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if not hastags:
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# create empty tags element
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newelements.append("<tags/>\n ")
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contents = contents[0:addelementsatposition] + newelements + contents[addelementsatposition:]
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# add .new for testing/safety purposes :P
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newtoolconffile = open(toolconffile, "w")
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newtoolconffile.writelines(contents)
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newtoolconffile.close()
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def addToToolDict(tool, sectionname, sectionindex, toolindex, currentlabel):
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toolfile = tool.attrib["file"]
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realtoolfile = os.path.join(os.getcwd(), "tools", toolfile)
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# define attributes for the toolboxposition xml-tag
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attribdict = {}
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if sectionname:
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attribdict["section"] = sectionname
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if currentlabel:
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attribdict["label"] = currentlabel
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if sectionindex:
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attribdict["sectionorder"] = str(sectionindex)
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if toolindex:
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attribdict["order"] = str(toolindex)
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tooldict[realtoolfile].append(attribdict)
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# Build a list of all toolconf xml files in the tools directory
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def getfnl(startdir):
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filenamelist = []
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for root, _dirs, files in os.walk(startdir):
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for fn in files:
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fullfn = os.path.join(root, fn)
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if fn.endswith(".xml"):
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try:
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doc = ET.parse(fullfn)
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except Exception as e:
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raise Exception(f"Oops, bad XML in '{fullfn}': {e}")
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rootelement = doc.getroot()
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# here we check if this xml file actually is a tool conf xml!
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if rootelement.tag == "tool":
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filenamelist.append(fullfn)
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return filenamelist
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if __name__ == "__main__":
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main()
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