Problem with "Manage Bibtex File" feature

[Jamie O'Sullivan]

Hi all,

I'm using Referencer on Suse 10.3, compiled from source. I'm trying to have a
bibtex file updated automatically with the"Manage Bibtex File" feature, but
when I save changes in my document library I get the following error.

Exception: Invalid URI

The operation underway was: "opening BibTex file"

I have indicated a .bib file I want updated using the "Manage Bibtex File"
dialog. I've tried with versions 1.0.4 and 1.1.5, and the "Export as Bibtex"
option works fine in 1.0.4 only.

Hope someone knows how to get this working,

Cheers,

Jamie

[John Spray]

Jamie,

If you run from a terminal you should see the filenames in use printed
just before this exception occurs: post that output.

John

[Jamie O'Sullivan]

Okay, here's the output from the terminal when I save the library

Updating relative filenames...
Set relfilename_ = Sternberg%201989ESASP.pdf
.
.
.
Set relfilename_ =
McCaughrean%20et%20al%201994%20molecular%20jet%20observations.pdf
Done.
Generating XML...
Done.
TagWindow::onExportBibtex: exception in create 'Invalid URI'

Jamie

Post by John Spray
Jamie,
If you run from a terminal you should see the filenames in use printed
just before this exception occurs: post that output.
John
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[Jamie O'Sullivan]

Sorry, I forgot to paste this output which appeared on startup:

(referencer:12929): Gtk-CRITICAL **: gtk_box_pack_start: assertion
`child->parent == NULL' failed
TagWindow::docSelectionChanged >>

Jamie

Post by Jamie O'Sullivan
Okay, here's the output from the terminal when I save the library
Updating relative filenames...
Set relfilename_ = Sternberg%201989ESASP.pdf
.
.
.
Set relfilename_ =
McCaughrean%20et%20al%201994%20molecular%20jet%20observations.pdf
Done.
Generating XML...
Done.
TagWindow::onExportBibtex: exception in create 'Invalid URI'
Jamie

Post by John Spray
Jamie,
If you run from a terminal you should see the filenames in use printed
just before this exception occurs: post that output.
John
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[John Spray]

That output doesn't appear to come from referencer 1.1.5, "TagWindow"
hasn't existed for several versions.

John

[Jamie O'Sullivan]

Sorry, that output was from 1.0.4. Here's the output from 1.1.5.

int main(int, char**):
setting pythonPath
to :/home/josulliv/Work/Visualisation/Local_Vis:./plugins:/home/josulliv/.referencer/plugins:/usr/local/lib/referencer:
void PluginManager::scan(const std::string&):
found module pubmed
virtual void PythonPlugin::load(const std::string&):
No actions in
successfully loaded pubmed
void PluginManager::scan(const std::string&):
found module lyx
virtual void PythonPlugin::load(const std::string&):
no metadata capabilities in lyx
Glib::ustring PluginManager::findDataFile(Glib::ustring):
Trying /usr/local/lib/referencer/lyx.png
virtual void PythonPlugin::load(const std::string&):
successfully loaded lyx
Preferences::Preferences():
disabling plugin crossref
std::pair<Glib::ustring, int> Preferences::getListSort():
Got column 'title'
DocumentView::DocumentView(RefWindow&, Library&, bool):
Initialising sort column to title
void DocumentView::onSortColumnChanged():
Activated action for column name title
bool Library::load(const Glib::ustring&):
Reading XML...
Done, got 67 docs
Glib::RefPtr<Gdk::Pixbuf> ThumbnailGenerator::lookupThumb(const
Glib::ustring&):
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Jet%20Simulations/Moraghan%20et%20al%202006%20MNRAS.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Jet%20Simulations/Moraghan%20et%20al%202006%20MNRAS.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Observations%20-%20Molecular%20jets/Garcia%20Lopez%20et%20al%202008%20A&A.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Observations%20-%20Molecular%20jets/Garcia%20Lopez%20et%20al%202008%20A&A.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Referencer_libs/Blondin%20et%20al%201990ApJ.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Referencer_libs/Blondin%20et%20al%201990ApJ.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Referencer_libs/Bromm%20et%20al%20ApJ%202002.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Referencer_libs/Bromm%20et%20al%20ApJ%202002.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Referencer_libs/cen%201992%20ApJS.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Referencer_libs/cen%201992%20ApJS.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Referencer_libs/Draine%20%26%20McKee%201993ARA%2BA.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Referencer_libs/Draine%20%26%20McKee%201993ARA%2BA.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Referencer_libs/Glover%20%26%20Abel%202008%20arxiv.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Referencer_libs/Glover%20%26%20Abel%202008%20arxiv.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Referencer_libs/Hollenbach%20%26%20McKee%201979ApJS.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Referencer_libs/Hollenbach%20%26%20McKee%201979ApJS.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Referencer_libs/Kirk%20H%2C%20Johnstone%2C%20Tafalla%202007ApJ.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Referencer_libs/Kirk%20H%2C%20Johnstone%2C%20Tafalla%202007ApJ.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Referencer_libs/Martin%20Schwarz%20Mandy%201996ApJ.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Referencer_libs/Martin%20Schwarz%20Mandy%201996ApJ.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Referencer_libs/O'Connell%20et%20al%202005%20A%26A.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Referencer_libs/O'Connell%20et%20al%202005%20A%26A.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Referencer_libs/O'Sullivan%20%26%20Ray%202000%20A%26A.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Referencer_libs/O'Sullivan%20%26%20Ray%202000%20A%26A.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Referencer_libs/Rosen%20%26%20Smith2003MNRAS.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Referencer_libs/Rosen%20%26%20Smith2003MNRAS.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Referencer_libs/Shapiro%20%26%20Kang%201987ApJ.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Referencer_libs/Shapiro%20%26%20Kang%201987ApJ.pdf'
Couldn't find
thumbnail:'file:///home/josulliv/Work/Documents/Referencer_libs/Sternberg%20%26%20Dalgarno%201989ApJ.pdf'
Has valid failed
thumbnail: 'file:///home/josulliv/Work/Documents/Referencer_libs/Sternberg%20%26%20Dalgarno%201989ApJ.pdf'

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_filter_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_sort_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_filter_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_sort_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_filter_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_sort_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_filter_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_sort_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_filter_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_sort_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_filter_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_sort_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_filter_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_sort_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_filter_real_unref_node:
assertion `elt->ref_count > 0' failed

(referencer:21777): Gtk-CRITICAL **: gtk_tree_model_sort_real_unref_node:
assertion `elt->ref_count > 0' failed
void RefWindow::run():
entering main loop
void RefWindow::onManageBibtex():
Got bibtextarget = Thesis%20Bibtex%2Fthesis.bib
Got absolute path =
Got relative path = Thesis Bibtex/thesis.bib
newtarget: Thesis%20Bibtex%2Fthesis.bib
bool Library::save(const Glib::ustring&):

file:///home/josulliv/Work/Documents/Thesis%20Bibliography/Thesis%20Bibliography.reflib
~
file:///home/josulliv/Work/Documents/Thesis%20Bibliography/Thesis%20Bibliography.reflib.save-tmp
Updating relative filenames...
void Document::updateRelFileName(const Glib::ustring&):
Set refilename_ 'Sternberg%201989ESASP.pdf'
Set refilename_ 'Flower%20%26%20Roueff%20JPhys%201998.pdf'
Set refilename_ 'suttner%20el%20al%201997A%26A.pdf'
Set refilename_ 'Flower%20et%20al%201989%20JPhysB.pdf'
Set refilename_ 'Hollenbach%20%26%20McKee%201979ApJS.pdf'
Set refilename_ 'Rosen%20%26%20Smith2003MNRAS.pdf'
Set refilename_ 'draine%20et%20al%201983%20ApJ.pdf'
Set refilename_ 'Mandy%20et%20al%201993ApJS.pdf'
Set refilename_ 'Yoshida%20et%20al%202006%20ApJ.pdf'
Set refilename_ 'Turner%20et%20al%201977ApJS.pdf'
Set refilename_ 'rosen%20%26%20smith%202004%20A%26A.pdf'
Set refilename_ 'Shapiro%20%26%20Kang%201987ApJ.pdf'
Set refilename_ 'O'Connell%20et%20al%202005%20A%26A.pdf'
Set refilename_ 'Martin%20Schwarz%20Mandy%201996ApJ.pdf'
Set refilename_ 'walmesley%20et%20al%202004%20A%26A.pdf'
Set refilename_ 'Lepp%20%26%20Shull%201983ApJ.pdf'
Set refilename_ 'yoshida%202007%20arxiv'
Set refilename_ 'Hartigan%20et%20al%201994%20ApJ.pdf'
Set refilename_ 'Le%20Bourlot%20et%20al%202002MNRAS.pdf'
Set refilename_ 'le%20bourlot%20et%20al%201999%20MNRAS.pdf'
Set refilename_ 'cen%201992%20ApJS.pdf'
Set refilename_ 'Blondin%20et%20al%201990ApJ.pdf'
Set refilename_ 'Flower%20et%20al%202007%20JPhysB.pdf'
Set refilename_ 'raga%20et%20al%202002%20A%26A.pdf'
Set refilename_ 'Shull%20%26%20Beckwith%201982%20annurev.aa.pdf'
Set refilename_ 'Schwartz%201975ApJ.pdf'
Set refilename_ 'Brand%20et%20al%201988ApJ.pdf'
Set refilename_ 'Smith%20%26%20Rosen%202003MNRAS.pdf'
Set refilename_ 'Glover%20%26%20Abel%202008%20arxiv.pdf'
Set refilename_ 'suttner%20el%20al%201997IAUS.pdf'
Set refilename_ 'Raga%20et%20al%202004%20ApJSS.pdf'
Set refilename_ 'le%20bourlot%20de%20forets%20flower%202000.pdf'
Set refilename_ 'Raga%20et%20al%201995A%26A.pdf'
Set refilename_ 'Flower%20et%20al%202003%20MNRAS.pdf'
Set refilename_ 'Glover%202003%20ApJ.pdf'
Set refilename_ 'Voelker%20et%20al%201999%20A%26A.pdf'
Set refilename_ 'Tine%20et%20al%201997%20ApJ.pdf'
Set refilename_ 'O'Sullivan%20%26%20Ray%202000%20A%26A.pdf'
Set refilename_ 'raga%20et%20al%202003%20RMAA.pdf'
Set refilename_ 'de%20gouveia%20dal%20pino%202005%20ASR.pdf'
Set refilename_ 'Flower%20et%20al%201986%20MNRAS'
Set refilename_ 'Draine%20%26%20McKee%201993ARA%2BA.pdf'
Set refilename_ 'Zinnecker%20et%20al%201997IAUS.pdf'
Set refilename_ 'Omukai%20et%20al%202000%20ApJ.pdf'
Set refilename_ 'Anninos%20et%20al%201997%20New%20Astronomy.pdf'
Set refilename_ 'Lee%20et%20al%20arxiv%202008.pdf'
Set refilename_ 'Lee%20et%20al%202007%20ApJ.pdf'
Set refilename_ 'Sternberg%20%26%20Dalgarno%201989ApJ.pdf'
Set refilename_ 'Smith%20et%20al%202007%20A%26A.pdf'
Set refilename_ 'raga%20et%20al%202004%20RMAA.pdf'
Set refilename_ 'raga%20et%20al%202000%20RMAA.pdf'
Set refilename_ 'Biro%20et%20al%201995MNRAS.pdf'
Set refilename_ 'Flower%20%26%20Roueff%201998%20JPhysB.pdf'
Set refilename_ 'Bromm%20et%20al%20ApJ%202002.pdf'
Set refilename_ 'nomura%20%26%20millar%202005%20A%26A.pdf'
Set refilename_ 'Smith%20et%20al%201997A%26A.pdf'
Set refilename_ 'Kirk%20H%2C%20Johnstone%2C%20Tafalla%202007ApJ.pdf'
Set refilename_ 'Flower%20et%20al%202000MNRAS.pdf'
Set refilename_ 'Galli%20%26%20Palla%20A%26A%201998.pdf'
Set refilename_ 'Glover%20%26%20MacLow%202007%20ApJ.pdf'
Set refilename_ 'Chang%20%26%20Martin%201991ApJ.pdf'
Set refilename_ 'rate06.pdf'
Set refilename_ 'Abel%20et%20al%20New%20Astronomy%201997.pdf'
Set refilename_ 'Moraghan%20et%20al%202006%20MNRAS.pdf'
Set refilename_ 'eisloeffel%2097'
Set refilename_ 'Garcia%20Lopez%20et%20al%202008%20A&A.pdf'
Set
refilename_ 'McCaughrean%20et%20al%201994%20molecular%20jet%20observations.pdf'
bool Library::save(const Glib::ustring&):
Done.
Generating XML...
Done.
Writing bibtex, manage_target_ = Thesis%20Bibtex%2Fthesis.bib
bibtextarget =
file:///home/josulliv/Work/Documents/Thesis%20Bibliography/Thesis%20Bibtex%2Fthesis.bib
void Library::writeBibtex(const Glib::ustring&, const std::vector<Document*,
std::allocator<Document*> >&, bool, bool):

file:///home/josulliv/Work/Documents/Thesis%20Bibliography/Thesis%20Bibtex%2Fthesis.bib
~
file:///home/josulliv/Work/Documents/Thesis%20Bibliography/Thesis%20Bibtex%2Fthesis.bib.export-tmp
exception in create Invalid URI
bool Library::save(const Glib::ustring&):
Done.

Post by John Spray
That output doesn't appear to come from referencer 1.1.5, "TagWindow"
hasn't existed for several versions.
John
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[Jamie O'Sullivan]

Hi,

After doing some reorganizing of my directories and starting a new library
from scratch, I found that I wasn't getting the error anymore. This appears
to me to have something to do with the directory names, in particular the
value of "bibtextarget". Whereas before I had directories with spaces or
underscores, now the directory names don't contain any special characters.

Could this have been the cause of the problem?? This is the only thing I can
see that changed in my case, and comparing the outputs (the new output is
pasted below) the error seemed to occur right after the file paths for
thesis.bib and thesis.bib.export-tmp were output.

If it is the case, well for the moment having no spaces is a small price to
pay for having this working! :-)

Jamie



void RefWindow::onManageBibtex():
Got bibtextarget =
Got absolute path =
Got relative path =
void RefWindow::manageBrowseDialog(Gtk::Entry*):
manage path:
file:///home/josulliv/Work/Thesis/mythesis/references/thesis.bib
library path:
file:///home/josulliv/Work/Thesis/mythesis/references/thesis.reflib
relative path: thesis.bib
void RefWindow::onManageBibtex():
newtarget: thesis.bib
bool Library::save(const Glib::ustring&):
file:///home/josulliv/Work/Thesis/mythesis/references/thesis.reflib ~
file:///home/josulliv/Work/Thesis/mythesis/references/thesis.reflib.save-tmp
Updating relative filenames...
void Document::updateRelFileName(const Glib::ustring&):
Set refilename_ 'Papers/suttner%20el%20al%201997A%26A.pdf'
Set refilename_ 'Papers/Rosen%20%26%20Smith2003MNRAS.pdf'
Set refilename_ 'Papers/Smith%20%26%20Rosen%202003MNRAS.pdf'
Set refilename_ 'Papers/suttner%20el%20al%201997IAUS.pdf'
Set refilename_ 'Papers/Smith%20et%20al%202007%20A&A.pdf'
Set refilename_ 'Papers/Smith%20et%20al%201997A%26A.pdf'
Set refilename_ 'Papers/O'Connell04.pdf'
bool Library::save(const Glib::ustring&):
Done.
Generating XML...
Done.
Writing bibtex, manage_target_ = thesis.bib
bibtextarget =
file:///home/josulliv/Work/Thesis/mythesis/references/thesis.bib
void Library::writeBibtex(const Glib::ustring&, const std::vector<Document*,
std::allocator<Document*> >&, bool, bool):
file:///home/josulliv/Work/Thesis/mythesis/references/thesis.bib ~
file:///home/josulliv/Work/Thesis/mythesis/references/thesis.bib.export-tmp
bool Library::save(const Glib::ustring&):
Done.