zeliboba7 / gpapers Goto Github PK

There hasn't been a commit for over a year, so i think this is unmaintained.

What steps will reproduce the problem?
1. Select a paper with a full-text PDF available.
2. Open the PDF.
3. Alt-Tab back to the gpapers window or close the PDF

What is the expected output? What do you see instead?

The paper should remain selected, but it gets unselected within a few seconds 
of opening the PDF.

What version of the product are you using? On what operating system?
I am using the latest git revision (7728031bc509) on Ubuntu 12.04.

Please provide any additional information below.

As far as I can tell, this happens because the paper's "read count" attribute 
gets updated when a user opens the associated PDF. I'm guessing that this 
change causes the list of papers to refresh and clear the selection.

My patch just manually re-selects the current paper after updating the "read 
count". I'm not sure if there's a better way to do this--I'm a GTK n00b and I'm 
not particularly well-versed in how the tree widget works.

Traceback (most recent call last):
  File "/usr/bin/gpapers", line 28, in <module>
    import gpapers
  File "/usr/lib/python2.7/site-packages/gpapers/__init__.py", line 50, in <module>
    from gpapers.importer import bibtex, pdf_file
  File "/usr/lib/python2.7/site-packages/gpapers/importer/pdf_file.py", line 24, in <module>
    from pdfminer.pdfparser import PDFParser, PDFDocument, resolve1
ImportError: cannot import name PDFDocument



just tried to install gpapers on fedora 20. Pdfminer is not in fedora repos, 
therefore I had to install it from source pdfminer-20131113, gpapers seem to 
not like something about that. Let me know how can I help you to track down the 
problem. 

gpaper fails to detect duplicates copies of the same paper
I see it computes md5sums of the files imported.
Shouldn't use them to check for duplicates in the library before 
importing the same paper twice?

What steps will reproduce the problem?
1. Import one paper once (for instance from the arxiv)
2. import it again
3. then you have two copies in the local library!

What version of the product are you using? On what operating system?

0.5dev on Debian/GNU linux

What steps will reproduce the problem?
1. Open gpapers
2. Select File->Import DOI...
3. Enter a valid DOI and press OK

What is the expected output? What do you see instead?

The dialog should close and the paper referred to by the DOI should be 
retrieved in the background.  Instead, the dialog stops responding to button 
presses.  The program must then be killed from the system monitor.

What version of the product are you using? On what operating system?

I am using a copy pulled via mercurial on 7/25/2012 (Revision ID:1638d25e2632) 
which I installed on Ubuntu 12.04. I use Python version 2.7.3

Please provide any additional information below.

I noticed a NameError in the import_from_url method in 
gpapers.importer.__init__.py, so I did a little debugging and found that the 
package-global variable 'active_threads' hadn't been declared global in that 
method.  I fixed the problem and now the dialog works as expected.  I have 
attached a patch file which contains the required changes.

pubmed changed their website, so our screen scraping fails.

Thanks for the renewed effort to keep tools like this alive!

I tried starting the current development build but it complains that it can not 
import "Poppler". I tried installing python-poppler but it seems that is not 
the library currently used.

What do I need to install to use it on Ubuntu?

What steps will reproduce the problem?
1. Select File -> Import DOI... and enter 10.1086/648726
2. Press OK and wait.

What is the expected output? What do you see instead?
This should download a paper from the journal "Clinical Infectious Diseases". 
Instead, the job appears to go through (the busy spinner stops) and the GUI 
refuses to respond until forcibly closed and restarted. Upon restarting, a 
blank entry is visible with the correct DOI and an incorrect PDF.

What version of the product are you using? On what operating system?
I am using the latest version from git (1dbb66ebecfb) on Ubuntu 12.04. I have 
pyparsing version 1.5.2-2ubuntu1 installed through my package manager.

Please provide any additional information below.

I haven't figured out what causes this bug, but when I run gpapers in a 
debugger, I can see that it gets stuck calling into the pyparsing library at 
line 146 of the importer.bibtex module (method parse_string(str)).  I'm 
guessing there is either a bug in your grammar or a bug in the pyparsing 
module, but I am not certain, since I've never used that library.

I attached a literal copy of the string being parsed.  Maybe the newline 
characters in the title are the problem?

What steps will reproduce the problem?
1. trying to download individual referenced paper

What is the expected output? What do you see instead?
I would like to see the paper that I want to download.
As well as the drop down should always be in the same order.

What version of the product are you using? On what operating system?
I don't know what version. On Linux

Please provide any additional information below.

What steps will reproduce the problem?
1. start gpapers from a terminal
2. In the File menu, select "Import Files"
3. Select several PDF files
4. The gtk-based GUI seems to hang during the import operation (which takes a 
long time). However, the debug informating sent to the terminal shows that 
gpapers has not hung.

What is the expected output? What do you see instead?

It would be nice to show the progress of the operation in user-friendy way 
using a progress bar (gtk progresbar).

What version of the product are you using? On what operating system?

0.5dev [mercurial changeset f16e6fdafb4d ] on Debian GNU/Linux [wheeze, very up 
to date]

Can you please make a tarball of your source and release it?  This would
facilitate the packaging of your project into the Fedora Package Collection.

Thanks in advance

I put mine here:
  http://code.google.com/p/scholarse
Cheers

I'm trying to run gPapers on my archlinux (build from aur: 
http://aur.archlinux.org/packages.php?ID=23256)
Here is the pythong traceback I'm getting:

$ gpapers 
/usr/lib/python2.7/gpapers ~

note: django provides a web-based administrative tool for your database.  to 
use it, uncomment the commented-out lines under INSTALLED_APPS in settings.py 
and run the following:
     ./manage.py runserver
    then go to http://127.0.0.1:8000/admin/

Traceback (most recent call last):
  File "gPapers.py", line 78, in <module>
    from django.db.models import Q
  File "/usr/lib/python2.7/site-packages/django/db/__init__.py", line 78, in <module>
    connection = connections[DEFAULT_DB_ALIAS]
  File "/usr/lib/python2.7/site-packages/django/db/utils.py", line 93, in __getitem__
    backend = load_backend(db['ENGINE'])
  File "/usr/lib/python2.7/site-packages/django/db/utils.py", line 33, in load_backend
    return import_module('.base', backend_name)
  File "/usr/lib/python2.7/site-packages/django/utils/importlib.py", line 35, in import_module
    __import__(name)
  File "/usr/lib/python2.7/site-packages/django/db/backends/sqlite3/base.py", line 14, in <module>
    from django.db import utils
ImportError: cannot import name utils
~

What steps will reproduce the problem?
1. cd /usr/local/src
2. sudo apt-get install mercurial
3. hg clone https://code.google.com/p/gpapers/ 
4. cd gpapers
5. chmod +x setup.py
6. ./setup.py build
7. sudo ./setup.py install
8. gpapers.py

There were no discernable errors during setup or install (console log attached).

What is the expected output? 

I expected the program to display a GUI interface.

What do you see instead?

Traceback (most recent call last):
  File "/usr/local/bin/gpapers.py", line 30, in <module>
    import gpapers
  File "/usr/local/bin/gpapers.py", line 37, in <module>
    gpapers.main(sys.argv)
AttributeError: 'module' object has no attribute 'main'

What version of the product are you using? 

Whatever is provided at https://code.google.com/p/gpapers/

On what operating system?

Ubuntu 12.04

Please provide any additional information below.

gpapers appears to be broken, at least for non-Python programmers.

What steps will reproduce the problem?
1. Display a paper in gpapers
2. Begin typing in the paper notes text box.

What is the expected output? What do you see instead?
The bookmark or note should be saved to the paper as I type. Instead, the save 
operation takes so long that it is difficult to type. If the general paper 
notes are being edited, the paper gets de-selected every time a single letter 
is saved.

What version of the product are you using? On what operating system?
I am using the latest version from git (Revision 1dbb66ebecfb) on Ubuntu 12.04.

Please provide any additional information below.

I have included a patch which makes a number of changes:
1. Notes and bookmarks are no longer saved automatically when the text box is 
edited.

2. A save button appears next to the 'add bookmark' button when appropriate. 
When clicked, it saves the current text to the paper notes or a bookmark if one 
is selected.

3. When a paper note is saved, the current paper is manually re-selected to 
prevent it from being unselected. This isn't a permanent solution, but it works 
for now.


I realize this isn't the sort of functionality you originally intended, but I 
thought this might work better for people like me with slow computers.

What steps will reproduce the problem?
1. Open gpapers
2. Select File->Import DOI...
3. Enter 10.1021/jm049029u and press OK

What is the expected output? What do you see instead?

I expect the only PDF URL on the target page to be downloaded and added to my 
library.  Instead, the program fails to locate the URL because it has the MIME 
type "application/pdf; charset=UTF-8" rather than just "application/pdf".

What version of the product are you using? On what operating system?

I am using a local copy of revision #1638d25e2632 on Ubuntu 12.04 with Python 
2.7.3

Please provide any additional information below.

I changed the MIME type analysis so it looks for types which start with 
"application/pdf", and this resolves the problem.

It is also worth noting that if you don't have access to the full-text article, 
the file which gets downloaded for this DOI is another PDF which happens to 
also be linked on the article's page.  That is a much more complicated problem 
which might merit its own bug report.

What steps will reproduce the problem?
1. Choose an URL of some abstract from the Arxiv like 

http://arxiv.org/abs/1302.3127

2.Go to the file menu and choose 

"Import URL"

and type "http://arxiv.org/abs/1302.3127"

3. The paper is imported into gpapers local library as expected 
(the imported recognizes that there is a PDF somewhere). However, 
the imported fails to recognize the URL as one from the arxiv an 
fill in the metadata correctly (like title, author,...) as one would
expect (and as what happens when you add it using the built-in arxiv
search facility).

What is the expected output? What do you see instead?

Go to "recently added" and look for the imported paper, you will see something 
like

Title: Arxiv: 1302.3127v2 [math.NT] 14 Feb. 2013
Authors: 
Status: Full text saved in local library.

instead of the correct metadata

Tilte: 
Weighted spectral large sieve inequalities for Hecke congruence subgroups of 
SL(2,Z[i])

Authors: Nigel Watt


What version of the product are you using? On what operating system?

0.5dev [revision f16e6fdafb4d] on Debian GNU/Linux

What steps will reproduce the problem?
1. Create a new collection (click on green plus sign in bottom left corner).
2. Drag an already imported paper from the main window and drop it onto the new 
collection.
3. Click on the new collection to view its contents.

What is the expected output? What do you see instead?
Expect to see that selected paper has been added to that collection.  Instead, 
the collection remains empty.

What version of the product are you using? On what operating system?
gpapers 0.5dev, Ubuntu 12.04.1 LTS

Please provide any additional information below.
Scratching under the hood, I can't seem to get 
handle_left_pane_drag_data_received_event() to fire.  I do see event handlers 
triggering for drag and drop within the main window ("can only reorder 
playlists"), and a external drag and drop of a PDF imports just fine.  I really 
wish I was able to offer a patch, but I'm afraid it's got my meagre skill-set 
stumped.  Any assistance would be greatly appreciated.

I just did an 'svn up' for the first time in a long time today, and then
followed the new installation instructions. I notice that the database
changed from ~/.gPapers to ~/.gPapers-test. I already had a bunch of papers
in my database, so I put it back. Is this going to cause problems? 

Also, (this is very possibly related) I can preview pdfs in the right pane,
but I can't get them to open. Any attempt to do so (double-click the
listing, or right-click and choose 'Open') is met with: 

Traceback (most recent call last):
  File "gPapers.py", line 988, in handle_middle_top_pane_row_activated
    paper.open()
  File "/home/todd/bin/gpapers/gPapers/models.py", line 179, in open
    if full_text and os.path.isfile( self.full_text.path ):
NameError: global name 'full_text' is not defined

What steps will reproduce the problem?
1. Import pdf file

What is the expected output? What do you see instead?
Expect to import a pdf file.

Instead I get:
Traceback (most recent call last):
  File "./gPapers.py", line 332, in import_document
    paper.save_full_text_file(
defaultfilters.slugify(os.path.split(filename)[1].replace('.pdf',''))+'.pdf',
data )
AttributeError: 'Paper' object has no attribute 'save_full_text_file'


What version of the product are you using? On what operating system?
svn:143 on Ubuntu Intrepid (8.10)

Please provide any additional information below.
This issue has been noted by other users on the wiki

I am using debian testing and latest gpapers download

when I launch gpapers, I get the following message -

Traceback (most recent call last):
  File "/usr/local/bin/gpapers", line 28, in <module>
    import gpapers
  File "/usr/local/lib/python2.7/dist-packages/gpapers/__init__.py", line 43, in <module>
    django.core.management.setup_environ(gpapers.settings)
AttributeError: 'module' object has no attribute 'setup_environ'

Could you advise how I can correct this error.
Do I need to change the django-core settings? If so, I would be grateful if you 
can provide step-by-step instructions

Very many thanks
yours
Neil

Align SWNTs with AC