Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/gxformat2/markdown_parse.py @ 3:758bc20232e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
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1 """Utilities for parsing "Galaxy Flavored Markdown".
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2
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3 See markdown_util.py for loading objects and interacting with the rest of Galaxy.
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4 This file is meant to be relatively self contained and just used to "parse" and validate
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5 Galaxy Markdown. Keeping things isolated to allow re-use of these utilities in other
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6 projects (e.g. gxformat2).
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7 """
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8 import re
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9
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10 BLOCK_FENCE_START = re.compile(r'```.*')
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11 BLOCK_FENCE_END = re.compile(r'```[\s]*')
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12 GALAXY_FLAVORED_MARKDOWN_CONTAINER_LINE_PATTERN = re.compile(
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13 r"```\s*galaxy\s*"
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14 )
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15 VALID_CONTAINER_END_PATTERN = re.compile(r"^```\s*$")
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16 GALAXY_FLAVORED_MARKDOWN_CONTAINERS = [
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17 "history_dataset_display",
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18 "history_dataset_collection_display",
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19 "history_dataset_as_image",
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20 "history_dataset_peek",
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21 "history_dataset_info",
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22 "workflow_display",
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23 "job_metrics",
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24 "job_parameters",
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25 "tool_stderr",
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26 "tool_stdout",
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27 ]
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28 INVOCATION_SECTIONS = [
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29 "invocation_inputs",
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30 "invocation_outputs",
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31 ]
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32 ALL_CONTAINER_TYPES = GALAXY_FLAVORED_MARKDOWN_CONTAINERS + INVOCATION_SECTIONS
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33 GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = "(%s)" % "|".join(ALL_CONTAINER_TYPES)
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34
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35 ARG_VAL_REGEX = r'''[\w_\-]+|\"[^\"]+\"|\'[^\']+\''''
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36 FUNCTION_ARG = r'\s*\w+\s*=\s*(?:%s)\s*' % ARG_VAL_REGEX
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37 FUNCTION_CALL_LINE_TEMPLATE = r'\s*%s\s*\((?:' + FUNCTION_ARG + r')?\)\s*'
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38 GALAXY_MARKDOWN_FUNCTION_CALL_LINE = re.compile(FUNCTION_CALL_LINE_TEMPLATE % GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX)
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39 WHITE_SPACE_ONLY_PATTERN = re.compile(r"^[\s]+$")
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40
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41
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42 def validate_galaxy_markdown(galaxy_markdown, internal=True):
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43 """Validate the supplied markdown and throw an ValueError with reason if invalid."""
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44 expecting_container_close_for = None
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45 last_line_no = 0
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46 function_calls = 0
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47 for (line, fenced, open_fence, line_no) in _split_markdown_lines(galaxy_markdown):
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48 last_line_no = line_no
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49
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50 def invalid_line(template, **kwd):
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51 if "line" in kwd:
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52 kwd["line"] = line.rstrip("\r\n")
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53 raise ValueError("Invalid line %d: %s" % (line_no + 1, template.format(**kwd)))
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54
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55 expecting_container_close = expecting_container_close_for is not None
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56 if not fenced and expecting_container_close:
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57 invalid_line("[{line}] is not expected close line for [{expected_for}]", line=line, expected_for=expecting_container_close_for)
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58 continue
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59 elif not fenced:
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60 continue
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61 elif fenced and expecting_container_close and BLOCK_FENCE_END.match(line):
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62 # reset
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63 expecting_container_close_for = None
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64 function_calls = 0
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65 elif open_fence and GALAXY_FLAVORED_MARKDOWN_CONTAINER_LINE_PATTERN.match(line):
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66 if expecting_container_close:
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67 if not VALID_CONTAINER_END_PATTERN.match(line):
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68 invalid_line("Invalid command close line [{line}] for [{expected_for}]", line=line, expected_for=expecting_container_close_for)
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69 # else closing container and we're done
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70 expecting_container_close_for = None
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71 function_calls = 0
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72 continue
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73
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74 expecting_container_close_for = line
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75 continue
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76 elif fenced and line and expecting_container_close_for:
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77 if GALAXY_MARKDOWN_FUNCTION_CALL_LINE.match(line):
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78 function_calls += 1
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79 if function_calls > 1:
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80 invalid_line("Only one Galaxy directive is allowed per fenced Galaxy block (```galaxy)")
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81 continue
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82 else:
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83 invalid_line("Invalid embedded Galaxy markup line [{line}]", line=line)
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84
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85 # Markdown unrelated to Galaxy object containers.
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86 continue
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87
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88 if expecting_container_close_for:
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89 template = "Invalid line %d: %s"
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90 msg = template % (last_line_no, "close of block for [{expected_for}] expected".format(expected_for=expecting_container_close_for))
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91 raise ValueError(msg)
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92
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93
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94 def _split_markdown_lines(markdown):
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95 """Yield lines of a markdown document line-by-line keeping track of fencing.
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96
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97 'Fenced' lines are code-like block (e.g. between ```) that shouldn't contain
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98 Markdown markup.
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99 """
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100 block_fenced = False
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101 indent_fenced = False
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102 for line_number, line in enumerate(markdown.splitlines(True)):
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103 open_fence_this_iteration = False
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104 indent_fenced = line.startswith(" ") or (indent_fenced and WHITE_SPACE_ONLY_PATTERN.match(line))
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105 if not block_fenced:
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106 if BLOCK_FENCE_START.match(line):
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107 open_fence_this_iteration = True
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108 block_fenced = True
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109 yield (line, block_fenced or indent_fenced, open_fence_this_iteration, line_number)
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110 if not open_fence_this_iteration and BLOCK_FENCE_END.match(line):
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111 block_fenced = False
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112
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113
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114 __all__ = (
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115 'validate_galaxy_markdown',
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116 'GALAXY_MARKDOWN_FUNCTION_CALL_LINE',
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117 )