Zotero database browser for iOn

[stsu]

Zotero is a firefox extension to manage research resources.
I wrote a small program named "zbi" which browse the database of Zotero and open files by appropriate viewers in DR1000s.

Version 0.9_1
* The bug below is fixed.
* Some small bugs (hopefully) fixed.

Version 0.9
See the post below (dated 04-08?09?) for detail.
* Works for both zotero1 and zotero2.
* Query by any combination of collection, tag, creator etc is available.
* Optionally, you can add Publication column.
* Menu added.
* Appropriate tags only will be displayed.
* PC utilities to create zbi's database included.

* I found a small bug: Attachment files in "Trash" will be listed. I will fix it soon.


Version 0.7_1
* A small but maybe IMPORTANT modification. See the post below (dated 04-06) for detail. I recommend that version 0.7 users update zbi to this version or to version 0.9.
Corresponding new versions zbi2-0.7_1, zbi2-0.71_1 for zbi2 are also available.
* A small bug fix. Recently opened items would not doubly listed.


VERSION 0.7
* Recently opened 10 items are listed on starting the program.
You can change the number "10" by editing the file "zbi.history" in "_zbi/share/zbi". (This file is created after you first quit the program.)


WARNING!
This is the alpha release (and I am a beginner in programming),
so the program could have serious bugs.

REQUIRE:
DR1000S firmware 1.7.1
(Try zbiXX-1.6 if you are using firmware 1.6.)
Zotero 1.0
(I posted a version which might work for zotero 2.0 below.)

INSTALL:
Unpack the zip file, then you will get a directory named "Programs". Copy the "Programs" directory to the root of your SD card.
(SD-card-root/Programs/_zbi etc. )

USAGE:
1. Copy entire Zotero data directory (the default name is "zotero", which contains a file named "zotero.sqlite" and a directory named "storage") to the root of your SD card
(or wherever you want, in that case, edit the shortcut file zbi.desktop).
2. Go to Home > Documents > Programs and use the zbi shortcut to start it.
3. Use the stylus to select an item. (I have not yet implement key navigation.)
(1) Choose a collection. ("*" for all the collections.)
(2) Select Tag/Title-Creator buttons/Added button. Selection by Tag/Title-Creator/Added are exclusive.
(3) Select an item.
(4) Select an attachment file, then it will be opend by the default viewer for the file extension.

NOTES:
1. By default, zbi will create the metadata.db file (if not exists) at opening
an attachment file. If you do not want it, then add "0" to the end of
the last line of the shortcut file zbi.desktop as follows:

Exec=/media/mmcblk0p1/Programs/_zbi/bin/zbi /media/mmcblk0p1/zotero/zotero.sqlite 0

2. zbi opens the database file zotero.sqlite in read-only mode and does not affect the zotero data directory except creating medadata.db files as described above. However, I am not sure what happens if you sync the zotero data directory with your PC.
3. zbi looks /apps/er/sys/ctb/filetypes/ for the viewer command.

TODO(someday):
key navigation, multiple tag selection, internationalisation. ...

Comments and suggestions are welcome.
Enjoy!

[Mackx]

Hi stsu,

The user base for the DR1000 is rather low, and it seems not many of them use Zotero. Anyway (although I did not really look into it) great work and very nice of you to share it with us.

If you need help on some DR specific programming problems, feel free to ask them here, there are enough people that are able to help you on this forum.

[tjdean256]

Hi stsu,

This is very promising and may be an important part of being able to use the DR as a self-contained portable library. I installed Zotero and converted my 10,000+ literature file. I installed your program and transferred the sqlite database to my DR. However, when I launch zbi, the program, I get a "please wait" then it reverts back to the program list. I have double-checked the locations of the files against your instructions and am pretty sure I got them right. If this lets me find articles on my DR, this will be tremendous.

td

[stsu]

Hi Mackx,

Thank you for your comments.
I might port the program to DR800 and/or iLiad in the future.

Your article on porting Xournal and source code of mxSudoku were
quite nice starting points for me. I appreciate it.

[stsu]

Hi td,

Thank you for trying the program.
Could you check the following points?

1. My instruction and the file zipping might be bad. Directories should be located as follows:
SD-card-root/Programs/_zbi
SD-card-root/zotero
(I changed the way of zipping in the updated version.)

2. The firmware of my DR is 1.7.1. I think the program works on 1.7. However, on 1.6, it would not (for the change of libs). If you use the firmware 1.6, could you try zbi0.7-1.6.zip. It worked on the 1.6 emulator.

3. The version of zotero I am using is 1.0. If you are using zotero 2.0, then the program would not work because of the change of database structure. I would write some codes for zotero 2.0 in the future. (Sooner or later, I have to move to zotero 2.0.)

4. The number of items. My zotero library contains 1,000 - 2,000 items and in my case, the search time is quite short, but I am not sure if the program work well for big number of items.

I should have written some words on software versions. Sorry for inconvenience.

[tjdean256]

OK, I installed version 2 of Zotero. I will install ver 1.

I did unzip to the root directory, but it created a x:\zbi\programs directory. I just moved the contents of that directory to the programs directory - not a problem for me. I looked at the .desktop file and noticed that the program looks for the database in a x:\zotero directory. In trouble shooting I copied the Zotero database both the root and to this directory.

I will let you know how this goes.

Can zbi search the database?

Thanks for this program.
td

[tjdean256]

I installed version 1 of Zotero and installed your update. The desktop shortcut expects the database in a folder named zotero. The program starts and acts like it is reading the database but reverts back to the program folder listing. zbi seems to still be loaded because I have to bring up the menu and select return to folder to get the screen to respond to the stylus again.

Will try a smaller database next. The current sqlite database is 22MB.

td

[tjdean256]

I got the program to work. I cut the database from 11,000 entries to 1700. It's interesting that the size of the database only went down 6 MB from 22 MB. It worked with ~4000 but it seemed slow. It would be nice to see the publication along with the title and creator (author). A Soundex query on author or keyword would be immensely useful. It definitely looks promising.

td

[stsu]

Originally Posted by tjdean256

I got the program to work. I cut the database from 11,000 entries to 1700. It's interesting that the size of the database only went down 6 MB from 22 MB. It worked with ~4000 but it seemed slow. It would be nice to see the publication along with the title and creator (author). A Soundex query on author or keyword would be immensely useful. It definitely looks promising.

td

My native language is Japanese and it is difficult for me to design applications using Soundex, for I cannot make a Soundex query. It is often the case that I do not know how to pronounce the name of the author.

By the way, did you copy the entire zotero directory (not only zotero.sqlite) to DR?
zbi is not only a database browser but a file launcher. You can open attachment files from zbi.

[stsu]

I modified the code slightly for zotero 2.0. I tested it on the emulator and it seems to work with zotero 2.0. But I am not usig zotero 2.0, hence I am not sure if it goes well.

WARNING: This version does not work for zotero 1.0.

[tjdean256]

None of the entries in my literature citation database have attachments so I did not try out that feature. One of my primary uses of the DR1000S is to store PDFs of articles from scientific journals. I name them by the authors and date and keep them in folders named after the journal that published the article. I locate the files using a desktop program similar to EndNote. The ability to look up an article in a searchable database on the DR would help immensely when I am away from my office desktop computer. That is why I am interested in the utility you wrote. Just adding an additional column in the title - creator listing would greatly aid in locating an article since everything is stored according to the publication title. Being able to query the database based on any combination of creator, title, and keyword would be an added benefit.

I installed zbi2 and it runs fine. It still has trouble with the full 11,000 record database. One thing I found out is if a journal file exists in the same directory as the sqlite file, zbi will abort and return to the directory listing.

Thanks for you work on this program.

td

[stsu]

That's exactly the way I am using DR and that's why I wrote this program. In my case, I am using zotero to organize my PDFs and PDFs are, by default, treated as attachments in zotero.

Currently, query by the combination of creator, title and keywords etc. makes searching very slow, so that I disabled it. I hope to make it possible in the future. I also want to make this program be able to work with large number of items.

Here I attach a test version of zbi2 (for zotero 2.0) with publication title column. I have not tested it fully, but I think it may have the following bugs:
Items without publication title will not be listed.
On clicking Publ buttons, items without creator will not be listed.
The journal issue is not fixed at all.

I am going to be busy, so I cannot fix the bugs for a while. Sorry for inconvenience.

The attached file contains only the program zbi2 itself. Unpack and copy the file "zbi2" into "Programs/_zbi2/bin/".

WARNING: This is a test version.

[tjdean256]

Thanks. I will give this version a try as soon as I can and let you know how it goes. Every little bit helps.

Do you attach the PDF files in Zotero before you copy the database to the DR? That would take me forever because I now have a large number of PDF files.

Another question: I don't know much about sqlite. Is an index built within the file or does sqlite do a line by line search for matches of a query?

td

[tjdean256]

Hi Stsu,

I got a chance to work a little more with zbi2. If found that I need to rotate the screen to landscape to see all of the fields. Even then only a few letters of the publication name shows on the right.

It runs and filters fairly quick. I move my 22 MB Zotero database to the DR1000S and launched the program. It has difficulty updating the screen. If you didn't force an update (bring up the menu or show the battery) you wouldn't think it was working. It hangs when you filter on added. The other filters seem to work. I need to work with it some more. Wanted to give you some feedback since it had been a while since I last posted.

Lot's of potential with this program

td

[stsu]

Thank you for your information, td.

I largely changed the code and am testing it.
I would like to post the new version soon.

Do you attach the PDF files in Zotero before you copy the database to the DR? That would take me forever because I now have a large number of PDF files.

Zotero do most of the work automatically when you add a new item, specially when you get a new item from the web. I gradually adding my old files (before zotero) by hand. I do not know if there exist some ways to inporting the existing database to zotero.