import os, sys, time from xml.etree import ElementTree as ET # ------------------------------------------------------------------------------ class ModulesElementTree(ET.ElementTree): def __init__(self): ET.ElementTree.__init__(self, ET.Element("root")) def parseModulesDef(self, ifile): root = self.getroot() amounts = dict() tag_id_map = dict() modules_list = list() for line in ifile: stripped = line.strip().replace("\t", " ") if stripped and not stripped.startswith("#"): head, sep, tail = stripped.partition(" ") if sep != " ": self._string_error("No separating space:", line) value = tail.lstrip() unquoted = value.split('"') if len(unquoted) == 1: if value.find(" ") > 0: self._string_error("Unquoted text:", line) elif len(unquoted) == 3: if len(unquoted[0]) == 0 and len(unquoted[2]) == 0: value = unquoted[1] else: self._string_error("Quotation in text:", line) else: self._string_error("Incorrect quotation:", line) tag_key, sep2, id = head.partition(",") tag, sep1, key = tag_key.partition("_") if sep1 == "_": if sep2 == ",": tag_id = ",".join((tag, id)) element = tag_id_map.get(tag_id) if element is None: element = ET.Element(tag) tag_id_map[tag_id] = element element.attrib["ID"] = id attrib = element.attrib if key in attrib: self._string_error("Repeated entry:", line) else: attrib[key] = value elif tag == "N": if amounts.get(key): self._string_error("Duplicated entry:", line) elif not value.isdigit(): self._string_error("Numeric value expected:", line) else: amounts[key] = [int(value), 0] elif tag_key == "MODULE_LIST": modules_list = self._split_line(value) else: self._string_error("Unrecognised record", line) elif tag_key == "PROJECT": root.tag = value elif tag_key == "TITLE": root.attrib[tag_key] = value else: self._string_error("Unrecognised record", line) elements = tag_id_map.values() modules_map = dict() mod_tit_map = dict() for element in elements: occurance = amounts.get(element.tag + "S") if not occurance: self._element_error("Unrecognised element", element) else: name = element.get("NAME") module = element.get("MODULE") title = element.get("TITLE") key = None map = None if name and element.tag == "MODULE": key = name map = modules_map elif module and title: key = " ".join((module, title)) map = mod_tit_map if not key: self._element_error("Ignoring:", element) else: occurance[1] += 1 if key in map: self._element_error("Element duplication", element) else: map[key] = element print for tag, occurance in amounts.items(): declared, actual = occurance print "No of %7s: %3d declared and %3d found" % (tag, declared, actual) for element in elements: attrib = element.attrib titles = self._split_line(attrib.pop("TASK_LIST", "")) if titles: module = attrib.get("MODULE") if element.tag == "MODULE": module = attrib.get("NAME") if not module: self._element_error("Missing TITLE or NAME:", element) else: for title in titles: key = " ".join((module, title)) child = mod_tit_map.pop(key, None) if child == None: self._string_error("Undefined task in module %s:" %module, title) else: element.append(child) for element in mod_tit_map.values(): self._element_error("Unreferenced task:", element) for module_name in modules_list: if not module_name.strip(): root.append(ET.Element("SEPARATOR")) else: element = modules_map.pop(module_name, None) if element == None: self._string_error("Declared MODULE is not defined: ", module_name) else: root.append(element) self._add_indents(root, "\n") self._check_modules(root, None) print def _split_line(self, line): parts = line.split("{") words = parts[0].split() for part in parts[1:]: head, sep, tail = part.partition("}") words.append(head) words.extend(tail.split()) return words def _add_indents(self, e0, t0): e0.tail = t0 if len(e0) > 0: t1 = t0 + " " e0.text = t1 for e1 in e0: self._add_indents(e1, t1) e1.tail = t0 def _check_modules(self, e0, m0): a0 = e0.attrib m1 = a0.pop("MODULE", a0.get("NAME")) if m0 and m0 != m1: self._element_error("MODULE attribute missmatch:", e0) for e1 in e0: self._check_modules(e1, m1) def _string_error(self, message, string): print print message print string def _element_error(self, message, element): print print message print ET.tostring(ET.Element(element.tag, element.attrib)) def writeModulesDef(self, ofile): head_list = list() head_list.extend(("FOLDER_DESCRIPT", "FOLDER_MODULE", "FOLDER_NAME", "FOLDER_TASK_LIST", "FOLDER_TITLE",)) head_list.extend(("MODULE_LIST", "MODULE_NAME", "MODULE_TASK_LIST", "MODULE_TITLE",)) head_list.extend(("N_FOLDERS", "N_MODULES", "N_TASKS", "PROJECT",)) head_list.extend(("TASK_DESCRIPT", "TASK_MODULE", "TASK_NAME", "TASK_TITLE","TITLE",)) id_limit = 10000 element_list = list() self._add_to_list(self.getroot(), None, None, element_list, id_limit) element_list.append(ET.Element("MODULE", ID="0", NAME="", TITLE="", TASK_LIST="")) element_list.append(ET.Element("FOLDER", ID="0", NAME="", TITLE="", DESCRIPT="", MODULE="", TASK_LIST="")) element_list.append(ET.Element("TASK", ID="0", NAME="", TITLE="", DESCRIPT="", MODULE="")) element_list.sort(lambda x, y: cmp(int(x.get("ID")), int(y.get("ID")))) tag_counts = dict(MODULE=-1, FOLDER=-1, TASK=-1) moddef_list = list() moddef_list.append((head_list.index("PROJECT"), id_limit, "CCP4")) for element in element_list: tag = element.tag id = id_limit if tag in tag_counts: id = tag_counts[tag] + 1 tag_counts[tag] = id for key, value in element.attrib.items(): if key != "ID": head = "_".join((tag, key)) if tag == "CCP4": head = key if not head in head_list: self._element_error("Element implies unspecified record %s:" %head, element) else: moddef_list.append((head_list.index(head), id, value)) for tag, count in tag_counts.items(): head = "N_%sS" %tag if head in head_list: moddef_list.append((head_list.index(head), id_limit, str(count))) moddef_list.sort(lambda x, y: cmp((1 + id_limit)* x[0] + x[1], (1 + id_limit)* y[0] + y[1])) ofile.write("#CCP4I DATE 20 Mar 2014 17:10:45\n") # ofile.write(time.strftime("#CCP4I DATE %d %b %Y %H:%M:%S\n", time.localtime(time.time()))) ofile.write("#CCP4I SCRIPT DEF modules\n") ofile.write("#CCP4I USER %s\n" %os.environ.get("USER", "unknown")) ofile.write("#CCP4I VERSION CCP4Interface 2.2.1\n") for ind, id, value in moddef_list: key = head_list[ind] if id < id_limit: key = "%s,%d" %(key, id) if not value or value.find(" ") > 0: value = "\"%s\"" %value ofile.write("%-25s %s\n" %(key, value)) ofile.write("\n") print def _add_to_list(self, e0, m0, k0, element_list, id_limit): if not e0.tag.strip(): self._element_error("Missing tag:", e0) return id = e0.get("ID", str(id_limit)) if not id.isdigit(): self._element_error("Non-integer ID:", e0) return e0.attrib["ID"] = id is_ccp4 = e0.tag == "CCP4" is_module = e0.tag == "MODULE" is_folder = e0.tag == "FOLDER" is_task = e0.tag == "TASK" is_separator = e0.tag == "SEPARATOR" m1 = m0 if is_module: m1 = e0.get("NAME", "") k1 = None if is_ccp4 or is_module or is_folder: k1 = list() if is_module or is_folder or is_task: key = e0.get("TITLE").strip() if is_module: key = e0.get("NAME").strip() if not key: self._element_error("Missing TITLE:", element) else: if key.find(" ") > 0: key = "{%s}" %(key) k0.append(key) if is_separator: k0.append("{}") for e1 in e0: self._add_to_list(e1, m1, k1, element_list, id_limit) element = ET.Element(e0.tag) element.attrib.update(e0.attrib) if is_ccp4: element.attrib["MODULE_LIST"] = " ".join(k1) if is_module or is_folder: element.attrib["TASK_LIST"] = " ".join(k1) if is_folder or is_task: element.attrib["MODULE"] = m0 element.tail = "\n" element_list.append(element) # ------------------------------------------------------------------------------ def access_node(self, action, path): name_list = path.replace('/', ' ').split() if not name_list: return node_tail = '\n' + len(name_list)* 3* ' ' root = self.getroot() cnode = root for name in name_list: pnode = cnode cou = 0 for cnode in list(pnode): cou += 1 if cnode.get('NAME') == name: break if pnode is cnode: return inode = None if action == 'get': inode = cnode elif action == 'remove': pnode.remove(cnode) inode = cnode elif action == 'before': inode = ET.Element('SEPARATOR') pnode.insert(cou - 1, inode) elif action == 'after': inode = ET.Element('SEPARATOR') pnode.insert(cou, inode) self._add_indents(root, "\n") return inode # ------------------------------------------------------------------------------ if __name__ == '__main__': print argmap = dict() for key, value in zip(sys.argv[1::2], sys.argv[2::2]): value = os.path.abspath(value) print "%-9s %s" %(key + ":", value) argmap[key.lower()] = value defin = argmap.get("defin") xmlin = argmap.get("xmlin") defout = argmap.get("defout") xmlout = argmap.get("xmlout") if defin and xmlin or not defin and not xmlin: print " usage:" print " python modules_def_xml.py defin in.def [defout ] [xmlout ]" print " or:" print " python modules_def_xml.py xmlin in.xml [defout ] [xmlout ]" print print " Do NOT define any ID attribute when adding new elements to XMLIN to preserve existing numbering" print else: tree = ModulesElementTree() if defin: with open(defin) as ifile: tree.parseModulesDef(ifile) elif xmlin: with open(xmlin) as ifile: tree.parse(ifile) if defout: with open(defout, "w") as ofile: tree.writeModulesDef(ofile) elif xmlout: with open(xmlout, "w") as ofile: tree.write(ofile) # ------------------------------------------------------------------------------