Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/cwltool/provenance_profile.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 import copy
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2 import datetime
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3 import logging
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4 import urllib
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5 import uuid
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6 from io import BytesIO
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7 from pathlib import PurePath, PurePosixPath
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8 from socket import getfqdn
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9 from typing import List, MutableMapping, MutableSequence, Optional, Tuple, Union, cast
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10
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11 from prov.identifier import Identifier
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12 from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity
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13 from schema_salad.sourceline import SourceLine
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14 from typing_extensions import TYPE_CHECKING
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15
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16 from .errors import WorkflowException
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17 from .job import CommandLineJob, JobBase
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18 from .loghandler import _logger
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19 from .process import Process, shortname
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20 from .provenance_constants import (
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21 ACCOUNT_UUID,
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22 CWLPROV,
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23 ENCODING,
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24 FOAF,
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25 METADATA,
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26 ORE,
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27 PROVENANCE,
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28 RO,
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29 SCHEMA,
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30 SHA1,
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31 SHA256,
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32 TEXT_PLAIN,
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33 UUID,
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34 WF4EVER,
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35 WFDESC,
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36 WFPROV,
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37 )
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38 from .stdfsaccess import StdFsAccess
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39 from .utils import (
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40 CWLObjectType,
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41 CWLOutputType,
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42 JobsType,
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43 get_listing,
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44 posix_path,
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45 versionstring,
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46 )
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47 from .workflow_job import WorkflowJob
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48
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49 if TYPE_CHECKING:
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50 from .provenance import ResearchObject
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51
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52
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53 def copy_job_order(
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54 job: Union[Process, JobsType], job_order_object: CWLObjectType
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55 ) -> CWLObjectType:
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56 """Create copy of job object for provenance."""
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57 if not isinstance(job, WorkflowJob):
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58 # direct command line tool execution
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59 return job_order_object
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60 customised_job = {} # type: CWLObjectType
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61 # new job object for RO
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62 for each, i in enumerate(job.tool["inputs"]):
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63 with SourceLine(
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64 job.tool["inputs"],
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65 each,
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66 WorkflowException,
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67 _logger.isEnabledFor(logging.DEBUG),
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68 ):
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69 iid = shortname(i["id"])
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70 if iid in job_order_object:
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71 customised_job[iid] = copy.deepcopy(job_order_object[iid])
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72 # add the input element in dictionary for provenance
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73 elif "default" in i:
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74 customised_job[iid] = copy.deepcopy(i["default"])
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75 # add the default elements in the dictionary for provenance
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76 else:
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77 pass
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78 return customised_job
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79
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80
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81 class ProvenanceProfile:
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82 """
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83 Provenance profile.
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84
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85 Populated as the workflow runs.
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86 """
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87
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88 def __init__(
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89 self,
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90 research_object: "ResearchObject",
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91 full_name: str,
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92 host_provenance: bool,
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93 user_provenance: bool,
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94 orcid: str,
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95 fsaccess: StdFsAccess,
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96 run_uuid: Optional[uuid.UUID] = None,
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97 ) -> None:
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98 """Initialize the provenance profile."""
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99 self.fsaccess = fsaccess
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100 self.orcid = orcid
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101 self.research_object = research_object
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102 self.folder = self.research_object.folder
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103 self.document = ProvDocument()
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104 self.host_provenance = host_provenance
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105 self.user_provenance = user_provenance
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106 self.engine_uuid = research_object.engine_uuid # type: str
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107 self.add_to_manifest = self.research_object.add_to_manifest
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108 if self.orcid:
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109 _logger.debug("[provenance] Creator ORCID: %s", self.orcid)
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110 self.full_name = full_name
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111 if self.full_name:
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112 _logger.debug("[provenance] Creator Full name: %s", self.full_name)
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113 self.workflow_run_uuid = run_uuid or uuid.uuid4()
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114 self.workflow_run_uri = self.workflow_run_uuid.urn # type: str
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115 self.generate_prov_doc()
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116
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117 def __str__(self) -> str:
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118 """Represent this Provenvance profile as a string."""
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119 return "ProvenanceProfile <{}> in <{}>".format(
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120 self.workflow_run_uri,
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121 self.research_object,
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122 )
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123
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124 def generate_prov_doc(self) -> Tuple[str, ProvDocument]:
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125 """Add basic namespaces."""
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126
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127 def host_provenance(document: ProvDocument) -> None:
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128 """Record host provenance."""
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129 document.add_namespace(CWLPROV)
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130 document.add_namespace(UUID)
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131 document.add_namespace(FOAF)
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132
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133 hostname = getfqdn()
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134 # won't have a foaf:accountServiceHomepage for unix hosts, but
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135 # we can at least provide hostname
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136 document.agent(
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137 ACCOUNT_UUID,
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138 {
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139 PROV_TYPE: FOAF["OnlineAccount"],
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140 "prov:location": hostname,
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141 CWLPROV["hostname"]: hostname,
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142 },
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143 )
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144
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145 self.cwltool_version = "cwltool %s" % versionstring().split()[-1]
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146 self.document.add_namespace("wfprov", "http://purl.org/wf4ever/wfprov#")
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147 # document.add_namespace('prov', 'http://www.w3.org/ns/prov#')
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148 self.document.add_namespace("wfdesc", "http://purl.org/wf4ever/wfdesc#")
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149 # TODO: Make this ontology. For now only has cwlprov:image
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150 self.document.add_namespace("cwlprov", "https://w3id.org/cwl/prov#")
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151 self.document.add_namespace("foaf", "http://xmlns.com/foaf/0.1/")
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152 self.document.add_namespace("schema", "http://schema.org/")
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153 self.document.add_namespace("orcid", "https://orcid.org/")
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154 self.document.add_namespace("id", "urn:uuid:")
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155 # NOTE: Internet draft expired 2004-03-04 (!)
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156 # https://tools.ietf.org/html/draft-thiemann-hash-urn-01
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157 # TODO: Change to nih:sha-256; hashes
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158 # https://tools.ietf.org/html/rfc6920#section-7
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159 self.document.add_namespace("data", "urn:hash::sha1:")
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160 # Also needed for docker images
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161 self.document.add_namespace(SHA256, "nih:sha-256;")
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162
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163 # info only, won't really be used by prov as sub-resources use /
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164 self.document.add_namespace("researchobject", self.research_object.base_uri)
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165 # annotations
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166 self.metadata_ns = self.document.add_namespace(
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167 "metadata", self.research_object.base_uri + METADATA + "/"
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168 )
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169 # Pre-register provenance directory so we can refer to its files
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170 self.provenance_ns = self.document.add_namespace(
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171 "provenance", self.research_object.base_uri + posix_path(PROVENANCE) + "/"
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172 )
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173 ro_identifier_workflow = self.research_object.base_uri + "workflow/packed.cwl#"
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174 self.wf_ns = self.document.add_namespace("wf", ro_identifier_workflow)
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175 ro_identifier_input = (
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176 self.research_object.base_uri + "workflow/primary-job.json#"
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177 )
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178 self.document.add_namespace("input", ro_identifier_input)
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179
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180 # More info about the account (e.g. username, fullname)
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181 # may or may not have been previously logged by user_provenance()
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182 # .. but we always know cwltool was launched (directly or indirectly)
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183 # by a user account, as cwltool is a command line tool
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184 account = self.document.agent(ACCOUNT_UUID)
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185 if self.orcid or self.full_name:
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186 person = {PROV_TYPE: PROV["Person"], "prov:type": SCHEMA["Person"]}
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187 if self.full_name:
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188 person["prov:label"] = self.full_name
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189 person["foaf:name"] = self.full_name
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190 person["schema:name"] = self.full_name
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191 else:
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192 # TODO: Look up name from ORCID API?
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193 pass
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194 agent = self.document.agent(self.orcid or uuid.uuid4().urn, person)
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195 self.document.actedOnBehalfOf(account, agent)
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196 else:
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197 if self.host_provenance:
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198 host_provenance(self.document)
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199 if self.user_provenance:
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200 self.research_object.user_provenance(self.document)
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201 # The execution of cwltool
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202 wfengine = self.document.agent(
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203 self.engine_uuid,
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204 {
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205 PROV_TYPE: PROV["SoftwareAgent"],
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206 "prov:type": WFPROV["WorkflowEngine"],
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207 "prov:label": self.cwltool_version,
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208 },
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209 )
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210 # FIXME: This datetime will be a bit too delayed, we should
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211 # capture when cwltool.py earliest started?
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212 self.document.wasStartedBy(wfengine, None, account, datetime.datetime.now())
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213 # define workflow run level activity
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214 self.document.activity(
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215 self.workflow_run_uri,
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216 datetime.datetime.now(),
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217 None,
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218 {
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219 PROV_TYPE: WFPROV["WorkflowRun"],
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220 "prov:label": "Run of workflow/packed.cwl#main",
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221 },
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222 )
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223 # association between SoftwareAgent and WorkflowRun
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224 main_workflow = "wf:main"
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225 self.document.wasAssociatedWith(
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226 self.workflow_run_uri, self.engine_uuid, main_workflow
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227 )
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228 self.document.wasStartedBy(
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229 self.workflow_run_uri, None, self.engine_uuid, datetime.datetime.now()
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230 )
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231 return (self.workflow_run_uri, self.document)
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232
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233 def evaluate(
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234 self,
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235 process: Process,
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236 job: JobsType,
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237 job_order_object: CWLObjectType,
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238 research_obj: "ResearchObject",
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239 ) -> None:
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240 """Evaluate the nature of job."""
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241 if not hasattr(process, "steps"):
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242 # record provenance of independent commandline tool executions
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243 self.prospective_prov(job)
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244 customised_job = copy_job_order(job, job_order_object)
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245 self.used_artefacts(customised_job, self.workflow_run_uri)
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246 research_obj.create_job(customised_job)
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247 elif hasattr(job, "workflow"):
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248 # record provenance of workflow executions
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249 self.prospective_prov(job)
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250 customised_job = copy_job_order(job, job_order_object)
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251 self.used_artefacts(customised_job, self.workflow_run_uri)
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252
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253 def record_process_start(
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254 self, process: Process, job: JobsType, process_run_id: Optional[str] = None
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255 ) -> Optional[str]:
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256 if not hasattr(process, "steps"):
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257 process_run_id = self.workflow_run_uri
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258 elif not hasattr(job, "workflow"):
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259 # commandline tool execution as part of workflow
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260 name = ""
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261 if isinstance(job, (CommandLineJob, JobBase, WorkflowJob)):
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262 name = job.name
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263 process_name = urllib.parse.quote(name, safe=":/,#")
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264 process_run_id = self.start_process(process_name, datetime.datetime.now())
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265 return process_run_id
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266
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267 def start_process(
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268 self,
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269 process_name: str,
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270 when: datetime.datetime,
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271 process_run_id: Optional[str] = None,
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272 ) -> str:
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273 """Record the start of each Process."""
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274 if process_run_id is None:
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275 process_run_id = uuid.uuid4().urn
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276 prov_label = "Run of workflow/packed.cwl#main/" + process_name
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277 self.document.activity(
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278 process_run_id,
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279 None,
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280 None,
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281 {PROV_TYPE: WFPROV["ProcessRun"], PROV_LABEL: prov_label},
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282 )
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283 self.document.wasAssociatedWith(
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284 process_run_id, self.engine_uuid, str("wf:main/" + process_name)
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285 )
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286 self.document.wasStartedBy(
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287 process_run_id, None, self.workflow_run_uri, when, None, None
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288 )
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289 return process_run_id
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290
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291 def record_process_end(
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292 self,
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293 process_name: str,
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294 process_run_id: str,
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295 outputs: Union[CWLObjectType, MutableSequence[CWLObjectType], None],
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296 when: datetime.datetime,
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297 ) -> None:
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298 self.generate_output_prov(outputs, process_run_id, process_name)
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299 self.document.wasEndedBy(process_run_id, None, self.workflow_run_uri, when)
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300
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301 def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, str]:
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302 if value["class"] != "File":
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303 raise ValueError("Must have class:File: %s" % value)
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304 # Need to determine file hash aka RO filename
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305 entity = None # type: Optional[ProvEntity]
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306 checksum = None
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307 if "checksum" in value:
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308 csum = cast(str, value["checksum"])
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309 (method, checksum) = csum.split("$", 1)
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310 if method == SHA1 and self.research_object.has_data_file(checksum):
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311 entity = self.document.entity("data:" + checksum)
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312
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313 if not entity and "location" in value:
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314 location = str(value["location"])
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315 # If we made it here, we'll have to add it to the RO
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316 with self.fsaccess.open(location, "rb") as fhandle:
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317 relative_path = self.research_object.add_data_file(fhandle)
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318 # FIXME: This naively relies on add_data_file setting hash as filename
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319 checksum = PurePath(relative_path).name
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320 entity = self.document.entity(
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321 "data:" + checksum, {PROV_TYPE: WFPROV["Artifact"]}
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322 )
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323 if "checksum" not in value:
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324 value["checksum"] = f"{SHA1}${checksum}"
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325
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326 if not entity and "contents" in value:
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327 # Anonymous file, add content as string
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328 entity, checksum = self.declare_string(cast(str, value["contents"]))
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329
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330 # By here one of them should have worked!
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331 if not entity or not checksum:
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332 raise ValueError(
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333 "class:File but missing checksum/location/content: %r" % value
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334 )
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335
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336 # Track filename and extension, this is generally useful only for
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337 # secondaryFiles. Note that multiple uses of a file might thus record
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338 # different names for the same entity, so we'll
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339 # make/track a specialized entity by UUID
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340 file_id = value.setdefault("@id", uuid.uuid4().urn)
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341 # A specialized entity that has just these names
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342 file_entity = self.document.entity(
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343 file_id,
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344 [(PROV_TYPE, WFPROV["Artifact"]), (PROV_TYPE, WF4EVER["File"])],
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345 ) # type: ProvEntity
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346
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347 if "basename" in value:
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348 file_entity.add_attributes({CWLPROV["basename"]: value["basename"]})
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349 if "nameroot" in value:
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350 file_entity.add_attributes({CWLPROV["nameroot"]: value["nameroot"]})
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351 if "nameext" in value:
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352 file_entity.add_attributes({CWLPROV["nameext"]: value["nameext"]})
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353 self.document.specializationOf(file_entity, entity)
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354
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355 # Check for secondaries
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356 for sec in cast(
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357 MutableSequence[CWLObjectType], value.get("secondaryFiles", [])
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358 ):
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359 # TODO: Record these in a specializationOf entity with UUID?
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360 if sec["class"] == "File":
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361 (sec_entity, _, _) = self.declare_file(sec)
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362 elif sec["class"] == "Directory":
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363 sec_entity = self.declare_directory(sec)
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364 else:
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365 raise ValueError(f"Got unexpected secondaryFiles value: {sec}")
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366 # We don't know how/when/where the secondary file was generated,
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367 # but CWL convention is a kind of summary/index derived
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368 # from the original file. As its generally in a different format
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369 # then prov:Quotation is not appropriate.
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370 self.document.derivation(
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371 sec_entity,
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372 file_entity,
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373 other_attributes={PROV["type"]: CWLPROV["SecondaryFile"]},
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374 )
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375
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376 return file_entity, entity, checksum
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377
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378 def declare_directory(self, value: CWLObjectType) -> ProvEntity:
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379 """Register any nested files/directories."""
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diff changeset
380 # FIXME: Calculate a hash-like identifier for directory
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diff changeset
381 # so we get same value if it's the same filenames/hashes
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diff changeset
382 # in a different location.
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383 # For now, mint a new UUID to identify this directory, but
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384 # attempt to keep it inside the value dictionary
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385 dir_id = cast(str, value.setdefault("@id", uuid.uuid4().urn))
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386
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387 # New annotation file to keep the ORE Folder listing
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388 ore_doc_fn = dir_id.replace("urn:uuid:", "directory-") + ".ttl"
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389 dir_bundle = self.document.bundle(self.metadata_ns[ore_doc_fn])
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390
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391 coll = self.document.entity(
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392 dir_id,
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393 [
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394 (PROV_TYPE, WFPROV["Artifact"]),
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395 (PROV_TYPE, PROV["Collection"]),
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396 (PROV_TYPE, PROV["Dictionary"]),
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397 (PROV_TYPE, RO["Folder"]),
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398 ],
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399 )
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400 # ORE description of ro:Folder, saved separately
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401 coll_b = dir_bundle.entity(
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402 dir_id,
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403 [(PROV_TYPE, RO["Folder"]), (PROV_TYPE, ORE["Aggregation"])],
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404 )
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405 self.document.mentionOf(dir_id + "#ore", dir_id, dir_bundle.identifier)
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406
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407 # dir_manifest = dir_bundle.entity(
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408 # dir_bundle.identifier, {PROV["type"]: ORE["ResourceMap"],
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409 # ORE["describes"]: coll_b.identifier})
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410
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411 coll_attribs = [(ORE["isDescribedBy"], dir_bundle.identifier)]
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412 coll_b_attribs = [] # type: List[Tuple[Identifier, ProvEntity]]
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413
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414 # FIXME: .listing might not be populated yet - hopefully
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415 # a later call to this method will sort that
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416 is_empty = True
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417
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418 if "listing" not in value:
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419 get_listing(self.fsaccess, value)
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420 for entry in cast(MutableSequence[CWLObjectType], value.get("listing", [])):
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421 is_empty = False
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422 # Declare child-artifacts
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423 entity = self.declare_artefact(entry)
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424 self.document.membership(coll, entity)
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425 # Membership relation aka our ORE Proxy
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426 m_id = uuid.uuid4().urn
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427 m_entity = self.document.entity(m_id)
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428 m_b = dir_bundle.entity(m_id)
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429
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430 # PROV-O style Dictionary
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431 # https://www.w3.org/TR/prov-dictionary/#dictionary-ontological-definition
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432 # ..as prov.py do not currently allow PROV-N extensions
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433 # like hadDictionaryMember(..)
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434 m_entity.add_asserted_type(PROV["KeyEntityPair"])
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435
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436 m_entity.add_attributes(
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437 {
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438 PROV["pairKey"]: entry["basename"],
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439 PROV["pairEntity"]: entity,
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440 }
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441 )
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442
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443 # As well as a being a
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444 # http://wf4ever.github.io/ro/2016-01-28/ro/#FolderEntry
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445 m_b.add_asserted_type(RO["FolderEntry"])
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446 m_b.add_asserted_type(ORE["Proxy"])
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447 m_b.add_attributes(
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448 {
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449 RO["entryName"]: entry["basename"],
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450 ORE["proxyIn"]: coll,
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451 ORE["proxyFor"]: entity,
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452 }
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453 )
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454 coll_attribs.append((PROV["hadDictionaryMember"], m_entity))
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455 coll_b_attribs.append((ORE["aggregates"], m_b))
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456
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457 coll.add_attributes(coll_attribs)
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458 coll_b.add_attributes(coll_b_attribs)
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459
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460 # Also Save ORE Folder as annotation metadata
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461 ore_doc = ProvDocument()
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462 ore_doc.add_namespace(ORE)
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463 ore_doc.add_namespace(RO)
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464 ore_doc.add_namespace(UUID)
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465 ore_doc.add_bundle(dir_bundle)
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466 ore_doc = ore_doc.flattened()
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467 ore_doc_path = str(PurePosixPath(METADATA, ore_doc_fn))
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468 with self.research_object.write_bag_file(ore_doc_path) as provenance_file:
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469 ore_doc.serialize(provenance_file, format="rdf", rdf_format="turtle")
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470 self.research_object.add_annotation(
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471 dir_id, [ore_doc_fn], ORE["isDescribedBy"].uri
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472 )
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473
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474 if is_empty:
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475 # Empty directory
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476 coll.add_asserted_type(PROV["EmptyCollection"])
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477 coll.add_asserted_type(PROV["EmptyDictionary"])
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478 self.research_object.add_uri(coll.identifier.uri)
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479 return coll
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480
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481 def declare_string(self, value: str) -> Tuple[ProvEntity, str]:
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482 """Save as string in UTF-8."""
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483 byte_s = BytesIO(str(value).encode(ENCODING))
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484 data_file = self.research_object.add_data_file(byte_s, content_type=TEXT_PLAIN)
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485 checksum = PurePosixPath(data_file).name
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486 # FIXME: Don't naively assume add_data_file uses hash in filename!
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487 data_id = "data:%s" % PurePosixPath(data_file).stem
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488 entity = self.document.entity(
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489 data_id, {PROV_TYPE: WFPROV["Artifact"], PROV_VALUE: str(value)}
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490 ) # type: ProvEntity
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491 return entity, checksum
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492
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493 def declare_artefact(self, value: Optional[CWLOutputType]) -> ProvEntity:
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parents:
diff changeset
494 """Create data artefact entities for all file objects."""
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parents:
diff changeset
495 if value is None:
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parents:
diff changeset
496 # FIXME: If this can happen in CWL, we'll
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
497 # need a better way to represent this in PROV
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parents:
diff changeset
498 return self.document.entity(CWLPROV["None"], {PROV_LABEL: "None"})
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shellac
parents:
diff changeset
499
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parents:
diff changeset
500 if isinstance(value, (bool, int, float)):
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shellac
parents:
diff changeset
501 # Typically used in job documents for flags
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shellac
parents:
diff changeset
502
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shellac
parents:
diff changeset
503 # FIXME: Make consistent hash URIs for these
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shellac
parents:
diff changeset
504 # that somehow include the type
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shellac
parents:
diff changeset
505 # (so "1" != 1 != "1.0" != true)
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parents:
diff changeset
506 entity = self.document.entity(uuid.uuid4().urn, {PROV_VALUE: value})
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parents:
diff changeset
507 self.research_object.add_uri(entity.identifier.uri)
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parents:
diff changeset
508 return entity
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parents:
diff changeset
509
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parents:
diff changeset
510 if isinstance(value, (str, str)):
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shellac
parents:
diff changeset
511 (entity, _) = self.declare_string(value)
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parents:
diff changeset
512 return entity
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parents:
diff changeset
513
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parents:
diff changeset
514 if isinstance(value, bytes):
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parents:
diff changeset
515 # If we got here then we must be in Python 3
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parents:
diff changeset
516 byte_s = BytesIO(value)
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parents:
diff changeset
517 data_file = self.research_object.add_data_file(byte_s)
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shellac
parents:
diff changeset
518 # FIXME: Don't naively assume add_data_file uses hash in filename!
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shellac
parents:
diff changeset
519 data_id = "data:%s" % PurePosixPath(data_file).stem
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parents:
diff changeset
520 return self.document.entity(
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parents:
diff changeset
521 data_id,
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parents:
diff changeset
522 {PROV_TYPE: WFPROV["Artifact"], PROV_VALUE: str(value)},
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
523 )
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parents:
diff changeset
524
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parents:
diff changeset
525 if isinstance(value, MutableMapping):
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parents:
diff changeset
526 if "@id" in value:
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parents:
diff changeset
527 # Already processed this value, but it might not be in this PROV
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shellac
parents:
diff changeset
528 entities = self.document.get_record(value["@id"])
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shellac
parents:
diff changeset
529 if entities:
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shellac
parents:
diff changeset
530 return entities[0]
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shellac
parents:
diff changeset
531 # else, unknown in PROV, re-add below as if it's fresh
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shellac
parents:
diff changeset
532
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shellac
parents:
diff changeset
533 # Base case - we found a File we need to update
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
534 if value.get("class") == "File":
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shellac
parents:
diff changeset
535 (entity, _, _) = self.declare_file(value)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
536 value["@id"] = entity.identifier.uri
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
537 return entity
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shellac
parents:
diff changeset
538
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
539 if value.get("class") == "Directory":
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shellac
parents:
diff changeset
540 entity = self.declare_directory(value)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
541 value["@id"] = entity.identifier.uri
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shellac
parents:
diff changeset
542 return entity
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shellac
parents:
diff changeset
543 coll_id = value.setdefault("@id", uuid.uuid4().urn)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
544 # some other kind of dictionary?
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
545 # TODO: also Save as JSON
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
546 coll = self.document.entity(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
547 coll_id,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
548 [
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
549 (PROV_TYPE, WFPROV["Artifact"]),
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shellac
parents:
diff changeset
550 (PROV_TYPE, PROV["Collection"]),
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shellac
parents:
diff changeset
551 (PROV_TYPE, PROV["Dictionary"]),
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parents:
diff changeset
552 ],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
553 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
554
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
555 if value.get("class"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
556 _logger.warning("Unknown data class %s.", value["class"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
557 # FIXME: The class might be "http://example.com/somethingelse"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
558 coll.add_asserted_type(CWLPROV[value["class"]])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
559
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
560 # Let's iterate and recurse
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
561 coll_attribs = [] # type: List[Tuple[Identifier, ProvEntity]]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
562 for (key, val) in value.items():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
563 v_ent = self.declare_artefact(val)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
564 self.document.membership(coll, v_ent)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
565 m_entity = self.document.entity(uuid.uuid4().urn)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
566 # Note: only support PROV-O style dictionary
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
567 # https://www.w3.org/TR/prov-dictionary/#dictionary-ontological-definition
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
568 # as prov.py do not easily allow PROV-N extensions
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
569 m_entity.add_asserted_type(PROV["KeyEntityPair"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
570 m_entity.add_attributes(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
571 {PROV["pairKey"]: str(key), PROV["pairEntity"]: v_ent}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
572 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
573 coll_attribs.append((PROV["hadDictionaryMember"], m_entity))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
574 coll.add_attributes(coll_attribs)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
575 self.research_object.add_uri(coll.identifier.uri)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
576 return coll
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
577
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
578 # some other kind of Collection?
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
579 # TODO: also save as JSON
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
580 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
581 members = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
582 for each_input_obj in iter(value):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
583 # Recurse and register any nested objects
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
584 e = self.declare_artefact(each_input_obj)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
585 members.append(e)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
586
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
587 # If we reached this, then we were allowed to iterate
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
588 coll = self.document.entity(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
589 uuid.uuid4().urn,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
590 [
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
591 (PROV_TYPE, WFPROV["Artifact"]),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
592 (PROV_TYPE, PROV["Collection"]),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
593 ],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
594 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
595 if not members:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
596 coll.add_asserted_type(PROV["EmptyCollection"])
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shellac
parents:
diff changeset
597 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
598 for member in members:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
599 # FIXME: This won't preserve order, for that
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
600 # we would need to use PROV.Dictionary
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
601 # with numeric keys
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
602 self.document.membership(coll, member)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
603 self.research_object.add_uri(coll.identifier.uri)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
604 # FIXME: list value does not support adding "@id"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
605 return coll
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
606 except TypeError:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
607 _logger.warning("Unrecognized type %s of %r", type(value), value)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
608 # Let's just fall back to Python repr()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
609 entity = self.document.entity(uuid.uuid4().urn, {PROV_LABEL: repr(value)})
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
610 self.research_object.add_uri(entity.identifier.uri)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
611 return entity
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
612
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
613 def used_artefacts(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
614 self,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
615 job_order: Union[CWLObjectType, List[CWLObjectType]],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
616 process_run_id: str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
617 name: Optional[str] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
618 ) -> None:
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shellac
parents:
diff changeset
619 """Add used() for each data artefact."""
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parents:
diff changeset
620 if isinstance(job_order, list):
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parents:
diff changeset
621 for entry in job_order:
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parents:
diff changeset
622 self.used_artefacts(entry, process_run_id, name)
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parents:
diff changeset
623 else:
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parents:
diff changeset
624 # FIXME: Use workflow name in packed.cwl, "main" is wrong for nested workflows
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parents:
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625 base = "main"
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parents:
diff changeset
626 if name is not None:
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parents:
diff changeset
627 base += "/" + name
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parents:
diff changeset
628 for key, value in job_order.items():
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parents:
diff changeset
629 prov_role = self.wf_ns[f"{base}/{key}"]
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parents:
diff changeset
630 try:
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parents:
diff changeset
631 entity = self.declare_artefact(value)
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parents:
diff changeset
632 self.document.used(
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parents:
diff changeset
633 process_run_id,
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parents:
diff changeset
634 entity,
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parents:
diff changeset
635 datetime.datetime.now(),
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diff changeset
636 None,
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parents:
diff changeset
637 {"prov:role": prov_role},
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parents:
diff changeset
638 )
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parents:
diff changeset
639 except OSError:
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parents:
diff changeset
640 pass
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641
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parents:
diff changeset
642 def generate_output_prov(
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parents:
diff changeset
643 self,
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644 final_output: Union[CWLObjectType, MutableSequence[CWLObjectType], None],
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645 process_run_id: Optional[str],
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parents:
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646 name: Optional[str],
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parents:
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647 ) -> None:
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parents:
diff changeset
648 """Call wasGeneratedBy() for each output,copy the files into the RO."""
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parents:
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649 if isinstance(final_output, MutableSequence):
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parents:
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650 for entry in final_output:
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parents:
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651 self.generate_output_prov(entry, process_run_id, name)
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parents:
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652 elif final_output is not None:
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parents:
diff changeset
653 # Timestamp should be created at the earliest
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parents:
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654 timestamp = datetime.datetime.now()
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parents:
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655
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parents:
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656 # For each output, find/register the corresponding
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657 # entity (UUID) and document it as generated in
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parents:
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658 # a role corresponding to the output
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parents:
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659 for output, value in final_output.items():
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parents:
diff changeset
660 entity = self.declare_artefact(value)
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parents:
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661 if name is not None:
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parents:
diff changeset
662 name = urllib.parse.quote(str(name), safe=":/,#")
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parents:
diff changeset
663 # FIXME: Probably not "main" in nested workflows
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parents:
diff changeset
664 role = self.wf_ns[f"main/{name}/{output}"]
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parents:
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665 else:
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666 role = self.wf_ns["main/%s" % output]
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667
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parents:
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668 if not process_run_id:
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parents:
diff changeset
669 process_run_id = self.workflow_run_uri
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670
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diff changeset
671 self.document.wasGeneratedBy(
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diff changeset
672 entity, process_run_id, timestamp, None, {"prov:role": role}
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673 )
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674
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675 def prospective_prov(self, job: JobsType) -> None:
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diff changeset
676 """Create prospective prov recording as wfdesc prov:Plan."""
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parents:
diff changeset
677 if not isinstance(job, WorkflowJob):
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diff changeset
678 # direct command line tool execution
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diff changeset
679 self.document.entity(
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parents:
diff changeset
680 "wf:main",
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diff changeset
681 {
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diff changeset
682 PROV_TYPE: WFDESC["Process"],
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parents:
diff changeset
683 "prov:type": PROV["Plan"],
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diff changeset
684 "prov:label": "Prospective provenance",
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diff changeset
685 },
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parents:
diff changeset
686 )
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parents:
diff changeset
687 return
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diff changeset
688
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diff changeset
689 self.document.entity(
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parents:
diff changeset
690 "wf:main",
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parents:
diff changeset
691 {
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diff changeset
692 PROV_TYPE: WFDESC["Workflow"],
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parents:
diff changeset
693 "prov:type": PROV["Plan"],
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parents:
diff changeset
694 "prov:label": "Prospective provenance",
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parents:
diff changeset
695 },
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parents:
diff changeset
696 )
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parents:
diff changeset
697
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parents:
diff changeset
698 for step in job.steps:
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parents:
diff changeset
699 stepnametemp = "wf:main/" + str(step.name)[5:]
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parents:
diff changeset
700 stepname = urllib.parse.quote(stepnametemp, safe=":/,#")
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parents:
diff changeset
701 provstep = self.document.entity(
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parents:
diff changeset
702 stepname,
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parents:
diff changeset
703 {PROV_TYPE: WFDESC["Process"], "prov:type": PROV["Plan"]},
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parents:
diff changeset
704 )
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parents:
diff changeset
705 self.document.entity(
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parents:
diff changeset
706 "wf:main",
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parents:
diff changeset
707 {
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parents:
diff changeset
708 "wfdesc:hasSubProcess": provstep,
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parents:
diff changeset
709 "prov:label": "Prospective provenance",
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parents:
diff changeset
710 },
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parents:
diff changeset
711 )
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parents:
diff changeset
712 # TODO: Declare roles/parameters as well
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parents:
diff changeset
713
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parents:
diff changeset
714 def activity_has_provenance(self, activity, prov_ids):
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shellac
parents:
diff changeset
715 # type: (str, List[Identifier]) -> None
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parents:
diff changeset
716 """Add http://www.w3.org/TR/prov-aq/ relations to nested PROV files."""
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parents:
diff changeset
717 # NOTE: The below will only work if the corresponding metadata/provenance arcp URI
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parents:
diff changeset
718 # is a pre-registered namespace in the PROV Document
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
719 attribs = [(PROV["has_provenance"], prov_id) for prov_id in prov_ids]
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shellac
parents:
diff changeset
720 self.document.activity(activity, other_attributes=attribs)
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shellac
parents:
diff changeset
721 # Tip: we can't use https://www.w3.org/TR/prov-links/#term-mention
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shellac
parents:
diff changeset
722 # as prov:mentionOf() is only for entities, not activities
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
723 uris = [i.uri for i in prov_ids]
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shellac
parents:
diff changeset
724 self.research_object.add_annotation(activity, uris, PROV["has_provenance"].uri)
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parents:
diff changeset
725
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parents:
diff changeset
726 def finalize_prov_profile(self, name):
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parents:
diff changeset
727 # type: (Optional[str]) -> List[Identifier]
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parents:
diff changeset
728 """Transfer the provenance related files to the RO."""
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parents:
diff changeset
729 # NOTE: Relative posix path
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parents:
diff changeset
730 if name is None:
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parents:
diff changeset
731 # main workflow, fixed filenames
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parents:
diff changeset
732 filename = "primary.cwlprov"
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parents:
diff changeset
733 else:
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parents:
diff changeset
734 # ASCII-friendly filename, avoiding % as we don't want %2520 in manifest.json
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parents:
diff changeset
735 wf_name = urllib.parse.quote(str(name), safe="").replace("%", "_")
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parents:
diff changeset
736 # Note that the above could cause overlaps for similarly named
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parents:
diff changeset
737 # workflows, but that's OK as we'll also include run uuid
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parents:
diff changeset
738 # which also covers thhe case of this step being run in
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parents:
diff changeset
739 # multiple places or iterations
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parents:
diff changeset
740 filename = f"{wf_name}.{self.workflow_run_uuid}.cwlprov"
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parents:
diff changeset
741
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parents:
diff changeset
742 basename = str(PurePosixPath(PROVENANCE) / filename)
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parents:
diff changeset
743
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shellac
parents:
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744 # TODO: Also support other profiles than CWLProv, e.g. ProvOne
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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745
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parents:
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746 # list of prov identifiers of provenance files
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shellac
parents:
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747 prov_ids = []
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parents:
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748
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shellac
parents:
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749 # https://www.w3.org/TR/prov-xml/
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shellac
parents:
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750 with self.research_object.write_bag_file(basename + ".xml") as provenance_file:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
751 self.document.serialize(provenance_file, format="xml", indent=4)
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shellac
parents:
diff changeset
752 prov_ids.append(self.provenance_ns[filename + ".xml"])
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parents:
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753
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shellac
parents:
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754 # https://www.w3.org/TR/prov-n/
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shellac
parents:
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755 with self.research_object.write_bag_file(
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parents:
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756 basename + ".provn"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
757 ) as provenance_file:
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shellac
parents:
diff changeset
758 self.document.serialize(provenance_file, format="provn", indent=2)
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shellac
parents:
diff changeset
759 prov_ids.append(self.provenance_ns[filename + ".provn"])
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shellac
parents:
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760
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shellac
parents:
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761 # https://www.w3.org/Submission/prov-json/
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shellac
parents:
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762 with self.research_object.write_bag_file(basename + ".json") as provenance_file:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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763 self.document.serialize(provenance_file, format="json", indent=2)
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shellac
parents:
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764 prov_ids.append(self.provenance_ns[filename + ".json"])
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765
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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766 # "rdf" aka https://www.w3.org/TR/prov-o/
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shellac
parents:
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767 # which can be serialized to ttl/nt/jsonld (and more!)
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shellac
parents:
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768
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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769 # https://www.w3.org/TR/turtle/
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shellac
parents:
diff changeset
770 with self.research_object.write_bag_file(basename + ".ttl") as provenance_file:
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shellac
parents:
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771 self.document.serialize(provenance_file, format="rdf", rdf_format="turtle")
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shellac
parents:
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772 prov_ids.append(self.provenance_ns[filename + ".ttl"])
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shellac
parents:
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773
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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774 # https://www.w3.org/TR/n-triples/
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shellac
parents:
diff changeset
775 with self.research_object.write_bag_file(basename + ".nt") as provenance_file:
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shellac
parents:
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776 self.document.serialize(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
777 provenance_file, format="rdf", rdf_format="ntriples"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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778 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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779 prov_ids.append(self.provenance_ns[filename + ".nt"])
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parents:
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780
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shellac
parents:
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781 # https://www.w3.org/TR/json-ld/
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shellac
parents:
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782 # TODO: Use a nice JSON-LD context
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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783 # see also https://eprints.soton.ac.uk/395985/
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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784 # 404 Not Found on https://provenance.ecs.soton.ac.uk/prov.jsonld :(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
785 with self.research_object.write_bag_file(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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786 basename + ".jsonld"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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787 ) as provenance_file:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
788 self.document.serialize(provenance_file, format="rdf", rdf_format="json-ld")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
789 prov_ids.append(self.provenance_ns[filename + ".jsonld"])
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shellac
parents:
diff changeset
790
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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791 _logger.debug("[provenance] added provenance: %s", prov_ids)
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shellac
parents:
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792 return prov_ids