Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/util/tool_shed/xml_util.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import logging |
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2 import os |
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3 import tempfile |
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4 |
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5 from galaxy.util import ( |
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6 etree, |
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7 parse_xml as galaxy_parse_xml, |
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8 unicodify, |
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9 xml_to_string, |
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10 ) |
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11 |
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12 log = logging.getLogger(__name__) |
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13 |
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14 |
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15 def create_and_write_tmp_file(elem): |
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16 tmp_str = xml_to_string(elem, pretty=True) |
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17 with tempfile.NamedTemporaryFile(prefix="tmp-toolshed-cawrf", delete=False) as fh: |
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18 tmp_filename = fh.name |
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19 with open(tmp_filename, mode='w', encoding='utf-8') as fh: |
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20 fh.write(tmp_str) |
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21 return tmp_filename |
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22 |
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23 |
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24 def create_element(tag, attributes=None, sub_elements=None): |
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25 """ |
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26 Create a new element whose tag is the value of the received tag, and whose attributes are all |
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27 key / value pairs in the received attributes and sub_elements. |
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28 """ |
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29 if tag: |
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30 elem = etree.Element(tag) |
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31 if attributes: |
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32 # The received attributes is an odict to preserve ordering. |
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33 for k, v in attributes.items(): |
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34 elem.set(k, v) |
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35 if sub_elements: |
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36 # The received attributes is an odict. These handle information that tends to be |
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37 # long text including paragraphs (e.g., description and long_description. |
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38 for k, v in sub_elements.items(): |
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39 # Don't include fields that are blank. |
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40 if v: |
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41 if k == 'packages': |
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42 # The received sub_elements is an odict whose key is 'packages' and whose |
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43 # value is a list of ( name, version ) tuples. |
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44 for v_tuple in v: |
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45 sub_elem = etree.SubElement(elem, 'package') |
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46 sub_elem_name, sub_elem_version = v_tuple |
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47 sub_elem.set('name', sub_elem_name) |
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48 sub_elem.set('version', sub_elem_version) |
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49 elif isinstance(v, list): |
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50 sub_elem = etree.SubElement(elem, k) |
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51 # If v is a list, then it must be a list of tuples where the first |
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52 # item is the tag and the second item is the text value. |
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53 for v_tuple in v: |
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54 if len(v_tuple) == 2: |
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55 v_tag = v_tuple[0] |
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56 v_text = v_tuple[1] |
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57 # Don't include fields that are blank. |
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58 if v_text: |
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59 v_elem = etree.SubElement(sub_elem, v_tag) |
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60 v_elem.text = v_text |
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61 else: |
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62 sub_elem = etree.SubElement(elem, k) |
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63 sub_elem.text = v |
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64 return elem |
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65 return None |
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66 |
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67 |
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68 def parse_xml(file_name, check_exists=True): |
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69 """Returns a parsed xml tree with comments intact.""" |
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70 error_message = '' |
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71 if check_exists and not os.path.exists(file_name): |
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72 return None, "File does not exist %s" % str(file_name) |
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73 try: |
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74 tree = galaxy_parse_xml(file_name, remove_comments=False, strip_whitespace=False) |
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75 except OSError: |
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76 raise |
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77 except Exception as e: |
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78 error_message = "Exception attempting to parse {}: {}".format(str(file_name), unicodify(e)) |
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79 log.exception(error_message) |
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80 return None, error_message |
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81 return tree, error_message |