PDF Indexing on Linux

rax_m
Hi

I recently installed Zotero on Ubuntu Linux (7.10). I really like the tool so far, but am having issues with the PDF full-text indexing.

I have my document repository on a windows share that is mounted on my linux computer. If I look at preferences, Zotero indicates that both pdftotext and pdfinfo are installed correctly. However, except for two web pages that have been indexed, nothing else seems to want to be indexed.

How do i check why this is happenning? Please give detailed instructions.. I tried enabling the zotero debug in about:config of firefox, but that hasn't showed any output when I restart firefox.

Thanks
Rax
  • rax_m
    Oops. You have to close all instances of firefox before the debug is enabled.

    Anyway, here's the output, the pdftotext and pdfinfo seem to be installed correctly to me :-/

    [code]
    rmistry@research43:~$ firefox -console
    zotero(3): Using data directory /home/rmistry/neptune-rmistry/Zotero

    zotero(3): Opening database 'zotero'

    zotero(3): pdftotext version 3.02pl1 registered at /home/rmistry/neptune-rmistry/Zotero/pdftotext-Linux-i686

    zotero(3): pdfinfo version 3.02pl1 registered at /home/rmistry/neptune-rmistry/Zotero/pdfinfo-Linux-i686

    zotero(5): SELECT version FROM version WHERE schema='userdata'

    zotero(5): Beginning DB transaction

    zotero(3): Beginning Notifier event queue

    zotero(5): SELECT version FROM version WHERE schema='system'

    zotero(5): Committing transaction

    zotero(3): Resetting Notifier event queue

    zotero(5): SELECT version FROM version WHERE schema='scrapers'

    zotero(3): Opening database 'zotero for dummy statement

    zotero(3): Initializing dummy statement for 'zotero'

    zotero(5): SELECT version FROM version WHERE schema='sync'

    zotero(5): SELECT version FROM version WHERE schema='lastcheck'

    zotero(4): Not enough time since last update -- not checking repository

    zotero(3): Setting repository check interval to 1294 seconds

    zotero(3): Integration HTTP server listening on 127.0.0.1:50001

    zotero(3): Registering URIContentListener for text/x-csl

    zotero(5): SELECT translatorID, translatorType, label, target, detectCode IS NULL as noDetectCode FROM translators ORDER BY priority, label

    zotero(5): SELECT translatorID, detectCode FROM translators WHERE target IS NULL

    zotero(4): Registering observer for [collection,search] in notifier with hash Xu'

    zotero(5): SELECT itemTypeID AS id, typeName AS name FROM itemTypes WHERE display=2 ORDER BY typeName

    zotero(5): SELECT itemTypeID AS id, typeName AS name FROM itemTypes WHERE display=1 ORDER BY typeName

    zotero(5): SELECT itemTypeID AS id, typeName AS name FROM itemTypes ORDER BY typeName

    zotero(3): Translate: binding sandbox to file:///usr/share/ubuntu-artwork/home/index.html

    zotero(3): Translate: searching for translators for file:///usr/share/ubuntu-artwork/home/index.html

    zotero(5): SELECT detectCode FROM translators WHERE translatorID = ?

    zotero(5): Binding parameter 1 of type string: "938ebe32-2b2e-4349-a5b3-b3a05d3de627"

    zotero(3): Translate: executed detectCode for ACS Publications

    zotero(5): SELECT detectCode FROM translators WHERE translatorID = ?

    zotero(5): Binding parameter 1 of type string: "e7e01cac-1e37-4da6-b078-a0e8343b0e98"

    zotero(3): Translate: executed detectCode for unAPI

    zotero(3): Translate: executed detectCode for COinS

    zotero(3): Translate: executed detectCode for Embedded RDF

    zotero(3): Translate: running handler 0 for translators

    zotero(3): Translate: searching for translators for /usr/share/ubuntu-artwork/home/index.html

    zotero(5): SELECT detectCode FROM translators WHERE translatorID = ?

    zotero(5): Binding parameter 1 of type string: "0e2235e7-babf-413c-9acf-f27cce5f059c"

    zotero(3): Translate: setting display option exportNotes to true

    zotero(3): Translate: executed detectCode for MODS

    zotero(5): SELECT detectCode FROM translators WHERE translatorID = ?

    zotero(5): Binding parameter 1 of type string: "9cb70025-a888-4a29-a210-93ec52da40d4"

    zotero(3): Translate: setting configure option dataMode to block

    zotero(3): Translate: setting display option UTF8 to true

    zotero(3): Translate: executed detectCode for BibTeX

    zotero(5): SELECT detectCode FROM translators WHERE translatorID = ?

    zotero(5): Binding parameter 1 of type string: "a6ee60df-1ddc-4aae-bb25-45e0537be973"

    zotero(3): Translate: executed detectCode for MARC

    zotero(5): SELECT detectCode FROM translators WHERE translatorID = ?

    zotero(5): Binding parameter 1 of type string: "5e3ad958-ac79-463d-812b-a86a9235c28f"

    zotero(3): Translate: setting configure option dataMode to rdf

    zotero(3): Translate: [Exception... "Component returned failure code: 0x80004002 (NS_NOINTERFACE) [nsIRDFService.GetDataSourceBlocking]" nsresult: "0x80004002 (NS_NOINTERFACE)" location: "JS frame :: chrome://zotero/content/xpcom/translate.js :: anonymous :: line 1566" data: no] in opening IO for RDF

    zotero(5): SELECT detectCode FROM translators WHERE translatorID = ?

    zotero(5): Binding parameter 1 of type string: "32d59d2d-b65a-4da4-b0a3-bdd3cfb979e7"

    zotero(3): Translate: setting configure option dataMode to line

    zotero(3): Translate: setting display option exportNotes to true

    zotero(3): Translate: executed detectCode for RIS

    zotero(5): SELECT detectCode FROM translators WHERE translatorID = ?

    zotero(5): Binding parameter 1 of type string: "881f60f2-0802-411a-9228-ce5f47b64c7d"

    zotero(3): Translate: setting configure option dataMode to line

    zotero(3): Translate: executed detectCode for Refer/BibIX

    zotero(3): Translate: running handler 0 for translators

    [/code]
  • dstillman
    What's the debug output when you try to import an item (for example, by dragging a PDF into Zotero)?
  • rax_m
    edited March 5, 2008
    Hi,

    Thanks for the reply Dan.

    I get the following output. Sometimes that first line is repeated quite a few times.
    EDIT: Oh and nothing actually happens within Zotero. I.e. The attachment is not added as a reference.

    Cheers
    Rax
    ------------------------------------

    (gecko:7182): Gtk-CRITICAL **: gtk_drag_get_data: assertion `GTK_IS_WIDGET (widget)' failed

    (gecko:7182): Gtk-CRITICAL **: gtk_drag_get_data: assertion `GTK_IS_WIDGET (widget)' failed
    zotero(5): SELECT I.itemID, I.itemTypeID, I.dateAdded, I.dateModified, COALESCE(CASE (SELECT COUNT(*) FROM itemCreators IC LEFT JOIN itemTypeCreatorTypes ITCT ON (IC.creatorTypeID=ITCT.creatorTypeID AND ITCT.itemTypeID=I.itemTypeID) WHERE itemID=I.itemID AND primaryField=1) WHEN 0 THEN NULL WHEN 1 THEN (SELECT lastName FROM itemCreators IC NATURAL JOIN creators LEFT JOIN itemTypeCreatorTypes ITCT ON (IC.creatorTypeID=ITCT.creatorTypeID AND ITCT.itemTypeID=I.itemTypeID) WHERE itemID=I.itemID AND primaryField=1) WHEN 2 THEN (SELECT (SELECT lastName FROM itemCreators IC NATURAL JOIN creators LEFT JOIN itemTypeCreatorTypes ITCT ON (IC.creatorTypeID=ITCT.creatorTypeID AND ITCT.itemTypeID=I.itemTypeID) WHERE itemID=I.itemID AND primaryField=1 ORDER BY orderIndex LIMIT 1) || ' and ' || (SELECT lastName FROM itemCreators IC NATURAL JOIN creators LEFT JOIN itemTypeCreatorTypes ITCT ON (IC.creatorTypeID=ITCT.creatorTypeID AND ITCT.itemTypeID=I.itemTypeID) WHERE itemID=I.itemID AND primaryField=1 ORDER BY orderIndex LIMIT 1,1)) ELSE (SELECT (SELECT lastName FROM itemCreators IC NATURAL JOIN creators LEFT JOIN itemTypeCreatorTypes ITCT ON (IC.creatorTypeID=ITCT.creatorTypeID AND ITCT.itemTypeID=I.itemTypeID) WHERE itemID=I.itemID AND primaryField=1 ORDER BY orderIndex LIMIT 1) || ' et al.' ) END, CASE (SELECT COUNT(*) FROM itemCreators NATURAL JOIN creatorTypes WHERE itemID=I.itemID AND creatorTypeID IN (3)) WHEN 0 THEN NULL WHEN 1 THEN (SELECT lastName FROM itemCreators NATURAL JOIN creators WHERE itemID=I.itemID AND creatorTypeID IN (3)) WHEN 2 THEN (SELECT (SELECT lastName FROM itemCreators NATURAL JOIN creators WHERE itemID=I.itemID AND creatorTypeID IN (3) ORDER BY orderIndex LIMIT 1) || ' and ' || (SELECT lastName FROM itemCreators NATURAL JOIN creators WHERE itemID=I.itemID AND creatorTypeID IN (3) ORDER BY orderIndex LIMIT 1,1) ) ELSE (SELECT (SELECT lastName FROM itemCreators NATURAL JOIN creators WHERE itemID=I.itemID AND creatorTypeID IN (3) ORDER BY orderIndex LIMIT 1) || ' et al.' ) END, CASE (SELECT COUNT(*) FROM itemCreators NATURAL JOIN creatorTypes WHERE itemID=I.itemID AND creatorTypeID IN (2)) WHEN 0 THEN NULL WHEN 1 THEN (SELECT lastName FROM itemCreators NATURAL JOIN creators WHERE itemID=I.itemID AND creatorTypeID IN (2)) WHEN 2 THEN (SELECT (SELECT lastName FROM itemCreators NATURAL JOIN creators WHERE itemID=I.itemID AND creatorTypeID IN (2) ORDER BY orderIndex LIMIT 1) || ' and ' || (SELECT lastName FROM itemCreators NATURAL JOIN creators WHERE itemID=I.itemID AND creatorTypeID IN (2) ORDER BY orderIndex LIMIT 1,1) ) ELSE (SELECT (SELECT lastName FROM itemCreators NATURAL JOIN creators WHERE itemID=I.itemID AND creatorTypeID IN (2) ORDER BY orderIndex LIMIT 1) || ' et al.' ) END) AS firstCreator, (SELECT COUNT(*) FROM itemNotes WHERE sourceItemID=I.itemID) AS numNotes, (SELECT COUNT(*) FROM itemAttachments WHERE sourceItemID=I.itemID) AS numAttachments FROM items I WHERE 1 AND I.itemID IN (sb/SAB%Bmsr@et)/msr/e%0oscmainvlm.d
  • rax_m
    anyone?
  • bigbreath
    Hi guys,

    I'm using Ubuntu 8.04 32bit and am experiencing a similar problem to rax_m. When I try to drag and drop pdfs into Zotero, no additional items appear in my library. The debug produces this:

    (firefox:18414): Gtk-CRITICAL **: gtk_drag_get_data: assertion `GTK_IS_WIDGET (widget)' failed

    (firefox:18414): Gtk-CRITICAL **: gtk_drag_get_data: assertion `GTK_IS_WIDGET (widget)' failed

    (firefox:18414): Gtk-CRITICAL **: gtk_drag_get_data: assertion `GTK_IS_WIDGET (widget)' failed

    (firefox:18414): Gtk-CRITICAL **: gtk_drag_get_data: assertion `GTK_IS_WIDGET (widget)' failed

    (firefox:18414): Gtk-CRITICAL **: gtk_drag_get_data: assertion `GTK_IS_WIDGET (widget)' failed

    (firefox:18414): Gtk-CRITICAL **: gtk_drag_get_data: assertion `GTK_IS_WIDGET (widget)' failed

    (firefox:18414): Gtk-CRITICAL **: gtk_drag_get_data: assertion `GTK_IS_WIDGET (widget)' failed

    (firefox:18414): Gtk-CRITICAL **: gtk_drag_get_data: assertion `GTK_IS_WIDGET (widget)' failed

    It seems that the error is similar in nature to rax_m's

    Any help would be great!

    Cheers!
  • bigbreath
    I forgot to mention that although the errors are occurring on Zotero Sync v1.5 sync2.2

    Thanks!
  • noksagt
    https://www.zotero.org/trac/ticket/1101
  • bigbreath
    Thanks for referring ticket 1101, the workaround for ubuntu is to click on "New item" "link to file" then right click "retrieve metadata for pdf"


    Hope you get ticket 1101 fixed

    Thanks heaps!
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