materialsCitation tagger issue: bug

[myrmoteras]

this is a case where the batch hung up - ie worked for a long time and did not move

GgImagine.20171031-0612.err.zip `Processing document 'E:\diglib\zootaxa\temp\zootaxa.4341.2.2.pdf'

• loaded PDF of 15686915 bytes Extracting page content Assessing font char usage Importing page words Sanitizing page words and graphics Handling flipped page content Analyzing words in relation to figures and graphics Storing custom fonts Assessing number punctuation Splitting page words Generating page images Generating pages Analyzing page structure Analyzing text stream structure
• PDF converted, document ID is 'AF06FFBCFF8B73222675FFCFFF90C85C' Storing conversion result to temporary folder Storing document data Storing page data Storing word data Storing region data Storing annotation data Storing font data Storing page images Storing page image data Storing supplement data Storing supplements Document stored to temporary folder
• assigned document style 'zootaxa.2013.journal_article' Running Image Markup Tool 'Detect Document Structure' Detecting document structure from 36 pages
• gathering data
• scoring page numbers:
• checking page number sequence:
• filling in missing page numbers:
• detecting page headers
• correcting empty tables
• detecting tables
• computing main text font size
• detecting captions
• detecting footnotes
• indexing paragraph end words
• de-hyphenating line breaks
• merging interrupted paragraphs
• identifying caption target areas
• merging tables within pages
• merging tables across pages
• marking caption citations
• marking headings and emphases Storing document data Storing page data Storing word data Storing region data Storing annotation data Storing font data Storing page images Storing page image data Storing supplement data Storing supplements Document stored to temporary folder Running Image Markup Tool 'Add Document Meta Data' Storing document data Storing page data Storing word data Storing region data Storing annotation data Storing font data Storing page images Storing page image data Storing supplement data Storing supplements Document stored to temporary folder Running Image Markup Tool 'Mark Taxonomic Keys' Storing document data Storing page data Storing word data Storing region data Storing annotation data Storing font data Storing page images Storing page image data Storing supplement data Storing supplements Document stored to temporary folder Running Image Markup Tool 'Parse Bibliography' Wrapping document Checking document Loading document processor Storing document data Storing page data Storing word data Storing region data Storing annotation data Storing font data Storing page images Storing page image data Storing supplement data Storing supplements Document stored to temporary folder Running Image Markup Tool 'Mark Bibliographic Citations' Wrapping document Checking document Loading document processor Processing document Storing document data Storing page data Storing word data Storing region data Storing annotation data Storing font data Storing page images Storing page image data Storing supplement data Storing supplements Document stored to temporary folder Running Image Markup Tool 'Mark Taxon Names' Wrapping document Checking document Loading document processor Collecting seed families and genera Collecting above-genus seeds Eliminating seeds from document head and bibliography Eliminating stop words Eliminating seeds with inappropriate suffixes Eliminating document local stop words Eliminating non-emphasis-start words Eliminating seeds occurring in lower case more often than capitalized Collecting labeled positives Doing catalog lookups for 27 seeds: Assessing catalog lookup results Building primary rank dictionaries Salvaging style eliminated seeds using lookup results Doing catalog lookups for 1 catalog salvaged seeds: Extending primary rank dictionaries Salvaging style eliminated seeds using style of catalog salvaged seeds Doing catalog lookups for 0 style salvaged seeds: Extending primary rank dictionaries Indexing epithet occurrences Indexing labeled epithets and potential epithets Indexing taxonomic status labels Indexing potential authorities Indexing name infixes and in-name symbols Assembling taxonomic names Expanding abbreviated genera and species Linking taxonomic names with non-catalog genera to families Linking taxonomic names to catalog data Getting taxonomic names Adding document authority for original names Adding or resetting verbatim authorities Bucketizing taxonomic names Merging equal buckets Merging compatible buckets Handling new combinations and status changes Transferring attributes already present in document Sorting out done-with buckets Loading authority data for 20 taxon names Storing document data Storing page data Storing word data Storing region data Storing annotation data Storing font data Storing page images Storing page image data Storing supplement data Storing supplements Document stored to temporary folder Running Image Markup Tool 'Clean Table Annotations' Storing document data Storing page data Storing word data Storing region data Storing annotation data Storing font data Storing page images Storing page image data Storing supplement data Storing supplements Document stored to temporary folder Running Image Markup Tool 'Remove Duplicate Annotations' Storing document data Storing page data Storing word data Storing region data Storing annotation data Storing font data Storing page images Storing page image data Storing supplement data Storing supplements Document stored to temporary folder Running Image Markup Tool 'Mark Treatments (Headings Only)' Wrapping document Checking document Loading document processor Storing document data Storing page data Storing word data Storing region data Storing annotation data Storing font data Storing page images Storing page image data Storing supplement data Storing supplements Document stored to temporary folder Running Image Markup Tool 'Extract Materials Citations' Wrapping document Checking document Loading document processor Detecting materials citation paragraphs Getting document person names Marking materials citations Setting materials citation attributes Detecting materials citation paragraphs Getting document person names Marking materials citations Setting materials citation attributes Detecting materials citation paragraphs Getting document person names Marking materials citations Setting materials citation attributes Detecting materials citation paragraphs Getting document person names Marking materials citations Setting materials citation attributes

D:\GoldenGateImagine20170823> zootaxa.4341.2.2.pdf `

[gsautter]

Setting the attributes of materials citations is a straightforward matter ... hard to tell how that one could take long or even hang. If any of the steps are prone to incurring excessive computational effort, it's marking the materials citations, but that one looks like having finished just fine.

Please try restarting the batch on the PDF in question. Thanks to storing intermediate results (which ends in the "Document stored to temporary folder" log entry), it should pick up right at the materials citations. Any change on the second run? If so, it most likely was a resource issue.