| 1 |
26772
|
marek.hors
|
<workflow-app xmlns="uri:oozie:workflow:0.4" name="mainworkflows_primary_processing">
|
| 2 |
20569
|
marek.hors
|
|
| 3 |
|
|
<parameters>
|
| 4 |
35057
|
marek.hors
|
<property>
|
| 5 |
|
|
<name>remove_sideproducts</name>
|
| 6 |
|
|
<value>true</value>
|
| 7 |
|
|
<description>flag indicating inference side products will be erased</description>
|
| 8 |
|
|
</property>
|
| 9 |
23440
|
marek.hors
|
<!-- processing modes -->
|
| 10 |
20569
|
marek.hors
|
<property>
|
| 11 |
23558
|
marek.hors
|
<name>active_referenceextraction_project</name>
|
| 12 |
23446
|
marek.hors
|
<value>true</value>
|
| 13 |
|
|
<description>flag indicating project reference extraction should be enabled</description>
|
| 14 |
|
|
</property>
|
| 15 |
|
|
<property>
|
| 16 |
23558
|
marek.hors
|
<name>active_referenceextraction_dataset</name>
|
| 17 |
23446
|
marek.hors
|
<value>true</value>
|
| 18 |
|
|
<description>flag indicating dataset reference extraction should be enabled</description>
|
| 19 |
|
|
</property>
|
| 20 |
|
|
<property>
|
| 21 |
24851
|
marek.hors
|
<!-- currently disabled by default -->
|
| 22 |
|
|
<name>active_referenceextraction_researchinitiative</name>
|
| 23 |
|
|
<value>false</value>
|
| 24 |
|
|
<description>flag indicating researchinitiative reference extraction should be enabled</description>
|
| 25 |
|
|
</property>
|
| 26 |
|
|
<property>
|
| 27 |
37432
|
marek.hors
|
<!-- currently disabled by default -->
|
| 28 |
|
|
<name>active_referenceextraction_pdb</name>
|
| 29 |
|
|
<value>false</value>
|
| 30 |
|
|
<description>flag indicating protein databank reference extraction should be enabled</description>
|
| 31 |
|
|
</property>
|
| 32 |
|
|
<property>
|
| 33 |
23558
|
marek.hors
|
<name>active_documentsclassification</name>
|
| 34 |
23446
|
marek.hors
|
<value>true</value>
|
| 35 |
|
|
<description>flag indicating documents classification should be enabled</description>
|
| 36 |
|
|
</property>
|
| 37 |
|
|
<property>
|
| 38 |
23558
|
marek.hors
|
<name>active_documentssimilarity</name>
|
| 39 |
23446
|
marek.hors
|
<value>true</value>
|
| 40 |
|
|
<description>flag indicating documents similarity should be enabled</description>
|
| 41 |
|
|
</property>
|
| 42 |
24465
|
marek.hors
|
<property>
|
| 43 |
|
|
<name>active_citationmatching</name>
|
| 44 |
|
|
<!-- currently disabled by default -->
|
| 45 |
|
|
<value>false</value>
|
| 46 |
|
|
<description>flag indicating citation matching should be enabled</description>
|
| 47 |
|
|
</property>
|
| 48 |
|
|
<property>
|
| 49 |
|
|
<name>active_statistics</name>
|
| 50 |
|
|
<!-- currently disabled by default -->
|
| 51 |
|
|
<value>false</value>
|
| 52 |
|
|
<description>flag indicating statistics generation should be enabled</description>
|
| 53 |
|
|
</property>
|
| 54 |
23446
|
marek.hors
|
<!-- input ports -->
|
| 55 |
|
|
<property>
|
| 56 |
20569
|
marek.hors
|
<name>input_document_metadata</name>
|
| 57 |
|
|
<description>input document metadata directory</description>
|
| 58 |
|
|
</property>
|
| 59 |
|
|
<property>
|
| 60 |
27488
|
marek.hors
|
<name>input_document_to_project</name>
|
| 61 |
|
|
<description>input document to project relation directory</description>
|
| 62 |
|
|
</property>
|
| 63 |
|
|
<property>
|
| 64 |
23418
|
marek.hors
|
<name>input_document_text</name>
|
| 65 |
|
|
<description>input document text directory</description>
|
| 66 |
|
|
</property>
|
| 67 |
|
|
<property>
|
| 68 |
29016
|
marek.hors
|
<name>input_document_text_wos</name>
|
| 69 |
|
|
<description>input document text directory holding WOS records</description>
|
| 70 |
|
|
</property>
|
| 71 |
|
|
<property>
|
| 72 |
20569
|
marek.hors
|
<name>input_project</name>
|
| 73 |
|
|
<description>input project directory</description>
|
| 74 |
|
|
</property>
|
| 75 |
|
|
<property>
|
| 76 |
|
|
<name>input_person</name>
|
| 77 |
|
|
<description>input person directory</description>
|
| 78 |
|
|
</property>
|
| 79 |
|
|
<property>
|
| 80 |
21313
|
marek.hors
|
<name>input_dataset</name>
|
| 81 |
|
|
<description>input dataset directory</description>
|
| 82 |
|
|
</property>
|
| 83 |
|
|
<property>
|
| 84 |
25563
|
marek.hors
|
<name>input_extracted_document_metadata</name>
|
| 85 |
|
|
<description>input extracted document metadata directory</description>
|
| 86 |
20664
|
marek.hors
|
</property>
|
| 87 |
|
|
<property>
|
| 88 |
28987
|
marek.hors
|
<name>input_citation_pmc</name>
|
| 89 |
|
|
<description>input directory holding citations extracted from PMC</description>
|
| 90 |
24465
|
marek.hors
|
</property>
|
| 91 |
33184
|
marek.hors
|
<property>
|
| 92 |
|
|
<name>input_project_concept</name>
|
| 93 |
|
|
<description>input project concept directory</description>
|
| 94 |
|
|
</property>
|
| 95 |
24609
|
marek.hors
|
<!-- citation matching related -->
|
| 96 |
24465
|
marek.hors
|
<property>
|
| 97 |
21313
|
marek.hors
|
<name>cit_genAuthorIdxJavaOpts</name>
|
| 98 |
|
|
<value>-Xmx8g</value>
|
| 99 |
|
|
<description>java opts for author index creation for citation purposes</description>
|
| 100 |
|
|
</property>
|
| 101 |
24609
|
marek.hors
|
<!-- document similarity related -->
|
| 102 |
|
|
<property>
|
| 103 |
|
|
<name>ds_parallel</name>
|
| 104 |
27909
|
marek.hors
|
<value>20</value>
|
| 105 |
24609
|
marek.hors
|
<description>document similarity pig parallel</description>
|
| 106 |
|
|
</property>
|
| 107 |
|
|
<property>
|
| 108 |
26161
|
marek.hors
|
<name>ds_mapredChildJavaOpts</name>
|
| 109 |
27909
|
marek.hors
|
<value>-Xmx20g</value>
|
| 110 |
26161
|
marek.hors
|
<description>mapred child java opts</description>
|
| 111 |
|
|
</property>
|
| 112 |
|
|
<property>
|
| 113 |
|
|
<name>ds_sample</name>
|
| 114 |
27551
|
marek.hors
|
<value>1.0</value>
|
| 115 |
26161
|
marek.hors
|
<description>sample rate</description>
|
| 116 |
|
|
</property>
|
| 117 |
|
|
<property>
|
| 118 |
24609
|
marek.hors
|
<name>ds_removal_rate</name>
|
| 119 |
27994
|
marek.hors
|
<value>0.99</value>
|
| 120 |
24609
|
marek.hors
|
<description>document similarity removal rate</description>
|
| 121 |
|
|
</property>
|
| 122 |
|
|
<property>
|
| 123 |
|
|
<name>ds_removal_least_used</name>
|
| 124 |
27551
|
marek.hors
|
<value>20</value>
|
| 125 |
24609
|
marek.hors
|
<description>document similarity least used removal</description>
|
| 126 |
|
|
</property>
|
| 127 |
27551
|
marek.hors
|
<property>
|
| 128 |
|
|
<name>ds_tfidfTopnTermPerDocument</name>
|
| 129 |
27994
|
marek.hors
|
<value>20</value>
|
| 130 |
27551
|
marek.hors
|
</property>
|
| 131 |
|
|
<property>
|
| 132 |
|
|
<name>ds_similarityTopnDocumentPerDocument</name>
|
| 133 |
|
|
<value>20</value>
|
| 134 |
|
|
</property>
|
| 135 |
24465
|
marek.hors
|
<!-- output ports -->
|
| 136 |
21313
|
marek.hors
|
<property>
|
| 137 |
26238
|
marek.hors
|
<name>output_document_to_project</name>
|
| 138 |
|
|
<description>project reference extraction output directory</description>
|
| 139 |
|
|
</property>
|
| 140 |
|
|
<property>
|
| 141 |
33184
|
marek.hors
|
<name>output_document_to_project_concepts</name>
|
| 142 |
|
|
<description>document to project concepts output directory</description>
|
| 143 |
|
|
</property>
|
| 144 |
|
|
<property>
|
| 145 |
26238
|
marek.hors
|
<name>output_document_to_dataset</name>
|
| 146 |
|
|
<description>dataset reference extraction output directory</description>
|
| 147 |
|
|
</property>
|
| 148 |
|
|
<property>
|
| 149 |
|
|
<name>output_document_to_research_initiatives</name>
|
| 150 |
|
|
<description>research initiatives reference extraction output directory</description>
|
| 151 |
|
|
</property>
|
| 152 |
|
|
<property>
|
| 153 |
37432
|
marek.hors
|
<name>output_document_to_pdb</name>
|
| 154 |
|
|
<description>protein databank reference extraction output directory</description>
|
| 155 |
|
|
</property>
|
| 156 |
|
|
<property>
|
| 157 |
26238
|
marek.hors
|
<name>output_document_to_document_classes</name>
|
| 158 |
|
|
<description>output document classification directory</description>
|
| 159 |
|
|
</property>
|
| 160 |
|
|
<property>
|
| 161 |
|
|
<name>output_citation</name>
|
| 162 |
29967
|
marek.hors
|
<description>output containing grouped citations coming from citation matching and pmc ingestion</description>
|
| 163 |
26238
|
marek.hors
|
</property>
|
| 164 |
|
|
<property>
|
| 165 |
20569
|
marek.hors
|
<name>output_document_similarity</name>
|
| 166 |
|
|
<description>output document similarity directory</description>
|
| 167 |
|
|
</property>
|
| 168 |
|
|
<property>
|
| 169 |
26238
|
marek.hors
|
<name>output_document_statistics</name>
|
| 170 |
|
|
<description>output document statistics directory</description>
|
| 171 |
20569
|
marek.hors
|
</property>
|
| 172 |
|
|
<property>
|
| 173 |
26238
|
marek.hors
|
<name>output_author_statistics</name>
|
| 174 |
|
|
<description>output author statistics directory</description>
|
| 175 |
20569
|
marek.hors
|
</property>
|
| 176 |
|
|
<property>
|
| 177 |
25414
|
marek.hors
|
<name>output_project_statistics</name>
|
| 178 |
|
|
<description>output project statistics directory</description>
|
| 179 |
|
|
</property>
|
| 180 |
20569
|
marek.hors
|
</parameters>
|
| 181 |
20051
|
marek.hors
|
|
| 182 |
26347
|
marek.hors
|
<global>
|
| 183 |
|
|
<job-tracker>${jobTracker}</job-tracker>
|
| 184 |
|
|
<name-node>${nameNode}</name-node>
|
| 185 |
|
|
<configuration>
|
| 186 |
|
|
<property>
|
| 187 |
|
|
<name>mapred.job.queue.name</name>
|
| 188 |
|
|
<value>${queueName}</value>
|
| 189 |
|
|
</property>
|
| 190 |
|
|
</configuration>
|
| 191 |
|
|
</global>
|
| 192 |
|
|
|
| 193 |
25563
|
marek.hors
|
<start to="forking" />
|
| 194 |
19628
|
marek.hors
|
|
| 195 |
|
|
<fork name="forking">
|
| 196 |
23446
|
marek.hors
|
<path start="decision-referenceextraction_project"/>
|
| 197 |
|
|
<path start="decision-referenceextraction_dataset"/>
|
| 198 |
24851
|
marek.hors
|
<path start="decision-referenceextraction_researchinitiative"/>
|
| 199 |
37432
|
marek.hors
|
<path start="decision-referenceextraction_pdb"/>
|
| 200 |
19628
|
marek.hors
|
<path start="transformers_metadatamerger"/>
|
| 201 |
|
|
</fork>
|
| 202 |
|
|
|
| 203 |
23446
|
marek.hors
|
<!-- start of project reference extraction block -->
|
| 204 |
|
|
<decision name="decision-referenceextraction_project">
|
| 205 |
|
|
<switch>
|
| 206 |
23861
|
marek.hors
|
<case to="referenceextraction_project">${active_referenceextraction_project eq "true"}</case>
|
| 207 |
23525
|
marek.hors
|
<default to="skip-referenceextraction_project"/>
|
| 208 |
23446
|
marek.hors
|
</switch>
|
| 209 |
|
|
</decision>
|
| 210 |
|
|
|
| 211 |
19980
|
marek.hors
|
<action name="referenceextraction_project">
|
| 212 |
|
|
<sub-workflow>
|
| 213 |
|
|
<app-path>${wf:appPath()}/referenceextraction_project</app-path>
|
| 214 |
|
|
<propagate-configuration/>
|
| 215 |
|
|
<configuration>
|
| 216 |
|
|
<property>
|
| 217 |
|
|
<name>workingDir</name>
|
| 218 |
|
|
<value>${workingDir}/referenceextraction_project/working_dir</value>
|
| 219 |
|
|
</property>
|
| 220 |
|
|
<property>
|
| 221 |
|
|
<name>input_document_text</name>
|
| 222 |
25563
|
marek.hors
|
<value>${input_document_text}</value>
|
| 223 |
19980
|
marek.hors
|
</property>
|
| 224 |
|
|
<property>
|
| 225 |
|
|
<name>input_project</name>
|
| 226 |
20051
|
marek.hors
|
<value>${input_project}</value>
|
| 227 |
19980
|
marek.hors
|
</property>
|
| 228 |
|
|
<property>
|
| 229 |
20186
|
marek.hors
|
<name>output_document_to_project</name>
|
| 230 |
19980
|
marek.hors
|
<!-- referenceextraction_project directory is created at subworkflow prepare phase -->
|
| 231 |
26238
|
marek.hors
|
<value>${output_document_to_project}</value>
|
| 232 |
19980
|
marek.hors
|
</property>
|
| 233 |
|
|
</configuration>
|
| 234 |
|
|
</sub-workflow>
|
| 235 |
33184
|
marek.hors
|
<ok to="transformers_project_toconcept"/>
|
| 236 |
|
|
<error to="fail" />
|
| 237 |
|
|
</action>
|
| 238 |
|
|
|
| 239 |
|
|
<action name="transformers_project_toconcept">
|
| 240 |
|
|
<sub-workflow>
|
| 241 |
|
|
<app-path>${wf:appPath()}/transformers_project_toconcept</app-path>
|
| 242 |
|
|
<propagate-configuration/>
|
| 243 |
|
|
<configuration>
|
| 244 |
|
|
<property>
|
| 245 |
|
|
<name>workingDir</name>
|
| 246 |
|
|
<value>${workingDir}/transformers_project_toconcept/working_dir</value>
|
| 247 |
|
|
</property>
|
| 248 |
|
|
<property>
|
| 249 |
|
|
<name>input_document_to_project</name>
|
| 250 |
|
|
<value>${output_document_to_project}</value>
|
| 251 |
|
|
</property>
|
| 252 |
|
|
<property>
|
| 253 |
|
|
<name>input_project</name>
|
| 254 |
|
|
<value>${input_project}</value>
|
| 255 |
|
|
</property>
|
| 256 |
|
|
<property>
|
| 257 |
|
|
<name>input_concept</name>
|
| 258 |
|
|
<value>${input_project_concept}</value>
|
| 259 |
|
|
</property>
|
| 260 |
|
|
<property>
|
| 261 |
|
|
<name>output</name>
|
| 262 |
|
|
<value>${workingDir}/transformers_project_toconcept/out</value>
|
| 263 |
|
|
</property>
|
| 264 |
|
|
</configuration>
|
| 265 |
|
|
</sub-workflow>
|
| 266 |
|
|
<ok to="transformers_concept_to_researchinitiatives"/>
|
| 267 |
|
|
<error to="fail" />
|
| 268 |
|
|
</action>
|
| 269 |
|
|
|
| 270 |
|
|
<action name="transformers_concept_to_researchinitiatives">
|
| 271 |
|
|
<sub-workflow>
|
| 272 |
|
|
<app-path>${wf:appPath()}/transformers_export_researchinitiatives</app-path>
|
| 273 |
|
|
<propagate-configuration/>
|
| 274 |
|
|
<configuration>
|
| 275 |
|
|
<property>
|
| 276 |
|
|
<name>workingDir</name>
|
| 277 |
|
|
<value>${workingDir}/transformers_concept_to_researchinitiatives/working_dir</value>
|
| 278 |
|
|
</property>
|
| 279 |
|
|
<property>
|
| 280 |
|
|
<name>input_document_to_research_initiative</name>
|
| 281 |
|
|
<value>${workingDir}/transformers_project_toconcept/out</value>
|
| 282 |
|
|
</property>
|
| 283 |
|
|
<property>
|
| 284 |
|
|
<name>output_document_to_research_initiatives</name>
|
| 285 |
|
|
<value>${output_document_to_project_concepts}</value>
|
| 286 |
|
|
</property>
|
| 287 |
|
|
</configuration>
|
| 288 |
|
|
</sub-workflow>
|
| 289 |
19980
|
marek.hors
|
<ok to="joining"/>
|
| 290 |
|
|
<error to="fail" />
|
| 291 |
|
|
</action>
|
| 292 |
|
|
|
| 293 |
23446
|
marek.hors
|
<action name="skip-referenceextraction_project">
|
| 294 |
|
|
<java>
|
| 295 |
|
|
<prepare>
|
| 296 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 297 |
|
|
<delete path="${nameNode}${workingDir}/referenceextraction_project" />
|
| 298 |
33184
|
marek.hors
|
<delete path="${nameNode}${workingDir}/transformers_project_toconcept" />
|
| 299 |
|
|
<delete path="${nameNode}${workingDir}/transformers_concept_to_researchinitiatives" />
|
| 300 |
26238
|
marek.hors
|
<delete path="${nameNode}${output_document_to_project}"/>
|
| 301 |
33184
|
marek.hors
|
<delete path="${nameNode}${output_document_to_project_concepts}"/>
|
| 302 |
34702
|
marek.hors
|
<mkdir path="${nameNode}${workingDir}/referenceextraction_project" />
|
| 303 |
26238
|
marek.hors
|
<mkdir path="${nameNode}${output_document_to_project}"/>
|
| 304 |
33184
|
marek.hors
|
<mkdir path="${nameNode}${output_document_to_project_concepts}"/>
|
| 305 |
23446
|
marek.hors
|
</prepare>
|
| 306 |
|
|
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
|
| 307 |
|
|
<arg>eu.dnetlib.iis.core.java.jsonworkflownodes.Producer</arg>
|
| 308 |
|
|
<arg>-C{referenceextraction_project,
|
| 309 |
|
|
eu.dnetlib.iis.referenceextraction.project.schemas.DocumentToProject,
|
| 310 |
|
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
| 311 |
33184
|
marek.hors
|
<arg>-C{document_to_project_concepts,
|
| 312 |
33249
|
marek.hors
|
eu.dnetlib.iis.export.schemas.DocumentToConceptIds,
|
| 313 |
33184
|
marek.hors
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
| 314 |
23446
|
marek.hors
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 315 |
26238
|
marek.hors
|
<arg>-Oreferenceextraction_project=${output_document_to_project}</arg>
|
| 316 |
33184
|
marek.hors
|
<arg>-Odocument_to_project_concepts=${output_document_to_project_concepts}</arg>
|
| 317 |
23446
|
marek.hors
|
</java>
|
| 318 |
|
|
<ok to="joining"/>
|
| 319 |
|
|
<error to="fail"/>
|
| 320 |
|
|
</action>
|
| 321 |
|
|
<!-- end of project reference extraction block -->
|
| 322 |
|
|
|
| 323 |
|
|
<!-- start of dataset reference extraction block -->
|
| 324 |
|
|
<decision name="decision-referenceextraction_dataset">
|
| 325 |
|
|
<switch>
|
| 326 |
23861
|
marek.hors
|
<case to="referenceextraction_dataset">${active_referenceextraction_dataset eq "true"}</case>
|
| 327 |
23525
|
marek.hors
|
<default to="skip-referenceextraction_dataset"/>
|
| 328 |
23446
|
marek.hors
|
</switch>
|
| 329 |
|
|
</decision>
|
| 330 |
|
|
|
| 331 |
21313
|
marek.hors
|
<action name="referenceextraction_dataset">
|
| 332 |
|
|
<sub-workflow>
|
| 333 |
|
|
<app-path>${wf:appPath()}/referenceextraction_dataset</app-path>
|
| 334 |
|
|
<propagate-configuration/>
|
| 335 |
|
|
<configuration>
|
| 336 |
|
|
<property>
|
| 337 |
|
|
<name>workingDir</name>
|
| 338 |
|
|
<value>${workingDir}/referenceextraction_dataset/working_dir</value>
|
| 339 |
|
|
</property>
|
| 340 |
|
|
<property>
|
| 341 |
|
|
<name>input_document_text</name>
|
| 342 |
25563
|
marek.hors
|
<value>${input_document_text}</value>
|
| 343 |
21313
|
marek.hors
|
</property>
|
| 344 |
|
|
<property>
|
| 345 |
|
|
<name>input_dataset</name>
|
| 346 |
|
|
<value>${input_dataset}</value>
|
| 347 |
|
|
</property>
|
| 348 |
|
|
<property>
|
| 349 |
|
|
<name>output_document_to_dataset</name>
|
| 350 |
|
|
<!-- referenceextraction_dataset directory is created at subworkflow prepare phase -->
|
| 351 |
26238
|
marek.hors
|
<value>${output_document_to_dataset}</value>
|
| 352 |
21313
|
marek.hors
|
</property>
|
| 353 |
|
|
</configuration>
|
| 354 |
|
|
</sub-workflow>
|
| 355 |
|
|
<ok to="joining"/>
|
| 356 |
|
|
<error to="fail" />
|
| 357 |
|
|
</action>
|
| 358 |
19980
|
marek.hors
|
|
| 359 |
23446
|
marek.hors
|
<action name="skip-referenceextraction_dataset">
|
| 360 |
|
|
<java>
|
| 361 |
|
|
<prepare>
|
| 362 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 363 |
|
|
<delete path="${nameNode}${workingDir}/referenceextraction_dataset" />
|
| 364 |
26238
|
marek.hors
|
<delete path="${nameNode}${output_document_to_dataset}"/>
|
| 365 |
34702
|
marek.hors
|
<mkdir path="${nameNode}${workingDir}/referenceextraction_dataset" />
|
| 366 |
26238
|
marek.hors
|
<mkdir path="${nameNode}${output_document_to_dataset}"/>
|
| 367 |
23446
|
marek.hors
|
</prepare>
|
| 368 |
|
|
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
|
| 369 |
|
|
<arg>eu.dnetlib.iis.core.java.jsonworkflownodes.Producer</arg>
|
| 370 |
|
|
<arg>-C{referenceextraction_dataset,
|
| 371 |
|
|
eu.dnetlib.iis.referenceextraction.dataset.schemas.DocumentToDataSet,
|
| 372 |
|
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
| 373 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 374 |
26238
|
marek.hors
|
<arg>-Oreferenceextraction_dataset=${output_document_to_dataset}</arg>
|
| 375 |
23446
|
marek.hors
|
</java>
|
| 376 |
|
|
<ok to="joining"/>
|
| 377 |
|
|
<error to="fail"/>
|
| 378 |
|
|
</action>
|
| 379 |
|
|
<!-- end of dataset reference extraction block -->
|
| 380 |
|
|
|
| 381 |
24851
|
marek.hors
|
<!-- start of researchinitiative reference extraction block -->
|
| 382 |
|
|
<decision name="decision-referenceextraction_researchinitiative">
|
| 383 |
|
|
<switch>
|
| 384 |
29016
|
marek.hors
|
<case to="referenceextraction_researchinitiative_collapser">${active_referenceextraction_researchinitiative eq "true"}</case>
|
| 385 |
24851
|
marek.hors
|
<default to="skip-referenceextraction_researchinitiative"/>
|
| 386 |
|
|
</switch>
|
| 387 |
|
|
</decision>
|
| 388 |
|
|
|
| 389 |
29016
|
marek.hors
|
<action name="referenceextraction_researchinitiative_collapser">
|
| 390 |
|
|
<sub-workflow>
|
| 391 |
|
|
<app-path>${wf:appPath()}/collapsers_multiple_input_collapser</app-path>
|
| 392 |
|
|
<propagate-configuration/>
|
| 393 |
|
|
<configuration>
|
| 394 |
|
|
<property>
|
| 395 |
|
|
<name>workingDir</name>
|
| 396 |
|
|
<value>${workingDir}/referenceextraction_researchinitiative_collapser/working_dir</value>
|
| 397 |
|
|
</property>
|
| 398 |
|
|
<property>
|
| 399 |
|
|
<name>origin_1</name>
|
| 400 |
|
|
<value>document_text</value>
|
| 401 |
|
|
</property>
|
| 402 |
|
|
<property>
|
| 403 |
|
|
<name>input_1</name>
|
| 404 |
|
|
<value>${input_document_text}</value>
|
| 405 |
|
|
</property>
|
| 406 |
|
|
<property>
|
| 407 |
|
|
<name>origin_2</name>
|
| 408 |
|
|
<value>document_text_wos</value>
|
| 409 |
|
|
</property>
|
| 410 |
|
|
<property>
|
| 411 |
|
|
<name>input_2</name>
|
| 412 |
|
|
<value>${input_document_text_wos}</value>
|
| 413 |
|
|
</property>
|
| 414 |
|
|
<property>
|
| 415 |
|
|
<name>blocking_field</name>
|
| 416 |
|
|
<value>id</value>
|
| 417 |
|
|
</property>
|
| 418 |
|
|
<property>
|
| 419 |
|
|
<name>schema_input</name>
|
| 420 |
|
|
<value>eu.dnetlib.iis.metadataextraction.schemas.DocumentText</value>
|
| 421 |
|
|
</property>
|
| 422 |
|
|
<property>
|
| 423 |
|
|
<name>output</name>
|
| 424 |
|
|
<value>${workingDir}/referenceextraction_researchinitiative_collapser/output</value>
|
| 425 |
|
|
</property>
|
| 426 |
|
|
<property>
|
| 427 |
|
|
<name>schema_input_envelope</name>
|
| 428 |
|
|
<value>eu.dnetlib.iis.collapsers.schemas.DocumentTextEnvelope</value>
|
| 429 |
|
|
</property>
|
| 430 |
|
|
<property>
|
| 431 |
|
|
<name>record_collapser</name>
|
| 432 |
|
|
<value>eu.dnetlib.iis.collapsers.origins.DocumentTextCollapser</value>
|
| 433 |
|
|
</property>
|
| 434 |
|
|
</configuration>
|
| 435 |
|
|
</sub-workflow>
|
| 436 |
|
|
<ok to="referenceextraction_researchinitiative"/>
|
| 437 |
|
|
<error to="fail"/>
|
| 438 |
|
|
</action>
|
| 439 |
|
|
|
| 440 |
24851
|
marek.hors
|
<action name="referenceextraction_researchinitiative">
|
| 441 |
|
|
<sub-workflow>
|
| 442 |
|
|
<app-path>${wf:appPath()}/referenceextraction_researchinitiative</app-path>
|
| 443 |
|
|
<propagate-configuration/>
|
| 444 |
|
|
<configuration>
|
| 445 |
|
|
<property>
|
| 446 |
|
|
<name>workingDir</name>
|
| 447 |
|
|
<value>${workingDir}/referenceextraction_researchinitiative/working_dir</value>
|
| 448 |
|
|
</property>
|
| 449 |
|
|
<property>
|
| 450 |
|
|
<name>input_document_text</name>
|
| 451 |
29016
|
marek.hors
|
<value>${workingDir}/referenceextraction_researchinitiative_collapser/output</value>
|
| 452 |
24851
|
marek.hors
|
</property>
|
| 453 |
|
|
<property>
|
| 454 |
|
|
<name>output_document_to_research_initiative</name>
|
| 455 |
26238
|
marek.hors
|
<value>${workingDir}/referenceextraction_researchinitiative/output</value>
|
| 456 |
24851
|
marek.hors
|
</property>
|
| 457 |
|
|
</configuration>
|
| 458 |
|
|
</sub-workflow>
|
| 459 |
26238
|
marek.hors
|
<ok to="transformers_export_researchinitiatives"/>
|
| 460 |
|
|
<error to="fail" />
|
| 461 |
|
|
</action>
|
| 462 |
|
|
|
| 463 |
|
|
<action name="transformers_export_researchinitiatives">
|
| 464 |
|
|
<sub-workflow>
|
| 465 |
|
|
<app-path>${wf:appPath()}/transformers_export_researchinitiatives</app-path>
|
| 466 |
|
|
<propagate-configuration/>
|
| 467 |
|
|
<configuration>
|
| 468 |
|
|
<property>
|
| 469 |
|
|
<name>workingDir</name>
|
| 470 |
|
|
<value>${workingDir}/transformers_export_researchinitiatives/working_dir</value>
|
| 471 |
|
|
</property>
|
| 472 |
|
|
<property>
|
| 473 |
|
|
<name>input_document_to_research_initiative</name>
|
| 474 |
|
|
<value>${workingDir}/referenceextraction_researchinitiative/output</value>
|
| 475 |
|
|
</property>
|
| 476 |
|
|
<property>
|
| 477 |
|
|
<name>output_document_to_research_initiatives</name>
|
| 478 |
|
|
<value>${output_document_to_research_initiatives}</value>
|
| 479 |
|
|
</property>
|
| 480 |
|
|
</configuration>
|
| 481 |
|
|
</sub-workflow>
|
| 482 |
|
|
|
| 483 |
24851
|
marek.hors
|
<ok to="joining"/>
|
| 484 |
|
|
<error to="fail" />
|
| 485 |
|
|
</action>
|
| 486 |
|
|
|
| 487 |
|
|
<action name="skip-referenceextraction_researchinitiative">
|
| 488 |
|
|
<java>
|
| 489 |
|
|
<prepare>
|
| 490 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 491 |
26238
|
marek.hors
|
<delete path="${nameNode}${workingDir}/transformers_export_researchinitiatives" />
|
| 492 |
|
|
<delete path="${nameNode}${output_document_to_research_initiatives}"/>
|
| 493 |
34702
|
marek.hors
|
<mkdir path="${nameNode}${workingDir}/transformers_export_researchinitiatives" />
|
| 494 |
26238
|
marek.hors
|
<mkdir path="${nameNode}${output_document_to_research_initiatives}"/>
|
| 495 |
24851
|
marek.hors
|
</prepare>
|
| 496 |
|
|
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
|
| 497 |
|
|
<arg>eu.dnetlib.iis.core.java.jsonworkflownodes.Producer</arg>
|
| 498 |
26238
|
marek.hors
|
<arg>-C{referenceextraction_researchinitiatives,
|
| 499 |
33249
|
marek.hors
|
eu.dnetlib.iis.export.schemas.DocumentToConceptIds,
|
| 500 |
24851
|
marek.hors
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
| 501 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 502 |
26238
|
marek.hors
|
<arg>-Oreferenceextraction_researchinitiatives=${output_document_to_research_initiatives}</arg>
|
| 503 |
24851
|
marek.hors
|
</java>
|
| 504 |
|
|
<ok to="joining"/>
|
| 505 |
|
|
<error to="fail"/>
|
| 506 |
|
|
</action>
|
| 507 |
|
|
<!-- end of researchinitiative reference extraction block -->
|
| 508 |
|
|
|
| 509 |
37432
|
marek.hors
|
<!-- start of pdb reference extraction block -->
|
| 510 |
|
|
<decision name="decision-referenceextraction_pdb">
|
| 511 |
|
|
<switch>
|
| 512 |
|
|
<case to="referenceextraction_pdb">${active_referenceextraction_pdb eq "true"}</case>
|
| 513 |
|
|
<default to="skip-referenceextraction_pdb"/>
|
| 514 |
|
|
</switch>
|
| 515 |
|
|
</decision>
|
| 516 |
|
|
|
| 517 |
|
|
<action name="referenceextraction_pdb">
|
| 518 |
|
|
<sub-workflow>
|
| 519 |
|
|
<app-path>${wf:appPath()}/referenceextraction_pdb</app-path>
|
| 520 |
|
|
<propagate-configuration/>
|
| 521 |
|
|
<configuration>
|
| 522 |
|
|
<property>
|
| 523 |
|
|
<name>workingDir</name>
|
| 524 |
|
|
<value>${workingDir}/referenceextraction_pdb/working_dir</value>
|
| 525 |
|
|
</property>
|
| 526 |
|
|
<property>
|
| 527 |
|
|
<name>input_document_text</name>
|
| 528 |
|
|
<value>${input_document_text}</value>
|
| 529 |
|
|
</property>
|
| 530 |
|
|
<property>
|
| 531 |
|
|
<name>output</name>
|
| 532 |
|
|
<value>${workingDir}/referenceextraction_pdb/output</value>
|
| 533 |
|
|
</property>
|
| 534 |
|
|
</configuration>
|
| 535 |
|
|
</sub-workflow>
|
| 536 |
|
|
<ok to="transformers_export_pdb"/>
|
| 537 |
|
|
<error to="fail" />
|
| 538 |
|
|
</action>
|
| 539 |
|
|
|
| 540 |
|
|
<action name="transformers_export_pdb">
|
| 541 |
|
|
<sub-workflow>
|
| 542 |
|
|
<app-path>${wf:appPath()}/transformers_export_researchinitiatives</app-path>
|
| 543 |
|
|
<propagate-configuration/>
|
| 544 |
|
|
<configuration>
|
| 545 |
|
|
<property>
|
| 546 |
|
|
<name>workingDir</name>
|
| 547 |
|
|
<value>${workingDir}/transformers_export_pdb/working_dir</value>
|
| 548 |
|
|
</property>
|
| 549 |
|
|
<property>
|
| 550 |
|
|
<name>input_document_to_research_initiative</name>
|
| 551 |
|
|
<value>${workingDir}/referenceextraction_pdb/output</value>
|
| 552 |
|
|
</property>
|
| 553 |
|
|
<property>
|
| 554 |
|
|
<name>output_document_to_research_initiatives</name>
|
| 555 |
|
|
<value>${output_document_to_pdb}</value>
|
| 556 |
|
|
</property>
|
| 557 |
|
|
</configuration>
|
| 558 |
|
|
</sub-workflow>
|
| 559 |
|
|
|
| 560 |
|
|
<ok to="joining"/>
|
| 561 |
|
|
<error to="fail" />
|
| 562 |
|
|
</action>
|
| 563 |
|
|
|
| 564 |
|
|
<action name="skip-referenceextraction_pdb">
|
| 565 |
|
|
<java>
|
| 566 |
|
|
<prepare>
|
| 567 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 568 |
|
|
<delete path="${nameNode}${workingDir}/transformers_export_pdb" />
|
| 569 |
|
|
<delete path="${nameNode}${output_document_to_pdb}"/>
|
| 570 |
|
|
<mkdir path="${nameNode}${workingDir}/transformers_export_pdb" />
|
| 571 |
|
|
<mkdir path="${nameNode}${output_document_to_pdb}"/>
|
| 572 |
|
|
</prepare>
|
| 573 |
|
|
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
|
| 574 |
|
|
<arg>eu.dnetlib.iis.core.java.jsonworkflownodes.Producer</arg>
|
| 575 |
|
|
<arg>-C{referenceextraction_pdb,
|
| 576 |
|
|
eu.dnetlib.iis.export.schemas.DocumentToConceptIds,
|
| 577 |
|
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
| 578 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 579 |
|
|
<arg>-Oreferenceextraction_pdb=${output_document_to_pdb}</arg>
|
| 580 |
|
|
</java>
|
| 581 |
|
|
<ok to="joining"/>
|
| 582 |
|
|
<error to="fail"/>
|
| 583 |
|
|
</action>
|
| 584 |
|
|
<!-- end of pdb reference extraction block -->
|
| 585 |
|
|
|
| 586 |
23527
|
marek.hors
|
<!-- metadatamerger branch -->
|
| 587 |
19628
|
marek.hors
|
<action name="transformers_metadatamerger">
|
| 588 |
|
|
<sub-workflow>
|
| 589 |
|
|
<app-path>${wf:appPath()}/transformers_metadatamerger</app-path>
|
| 590 |
|
|
<propagate-configuration/>
|
| 591 |
|
|
<configuration>
|
| 592 |
|
|
<property>
|
| 593 |
19980
|
marek.hors
|
<name>workingDir</name>
|
| 594 |
|
|
<value>${workingDir}/transformers_metadatamerger/working_dir</value>
|
| 595 |
|
|
</property>
|
| 596 |
|
|
<property>
|
| 597 |
19628
|
marek.hors
|
<name>input_base_metadata</name>
|
| 598 |
20051
|
marek.hors
|
<value>${input_document_metadata}</value>
|
| 599 |
19628
|
marek.hors
|
</property>
|
| 600 |
|
|
<property>
|
| 601 |
|
|
<name>input_extracted_metadata</name>
|
| 602 |
25563
|
marek.hors
|
<value>${input_extracted_document_metadata}</value>
|
| 603 |
19628
|
marek.hors
|
</property>
|
| 604 |
|
|
<property>
|
| 605 |
|
|
<name>output_merged_metadata</name>
|
| 606 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_metadatamerger/output_merged_metadata</value>
|
| 607 |
19628
|
marek.hors
|
</property>
|
| 608 |
|
|
</configuration>
|
| 609 |
|
|
</sub-workflow>
|
| 610 |
22848
|
marek.hors
|
|
| 611 |
27714
|
marek.hors
|
<ok to="decision-documentsclassification"/>
|
| 612 |
19628
|
marek.hors
|
<error to="fail" />
|
| 613 |
|
|
</action>
|
| 614 |
|
|
|
| 615 |
23446
|
marek.hors
|
<!-- start of documents classification part -->
|
| 616 |
|
|
<decision name="decision-documentsclassification">
|
| 617 |
|
|
<switch>
|
| 618 |
23861
|
marek.hors
|
<case to="transformers_documentsclassification">${active_documentsclassification eq "true"}</case>
|
| 619 |
23525
|
marek.hors
|
<default to="skip-documentsclassification"/>
|
| 620 |
23446
|
marek.hors
|
</switch>
|
| 621 |
|
|
</decision>
|
| 622 |
|
|
|
| 623 |
22402
|
marek.hors
|
<action name="transformers_documentsclassification">
|
| 624 |
|
|
<sub-workflow>
|
| 625 |
|
|
<app-path>${wf:appPath()}/transformers_documentsclassification</app-path>
|
| 626 |
|
|
<propagate-configuration/>
|
| 627 |
|
|
<configuration>
|
| 628 |
|
|
<property>
|
| 629 |
|
|
<name>workingDir</name>
|
| 630 |
|
|
<value>${workingDir}/transformers_documentsclassification/working_dir</value>
|
| 631 |
|
|
</property>
|
| 632 |
|
|
<property>
|
| 633 |
|
|
<name>input_merged_metadata</name>
|
| 634 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_metadatamerger/output_merged_metadata</value>
|
| 635 |
22402
|
marek.hors
|
</property>
|
| 636 |
|
|
<property>
|
| 637 |
|
|
<name>output_document_metadata</name>
|
| 638 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_documentsclassification/output_document_metadata</value>
|
| 639 |
22402
|
marek.hors
|
</property>
|
| 640 |
|
|
</configuration>
|
| 641 |
|
|
</sub-workflow>
|
| 642 |
|
|
<ok to="documentsclassification_main"/>
|
| 643 |
|
|
<error to="fail" />
|
| 644 |
|
|
</action>
|
| 645 |
|
|
|
| 646 |
|
|
<action name="documentsclassification_main">
|
| 647 |
|
|
<sub-workflow>
|
| 648 |
|
|
<app-path>${wf:appPath()}/documentsclassification_main</app-path>
|
| 649 |
|
|
<propagate-configuration/>
|
| 650 |
|
|
<configuration>
|
| 651 |
|
|
<property>
|
| 652 |
|
|
<name>workingDir</name>
|
| 653 |
|
|
<value>${workingDir}/documentsclassification_main/working_dir</value>
|
| 654 |
|
|
</property>
|
| 655 |
|
|
<property>
|
| 656 |
|
|
<name>input_document_metadata</name>
|
| 657 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_documentsclassification/output_document_metadata</value>
|
| 658 |
22402
|
marek.hors
|
</property>
|
| 659 |
|
|
<property>
|
| 660 |
|
|
<name>output_document_to_document_classes</name>
|
| 661 |
26238
|
marek.hors
|
<value>${output_document_to_document_classes}</value>
|
| 662 |
22402
|
marek.hors
|
</property>
|
| 663 |
|
|
</configuration>
|
| 664 |
|
|
</sub-workflow>
|
| 665 |
27714
|
marek.hors
|
<ok to="joining"/>
|
| 666 |
22402
|
marek.hors
|
<error to="fail" />
|
| 667 |
|
|
</action>
|
| 668 |
|
|
|
| 669 |
23446
|
marek.hors
|
<action name="skip-documentsclassification">
|
| 670 |
|
|
<java>
|
| 671 |
|
|
<prepare>
|
| 672 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 673 |
|
|
<delete path="${nameNode}${workingDir}/documentsclassification_main" />
|
| 674 |
26238
|
marek.hors
|
<delete path="${nameNode}${output_document_to_document_classes}"/>
|
| 675 |
34702
|
marek.hors
|
<mkdir path="${nameNode}${workingDir}/documentsclassification_main" />
|
| 676 |
26238
|
marek.hors
|
<mkdir path="${nameNode}${output_document_to_document_classes}"/>
|
| 677 |
23446
|
marek.hors
|
</prepare>
|
| 678 |
|
|
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
|
| 679 |
|
|
<arg>eu.dnetlib.iis.core.java.jsonworkflownodes.Producer</arg>
|
| 680 |
|
|
<arg>-C{documentsclassification,
|
| 681 |
|
|
eu.dnetlib.iis.documentsclassification.schemas.DocumentToDocumentClasses,
|
| 682 |
|
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
| 683 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 684 |
26238
|
marek.hors
|
<arg>-Odocumentsclassification=${output_document_to_document_classes}</arg>
|
| 685 |
23446
|
marek.hors
|
</java>
|
| 686 |
27714
|
marek.hors
|
<ok to="joining"/>
|
| 687 |
23446
|
marek.hors
|
<error to="fail"/>
|
| 688 |
|
|
</action>
|
| 689 |
|
|
<!-- end of documents classification part -->
|
| 690 |
|
|
|
| 691 |
27714
|
marek.hors
|
<join name="joining" to="decision-citationmatching"/>
|
| 692 |
|
|
|
| 693 |
24465
|
marek.hors
|
<!-- citation matching part -->
|
| 694 |
|
|
<decision name="decision-citationmatching">
|
| 695 |
|
|
<switch>
|
| 696 |
|
|
<case to="transformers_citationmatching">${active_citationmatching eq "true"}</case>
|
| 697 |
|
|
<default to="skip-citationmatching"/>
|
| 698 |
|
|
</switch>
|
| 699 |
|
|
</decision>
|
| 700 |
|
|
|
| 701 |
20623
|
marek.hors
|
<action name="transformers_citationmatching">
|
| 702 |
19628
|
marek.hors
|
<sub-workflow>
|
| 703 |
20623
|
marek.hors
|
<app-path>${wf:appPath()}/transformers_citationmatching</app-path>
|
| 704 |
19628
|
marek.hors
|
<propagate-configuration/>
|
| 705 |
|
|
<configuration>
|
| 706 |
|
|
<property>
|
| 707 |
19980
|
marek.hors
|
<name>workingDir</name>
|
| 708 |
20623
|
marek.hors
|
<value>${workingDir}/transformers_citationmatching/working_dir</value>
|
| 709 |
19980
|
marek.hors
|
</property>
|
| 710 |
|
|
<property>
|
| 711 |
19628
|
marek.hors
|
<name>input_metadata</name>
|
| 712 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_metadatamerger/output_merged_metadata</value>
|
| 713 |
19628
|
marek.hors
|
</property>
|
| 714 |
|
|
<property>
|
| 715 |
|
|
<name>input_person</name>
|
| 716 |
20051
|
marek.hors
|
<value>${input_person}</value>
|
| 717 |
19628
|
marek.hors
|
</property>
|
| 718 |
|
|
<property>
|
| 719 |
|
|
<name>output_citation_metadata</name>
|
| 720 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_citationmatching/output_citation_metadata</value>
|
| 721 |
19628
|
marek.hors
|
</property>
|
| 722 |
|
|
</configuration>
|
| 723 |
|
|
</sub-workflow>
|
| 724 |
|
|
<ok to="citationmatching_chain"/>
|
| 725 |
|
|
<error to="fail" />
|
| 726 |
|
|
</action>
|
| 727 |
|
|
|
| 728 |
|
|
<action name="citationmatching_chain">
|
| 729 |
|
|
<sub-workflow>
|
| 730 |
|
|
<app-path>${wf:appPath()}/citationmatching_chain</app-path>
|
| 731 |
|
|
<propagate-configuration/>
|
| 732 |
|
|
<configuration>
|
| 733 |
|
|
<property>
|
| 734 |
19980
|
marek.hors
|
<name>workingDir</name>
|
| 735 |
|
|
<value>${workingDir}/citationmatching_chain/working_dir</value>
|
| 736 |
|
|
</property>
|
| 737 |
|
|
<property>
|
| 738 |
19628
|
marek.hors
|
<name>input</name>
|
| 739 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_citationmatching/output_citation_metadata</value>
|
| 740 |
19628
|
marek.hors
|
</property>
|
| 741 |
|
|
<property>
|
| 742 |
|
|
<name>output</name>
|
| 743 |
29967
|
marek.hors
|
<value>${workingDir}/citationmatching_chain/output</value>
|
| 744 |
19628
|
marek.hors
|
</property>
|
| 745 |
21313
|
marek.hors
|
<property>
|
| 746 |
|
|
<name>cit_genAuthorIdxJavaOpts</name>
|
| 747 |
|
|
<value>${cit_genAuthorIdxJavaOpts}</value>
|
| 748 |
|
|
</property>
|
| 749 |
19628
|
marek.hors
|
</configuration>
|
| 750 |
|
|
</sub-workflow>
|
| 751 |
27714
|
marek.hors
|
<ok to="decision-documentssimilarity"/>
|
| 752 |
19628
|
marek.hors
|
<error to="fail" />
|
| 753 |
|
|
</action>
|
| 754 |
25765
|
marek.hors
|
|
| 755 |
|
|
<action name="skip-citationmatching">
|
| 756 |
|
|
<java>
|
| 757 |
|
|
<prepare>
|
| 758 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 759 |
|
|
<delete path="${nameNode}${workingDir}/citationmatching_chain" />
|
| 760 |
34702
|
marek.hors
|
<mkdir path="${nameNode}${workingDir}/citationmatching_chain" />
|
| 761 |
25765
|
marek.hors
|
</prepare>
|
| 762 |
|
|
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
|
| 763 |
|
|
<arg>eu.dnetlib.iis.core.java.jsonworkflownodes.Producer</arg>
|
| 764 |
|
|
<arg>-C{citation,
|
| 765 |
|
|
eu.dnetlib.iis.citationmatching.schemas.Citation,
|
| 766 |
|
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
| 767 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 768 |
29967
|
marek.hors
|
<arg>-Ocitation=${workingDir}/citationmatching_chain/output</arg>
|
| 769 |
25765
|
marek.hors
|
</java>
|
| 770 |
27714
|
marek.hors
|
<ok to="decision-documentssimilarity"/>
|
| 771 |
25765
|
marek.hors
|
<error to="fail"/>
|
| 772 |
|
|
</action>
|
| 773 |
|
|
<!-- end of citation matching part -->
|
| 774 |
19628
|
marek.hors
|
|
| 775 |
27530
|
marek.hors
|
<!-- start of documents similarity part -->
|
| 776 |
|
|
<!-- running documentsimilarity sequentially to all the other KDM modules
|
| 777 |
|
|
due to the lack of memory when executed in parallel -->
|
| 778 |
|
|
<decision name="decision-documentssimilarity">
|
| 779 |
|
|
<switch>
|
| 780 |
|
|
<case to="transformers_documentssimilarity">${active_documentssimilarity eq "true"}</case>
|
| 781 |
|
|
<default to="skip-documentssimilarity"/>
|
| 782 |
|
|
</switch>
|
| 783 |
|
|
</decision>
|
| 784 |
|
|
|
| 785 |
|
|
<action name="transformers_documentssimilarity">
|
| 786 |
|
|
<sub-workflow>
|
| 787 |
|
|
<app-path>${wf:appPath()}/transformers_documentssimilarity</app-path>
|
| 788 |
|
|
<propagate-configuration/>
|
| 789 |
|
|
<configuration>
|
| 790 |
|
|
<property>
|
| 791 |
|
|
<name>workingDir</name>
|
| 792 |
|
|
<value>${workingDir}/transformers_documentssimilarity/working_dir</value>
|
| 793 |
|
|
</property>
|
| 794 |
|
|
<property>
|
| 795 |
|
|
<name>input_person</name>
|
| 796 |
|
|
<value>${input_person}</value>
|
| 797 |
|
|
</property>
|
| 798 |
|
|
<property>
|
| 799 |
|
|
<name>input_metadata</name>
|
| 800 |
|
|
<value>${workingDir}/transformers_metadatamerger/output_merged_metadata</value>
|
| 801 |
|
|
</property>
|
| 802 |
|
|
<property>
|
| 803 |
|
|
<name>output_document_metadata</name>
|
| 804 |
|
|
<value>${workingDir}/transformers_documentssimilarity/output_document_metadata</value>
|
| 805 |
|
|
</property>
|
| 806 |
|
|
</configuration>
|
| 807 |
|
|
</sub-workflow>
|
| 808 |
|
|
<ok to="documentssimilarity_chain"/>
|
| 809 |
|
|
<error to="fail" />
|
| 810 |
|
|
</action>
|
| 811 |
|
|
|
| 812 |
|
|
<action name="documentssimilarity_chain">
|
| 813 |
|
|
<sub-workflow>
|
| 814 |
|
|
<app-path>${wf:appPath()}/documentssimilarity_chain</app-path>
|
| 815 |
|
|
<propagate-configuration/>
|
| 816 |
|
|
<configuration>
|
| 817 |
|
|
<property>
|
| 818 |
|
|
<name>workingDir</name>
|
| 819 |
|
|
<value>${workingDir}/documentssimilarity_chain/working_dir</value>
|
| 820 |
|
|
</property>
|
| 821 |
|
|
<property>
|
| 822 |
|
|
<name>input_document</name>
|
| 823 |
|
|
<value>${workingDir}/transformers_documentssimilarity/output_document_metadata</value>
|
| 824 |
|
|
</property>
|
| 825 |
|
|
<property>
|
| 826 |
|
|
<name>output_documents_similarity</name>
|
| 827 |
|
|
<value>${output_document_similarity}</value>
|
| 828 |
|
|
</property>
|
| 829 |
|
|
<property>
|
| 830 |
27551
|
marek.hors
|
<name>parallel</name>
|
| 831 |
27530
|
marek.hors
|
<value>${ds_parallel}</value>
|
| 832 |
|
|
</property>
|
| 833 |
|
|
<property>
|
| 834 |
27551
|
marek.hors
|
<name>mapredChildJavaOpts</name>
|
| 835 |
27530
|
marek.hors
|
<value>${ds_mapredChildJavaOpts}</value>
|
| 836 |
|
|
</property>
|
| 837 |
|
|
<property>
|
| 838 |
27551
|
marek.hors
|
<name>sample</name>
|
| 839 |
27530
|
marek.hors
|
<value>${ds_sample}</value>
|
| 840 |
|
|
</property>
|
| 841 |
|
|
<property>
|
| 842 |
27551
|
marek.hors
|
<name>removal_rate</name>
|
| 843 |
27530
|
marek.hors
|
<value>${ds_removal_rate}</value>
|
| 844 |
|
|
</property>
|
| 845 |
|
|
<property>
|
| 846 |
27551
|
marek.hors
|
<name>removal_least_used</name>
|
| 847 |
27530
|
marek.hors
|
<value>${ds_removal_least_used}</value>
|
| 848 |
|
|
</property>
|
| 849 |
27551
|
marek.hors
|
<property>
|
| 850 |
|
|
<name>tfidfTopnTermPerDocument</name>
|
| 851 |
|
|
<value>${ds_tfidfTopnTermPerDocument}</value>
|
| 852 |
|
|
</property>
|
| 853 |
|
|
<property>
|
| 854 |
|
|
<name>similarityTopnDocumentPerDocument</name>
|
| 855 |
|
|
<value>${ds_similarityTopnDocumentPerDocument}</value>
|
| 856 |
|
|
</property>
|
| 857 |
27530
|
marek.hors
|
</configuration>
|
| 858 |
|
|
</sub-workflow>
|
| 859 |
27714
|
marek.hors
|
<ok to="decision-statistics"/>
|
| 860 |
27530
|
marek.hors
|
<error to="fail" />
|
| 861 |
|
|
</action>
|
| 862 |
|
|
|
| 863 |
|
|
<action name="skip-documentssimilarity">
|
| 864 |
|
|
<java>
|
| 865 |
|
|
<prepare>
|
| 866 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 867 |
|
|
<delete path="${nameNode}${workingDir}/documentssimilarity_chain" />
|
| 868 |
|
|
<delete path="${nameNode}${output_document_similarity}" />
|
| 869 |
34702
|
marek.hors
|
<mkdir path="${nameNode}${workingDir}/documentssimilarity_chain" />
|
| 870 |
27530
|
marek.hors
|
<mkdir path="${nameNode}${output_document_similarity}" />
|
| 871 |
|
|
</prepare>
|
| 872 |
|
|
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
|
| 873 |
|
|
<arg>eu.dnetlib.iis.core.java.jsonworkflownodes.Producer</arg>
|
| 874 |
|
|
<arg>-C{documentssimilarity,
|
| 875 |
|
|
eu.dnetlib.iis.documentssimilarity.schemas.DocumentSimilarity,
|
| 876 |
|
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
| 877 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 878 |
|
|
<arg>-Odocumentssimilarity=${output_document_similarity}</arg>
|
| 879 |
|
|
</java>
|
| 880 |
27714
|
marek.hors
|
<ok to="decision-statistics"/>
|
| 881 |
27530
|
marek.hors
|
<error to="fail"/>
|
| 882 |
|
|
</action>
|
| 883 |
|
|
<!-- end of documents similarity part -->
|
| 884 |
27714
|
marek.hors
|
|
| 885 |
27530
|
marek.hors
|
<!-- statistics are calculated at the end, because they are taking two forked paths
|
| 886 |
|
|
outcome into account: transformers_metadatamerger and referenceextraction_project -->
|
| 887 |
25765
|
marek.hors
|
<!-- statistics part -->
|
| 888 |
|
|
<decision name="decision-statistics">
|
| 889 |
|
|
<switch>
|
| 890 |
|
|
<case to="transformers_statistics">${active_statistics eq "true"}</case>
|
| 891 |
|
|
<default to="skip-statistics"/>
|
| 892 |
|
|
</switch>
|
| 893 |
|
|
</decision>
|
| 894 |
|
|
|
| 895 |
27530
|
marek.hors
|
<action name="transformers_statistics">
|
| 896 |
19628
|
marek.hors
|
<sub-workflow>
|
| 897 |
24465
|
marek.hors
|
<app-path>${wf:appPath()}/transformers_statistics</app-path>
|
| 898 |
19628
|
marek.hors
|
<propagate-configuration/>
|
| 899 |
|
|
<configuration>
|
| 900 |
|
|
<property>
|
| 901 |
19980
|
marek.hors
|
<name>workingDir</name>
|
| 902 |
24465
|
marek.hors
|
<value>${workingDir}/transformers_statistics/working_dir</value>
|
| 903 |
19980
|
marek.hors
|
</property>
|
| 904 |
|
|
<property>
|
| 905 |
19628
|
marek.hors
|
<name>input_document</name>
|
| 906 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_metadatamerger/output_merged_metadata</value>
|
| 907 |
19628
|
marek.hors
|
</property>
|
| 908 |
|
|
<property>
|
| 909 |
|
|
<name>input_citation</name>
|
| 910 |
29967
|
marek.hors
|
<value>${workingDir}/citationmatching_chain/output</value>
|
| 911 |
19628
|
marek.hors
|
</property>
|
| 912 |
|
|
<property>
|
| 913 |
24465
|
marek.hors
|
<!-- NOTICE: reference extraction will have to be enabled to get this input -->
|
| 914 |
|
|
<name>input_document_to_project</name>
|
| 915 |
26238
|
marek.hors
|
<value>${output_document_to_project}</value>
|
| 916 |
24465
|
marek.hors
|
</property>
|
| 917 |
|
|
<property>
|
| 918 |
20253
|
marek.hors
|
<name>input_person</name>
|
| 919 |
|
|
<value>${input_person}</value>
|
| 920 |
|
|
</property>
|
| 921 |
|
|
<property>
|
| 922 |
24465
|
marek.hors
|
<name>input_project</name>
|
| 923 |
|
|
<value>${input_project}</value>
|
| 924 |
|
|
</property>
|
| 925 |
|
|
<property>
|
| 926 |
19628
|
marek.hors
|
<name>output_document_authors_citations</name>
|
| 927 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_statistics/output_document_authors_citations</value>
|
| 928 |
19628
|
marek.hors
|
</property>
|
| 929 |
20253
|
marek.hors
|
<property>
|
| 930 |
|
|
<name>output_person_id</name>
|
| 931 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_statistics/output_person_id</value>
|
| 932 |
20253
|
marek.hors
|
</property>
|
| 933 |
24465
|
marek.hors
|
<property>
|
| 934 |
|
|
<name>output_project_id</name>
|
| 935 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_statistics/output_project_id</value>
|
| 936 |
24465
|
marek.hors
|
</property>
|
| 937 |
19628
|
marek.hors
|
</configuration>
|
| 938 |
|
|
</sub-workflow>
|
| 939 |
25765
|
marek.hors
|
<ok to="statistics"/>
|
| 940 |
19628
|
marek.hors
|
<error to="fail" />
|
| 941 |
|
|
</action>
|
| 942 |
|
|
|
| 943 |
24465
|
marek.hors
|
<action name="statistics">
|
| 944 |
19628
|
marek.hors
|
<sub-workflow>
|
| 945 |
24465
|
marek.hors
|
<app-path>${wf:appPath()}/statistics</app-path>
|
| 946 |
19628
|
marek.hors
|
<propagate-configuration/>
|
| 947 |
|
|
<configuration>
|
| 948 |
|
|
<property>
|
| 949 |
19980
|
marek.hors
|
<name>workingDir</name>
|
| 950 |
24465
|
marek.hors
|
<value>${workingDir}/statistics/working_dir</value>
|
| 951 |
19980
|
marek.hors
|
</property>
|
| 952 |
|
|
<property>
|
| 953 |
24465
|
marek.hors
|
<name>input_document_authors_citations</name>
|
| 954 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_statistics/output_document_authors_citations</value>
|
| 955 |
19628
|
marek.hors
|
</property>
|
| 956 |
|
|
<property>
|
| 957 |
20253
|
marek.hors
|
<name>input_person_id</name>
|
| 958 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_statistics/output_person_id</value>
|
| 959 |
19628
|
marek.hors
|
</property>
|
| 960 |
|
|
<property>
|
| 961 |
24465
|
marek.hors
|
<name>input_project_id</name>
|
| 962 |
26567
|
marek.hors
|
<value>${workingDir}/transformers_statistics/output_project_id</value>
|
| 963 |
19628
|
marek.hors
|
</property>
|
| 964 |
|
|
<property>
|
| 965 |
24465
|
marek.hors
|
<name>output_document_statistics</name>
|
| 966 |
26286
|
marek.hors
|
<value>${output_document_statistics}</value>
|
| 967 |
19628
|
marek.hors
|
</property>
|
| 968 |
24465
|
marek.hors
|
<property>
|
| 969 |
|
|
<name>output_author_statistics</name>
|
| 970 |
26238
|
marek.hors
|
<value>${output_author_statistics}</value>
|
| 971 |
24465
|
marek.hors
|
</property>
|
| 972 |
|
|
<property>
|
| 973 |
|
|
<name>output_project_statistics</name>
|
| 974 |
25414
|
marek.hors
|
<value>${output_project_statistics}</value>
|
| 975 |
24465
|
marek.hors
|
</property>
|
| 976 |
|
|
<property>
|
| 977 |
|
|
<name>output_global_statistics</name>
|
| 978 |
26567
|
marek.hors
|
<value>${workingDir}/statistics/output_global_statistics</value>
|
| 979 |
24465
|
marek.hors
|
</property>
|
| 980 |
19628
|
marek.hors
|
</configuration>
|
| 981 |
|
|
</sub-workflow>
|
| 982 |
29967
|
marek.hors
|
<ok to="transformers_citations_from_matching"/>
|
| 983 |
19628
|
marek.hors
|
<error to="fail" />
|
| 984 |
|
|
</action>
|
| 985 |
19980
|
marek.hors
|
|
| 986 |
24465
|
marek.hors
|
<action name="skip-statistics">
|
| 987 |
|
|
<java>
|
| 988 |
|
|
<prepare>
|
| 989 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 990 |
|
|
<delete path="${nameNode}${workingDir}/statistics" />
|
| 991 |
26286
|
marek.hors
|
<delete path="${nameNode}${output_document_statistics}"/>
|
| 992 |
26238
|
marek.hors
|
<delete path="${nameNode}${output_author_statistics}"/>
|
| 993 |
|
|
<delete path="${nameNode}${output_project_statistics}"/>
|
| 994 |
34702
|
marek.hors
|
<mkdir path="${nameNode}${workingDir}/statistics" />
|
| 995 |
26286
|
marek.hors
|
<mkdir path="${nameNode}${output_document_statistics}"/>
|
| 996 |
26238
|
marek.hors
|
<mkdir path="${nameNode}${output_author_statistics}"/>
|
| 997 |
|
|
<mkdir path="${nameNode}${output_project_statistics}"/>
|
| 998 |
24465
|
marek.hors
|
</prepare>
|
| 999 |
|
|
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
|
| 1000 |
|
|
<arg>eu.dnetlib.iis.core.java.jsonworkflownodes.Producer</arg>
|
| 1001 |
|
|
<arg>-C{document_statistics,
|
| 1002 |
|
|
eu.dnetlib.iis.statistics.schemas.DocumentToDocumentStatistics,
|
| 1003 |
|
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
| 1004 |
|
|
<arg>-C{author_statistics,
|
| 1005 |
|
|
eu.dnetlib.iis.statistics.schemas.AuthorToAuthorStatistics,
|
| 1006 |
|
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
| 1007 |
|
|
<arg>-C{project_statistics,
|
| 1008 |
|
|
eu.dnetlib.iis.statistics.schemas.ProjectToProjectStatistics,
|
| 1009 |
|
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
| 1010 |
|
|
<!-- FIXME currently global statistics are not available -->
|
| 1011 |
|
|
<!--
|
| 1012 |
|
|
<arg>-C{global_statistics,
|
| 1013 |
|
|
eu.dnetlib.iis.statistics.schemas.,
|
| 1014 |
|
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
| 1015 |
|
|
-->
|
| 1016 |
|
|
<!-- notice: directory have to aligned with skipped action output -->
|
| 1017 |
26286
|
marek.hors
|
<arg>-Odocument_statistics=${output_document_statistics}</arg>
|
| 1018 |
26238
|
marek.hors
|
<arg>-Oauthor_statistics=${output_author_statistics}</arg>
|
| 1019 |
25414
|
marek.hors
|
<arg>-Oproject_statistics=${output_project_statistics}</arg>
|
| 1020 |
24465
|
marek.hors
|
<!-- FIXME currently global statistics are not available -->
|
| 1021 |
|
|
<!--
|
| 1022 |
26567
|
marek.hors
|
<arg>-Oglobal_statistics=${workingDir}/statistics/output_global_statistics</arg>
|
| 1023 |
24465
|
marek.hors
|
-->
|
| 1024 |
|
|
</java>
|
| 1025 |
29967
|
marek.hors
|
<ok to="transformers_citations_from_matching"/>
|
| 1026 |
24465
|
marek.hors
|
<error to="fail"/>
|
| 1027 |
|
|
</action>
|
| 1028 |
|
|
<!-- end of statistics part -->
|
| 1029 |
|
|
|
| 1030 |
29967
|
marek.hors
|
<!-- normalize and group citations part -->
|
| 1031 |
|
|
<action name="transformers_citations_from_matching">
|
| 1032 |
|
|
<sub-workflow>
|
| 1033 |
|
|
<app-path>${wf:appPath()}/transformers_citations_from_matching</app-path>
|
| 1034 |
|
|
<propagate-configuration/>
|
| 1035 |
|
|
<configuration>
|
| 1036 |
|
|
<property>
|
| 1037 |
|
|
<name>workingDir</name>
|
| 1038 |
|
|
<value>${workingDir}/transformers_citations_from_matching/working_dir</value>
|
| 1039 |
|
|
</property>
|
| 1040 |
|
|
<property>
|
| 1041 |
|
|
<name>input</name>
|
| 1042 |
|
|
<value>${workingDir}/citationmatching_chain/output</value>
|
| 1043 |
|
|
</property>
|
| 1044 |
|
|
<property>
|
| 1045 |
|
|
<name>output</name>
|
| 1046 |
|
|
<value>${workingDir}/transformers_citations_from_matching/output</value>
|
| 1047 |
|
|
</property>
|
| 1048 |
|
|
</configuration>
|
| 1049 |
|
|
</sub-workflow>
|
| 1050 |
|
|
<ok to="transformers_citations_from_ingestpmc"/>
|
| 1051 |
|
|
<error to="fail" />
|
| 1052 |
|
|
</action>
|
| 1053 |
|
|
|
| 1054 |
|
|
<action name="transformers_citations_from_ingestpmc">
|
| 1055 |
|
|
<sub-workflow>
|
| 1056 |
|
|
<app-path>${wf:appPath()}/transformers_citations_from_ingestpmc</app-path>
|
| 1057 |
|
|
<propagate-configuration/>
|
| 1058 |
|
|
<configuration>
|
| 1059 |
|
|
<property>
|
| 1060 |
|
|
<name>workingDir</name>
|
| 1061 |
|
|
<value>${workingDir}/transformers_citations_from_ingestpmc/working_dir</value>
|
| 1062 |
|
|
</property>
|
| 1063 |
|
|
<property>
|
| 1064 |
|
|
<name>input</name>
|
| 1065 |
|
|
<value>${input_citation_pmc}</value>
|
| 1066 |
|
|
</property>
|
| 1067 |
|
|
<property>
|
| 1068 |
|
|
<name>output</name>
|
| 1069 |
|
|
<value>${workingDir}/transformers_citations_from_ingestpmc/output</value>
|
| 1070 |
|
|
</property>
|
| 1071 |
|
|
</configuration>
|
| 1072 |
|
|
</sub-workflow>
|
| 1073 |
33098
|
marek.hors
|
<ok to="citations_collapser"/>
|
| 1074 |
29967
|
marek.hors
|
<error to="fail" />
|
| 1075 |
|
|
</action>
|
| 1076 |
|
|
|
| 1077 |
33098
|
marek.hors
|
<action name="citations_collapser">
|
| 1078 |
|
|
<sub-workflow>
|
| 1079 |
35042
|
marek.hors
|
<app-path>${wf:appPath()}/collapsers_multiple_input_collapser</app-path>
|
| 1080 |
29967
|
marek.hors
|
<propagate-configuration/>
|
| 1081 |
|
|
<configuration>
|
| 1082 |
33098
|
marek.hors
|
<property>
|
| 1083 |
29967
|
marek.hors
|
<name>workingDir</name>
|
| 1084 |
33098
|
marek.hors
|
<value>${workingDir}/citations_collapser/working_dir</value>
|
| 1085 |
29967
|
marek.hors
|
</property>
|
| 1086 |
33098
|
marek.hors
|
<!-- Input ports & parameters. -->
|
| 1087 |
|
|
<property>
|
| 1088 |
|
|
<name>origin_1</name>
|
| 1089 |
|
|
<value>ingested</value>
|
| 1090 |
|
|
</property>
|
| 1091 |
|
|
<property>
|
| 1092 |
|
|
<name>input_1</name>
|
| 1093 |
|
|
<value>${workingDir}/transformers_citations_from_ingestpmc/output</value>
|
| 1094 |
|
|
</property>
|
| 1095 |
|
|
<property>
|
| 1096 |
|
|
<name>origin_2</name>
|
| 1097 |
|
|
<value>matched</value>
|
| 1098 |
|
|
</property>
|
| 1099 |
|
|
<property>
|
| 1100 |
|
|
<name>input_2</name>
|
| 1101 |
|
|
<value>${workingDir}/transformers_citations_from_matching/output</value>
|
| 1102 |
|
|
</property>
|
| 1103 |
|
|
<property>
|
| 1104 |
|
|
<name>blocking_field</name>
|
| 1105 |
|
|
<value>sourceDocumentId</value>
|
| 1106 |
|
|
</property>
|
| 1107 |
|
|
<property>
|
| 1108 |
|
|
<name>schema_input</name>
|
| 1109 |
|
|
<value>eu.dnetlib.iis.common.citations.schemas.Citation</value>
|
| 1110 |
|
|
</property>
|
| 1111 |
|
|
<property>
|
| 1112 |
|
|
<name>output</name>
|
| 1113 |
|
|
<value>${workingDir}/citations_collapser/output</value>
|
| 1114 |
|
|
</property>
|
| 1115 |
|
|
<property>
|
| 1116 |
|
|
<name>schema_input_envelope</name>
|
| 1117 |
|
|
<value>eu.dnetlib.iis.common.citations.schemas.CitationEnvelope</value>
|
| 1118 |
|
|
</property>
|
| 1119 |
|
|
<property>
|
| 1120 |
|
|
<name>record_collapser</name>
|
| 1121 |
|
|
<value>eu.dnetlib.iis.collapsers.origins.PMCCitationCollapser</value>
|
| 1122 |
|
|
</property>
|
| 1123 |
29967
|
marek.hors
|
</configuration>
|
| 1124 |
|
|
</sub-workflow>
|
| 1125 |
|
|
<ok to="transformers_export_citations"/>
|
| 1126 |
|
|
<error to="fail" />
|
| 1127 |
|
|
</action>
|
| 1128 |
|
|
|
| 1129 |
|
|
<action name="transformers_export_citations">
|
| 1130 |
|
|
<sub-workflow>
|
| 1131 |
|
|
<app-path>${wf:appPath()}/transformers_export_citations</app-path>
|
| 1132 |
|
|
<propagate-configuration/>
|
| 1133 |
|
|
<configuration>
|
| 1134 |
|
|
<property>
|
| 1135 |
|
|
<name>workingDir</name>
|
| 1136 |
|
|
<value>${workingDir}/transformers_export_citations/working_dir</value>
|
| 1137 |
|
|
</property>
|
| 1138 |
|
|
<property>
|
| 1139 |
|
|
<name>input</name>
|
| 1140 |
33098
|
marek.hors
|
<value>${workingDir}/citations_collapser/output</value>
|
| 1141 |
29967
|
marek.hors
|
</property>
|
| 1142 |
|
|
<property>
|
| 1143 |
|
|
<name>output</name>
|
| 1144 |
|
|
<value>${output_citation}</value>
|
| 1145 |
|
|
</property>
|
| 1146 |
|
|
</configuration>
|
| 1147 |
|
|
</sub-workflow>
|
| 1148 |
|
|
<ok to="end"/>
|
| 1149 |
|
|
<error to="fail" />
|
| 1150 |
|
|
</action>
|
| 1151 |
|
|
|
| 1152 |
|
|
<!-- end of normalize and group citations part -->
|
| 1153 |
|
|
|
| 1154 |
19628
|
marek.hors
|
<kill name="fail">
|
| 1155 |
|
|
<message>Unfortunately, the process failed -- error message:
|
| 1156 |
|
|
[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
| 1157 |
|
|
</kill>
|
| 1158 |
|
|
<end name="end" />
|
| 1159 |
|
|
</workflow-app>
|