Can someone try the new version (1.0.6) and tell me whether the reported problems are solved? It works at my computer...

Zotfile 1.0.6 Changes:

- The filename for items which already have an attachment was not correctly determined (author_2000_titel23.pdf instead of author_2000_titel3.pdf when the file author_2000_titel2.pdf already exists)
- zotfile stopped working after using it a couple of times after starting firefox

can you check out whether 1.0.4 still works?

http://www.columbia.edu/~jpl2136/zotfile_104.xpi

I finally tested zotfile 1.0.5 under Zotero 2.0b7.2, Snow Leopard, and ff3.5.3 and it works great--I zotted 3 separate item/paper combinations with no troubles. Thanks Joscha! Despite the great rename from metadata feature of Zotero proper, I still find it more convenient to have Zotfile pull the file out of the downloads folder, attach it to the parent item, and do the renaming all in one step.

...106b did not work for me, but 1.0.4 works fine. Great tool!

I uninstalled 1.0.6 and installed version 1.0.4 --everything seems to be working fine.

Thanks
gary

Hi Joscha,

Sorry for the delay. No, 1.06 doesn't work for me either. This is firefox 3.5.3, zotero 2.0b7.4, and windows 2000SP4.

It is a small thing, but I notice that 1.06 shows up in the add-ons list as version 1.05. Also, 1.04 shows up as 1.03.

I will test again on linux. Maybe it is different there.

-Greg

I figured out the problem with attachments not working on linux. Here is the fix:

In moveFile, change this:

return(file.path);

to this:

dir.append (filename);
return dir;

Then, if you do the above, you can delete the stuff that creates "newfile" from "newfile_path". Instead you can just do this:

var newfile=this.moveFile(lastfile, this.prefs.getCharPref("dest_dir"), filename);

This is esp. to GregSharp -- I'm also using linux, and I'm also not having a problem where the file gets moved and renamed, but not attached. The item doesn't have other attachments, so that's not the problem. I tried following Gregsharp's instructions about modifying the extension, but I'm not sure I did it right--I edited file:///home/peter/.mozilla/firefox/lqs6604f.default/extensions/zotfile@columbia.edu/chrome/content/zotfile/zotfile.js
so it looks like this from line 260-337 ... any suggestions? did I not edit it correctly, or edit the wrong thing?

moveFile: function(file, destination, filename){
// create a nslFile Object of the destination folder
var dir = Components.classes["@mozilla.org/file/local;1"].
createInstance(Components.interfaces.nsILocalFile);
dir.initWithPath(destination);

// move file to new location
file.moveTo(dir, filename);
// changing this in hopes it fixes for linux: http://forums.zotero.org/discussion/5301/3/zotero-plugin-to-rename-move-and-attach-your-pdfs-to-zotero-items/
// return(file.path);
dir.append (filename);
return dir;

},

getFilename: function(item){
// create the new filename from the selected item
var item_type = item.getType();
var rename_rule=this.prefs.getCharPref("renameFormat");
if(item_type==19) var rename_rule=this.prefs.getCharPref("renameFormat_patent");
if (!this.prefs.getBoolPref("useZoteroToRename")) filename=this.createFilename(item, rename_rule);
if (this.prefs.getBoolPref("useZoteroToRename")) filename=Zotero.Attachments.getFileBaseNameFromItem(item.itemID);
return(filename);
},

zotfileAction: function(){
var items = ZoteroPane.getSelectedItems();
var item = items[0];

//check whether it really is an bibliographic item (no Attachment, note or collection)
if (!item.isAttachment() & !item.isCollection() & !item.isNote()) {

// create the new filename from the selected item
filename=this.getFilename(item);

// get the last modified file from a directory
lastfile=this.lastFileInDir(this.prefs.getCharPref("source_dir"), this.getpara("filetypes"));
if(lastfile!=-1 & lastfile!=-2 ) {
var lastfile_oldpath=lastfile.leafName;

// complete filename with extension and then move the file to destination
var filetype=this.getFiletype(lastfile.leafName);
var filename = filename + "." + filetype;

var confirmed=1;
if (this.prefs.getBoolPref("confirmation")) var confirmed=confirm("Do you want to rename and link the file \'" + lastfile_oldpath + "\' to the currently selected Zotero item?");
if(confirmed){
var newfile_path=this.moveFile(lastfile, this.prefs.getCharPref("dest_dir"), filename);

// recreate the lastfile nslFile Object
// (for some reason the Attachment is linked to the wrong location without recreation)
// changing based on suggestion here: http://forums.zotero.org/discussion/5301/3/zotero-plugin-to-rename-move-and-attach-your-pdfs-to-zotero-items/

// var newfile = Components.classes["@mozilla.org/file/local;1"].
// createInstance(Components.interfaces.nsILocalFile);
// newfile.initWithPath(newfile_path);

var newfile=this.moveFile(lastfile, this.prefs.getCharPref("dest_dir"), filename);

// Attach last file to selected Zotero item
if(this.prefs.getBoolPref("import")) {
// Attach last file to selected Zotero item
Zotero.Attachments.importFromFile(newfile, item.itemID);

//Delete the old file that is not longer needed
newfile.remove(false);
}
if(!this.prefs.getBoolPref("import")) Zotero.Attachments.linkFromFile(newfile, item.itemID);

// Show message
this.infoWindow("Zotfile","File \'" + lastfile_oldpath + "\' changed to \'" + newfile.leafName + "\' and added as an attachment.",8000);
}
}
else this.infoWindow("Zotfile Error","Unable to find file in " + this.prefs.getCharPref("source_dir"),8000);
}
else this.infoWindow("Zotfile Error","Selected item is either an Attachment, a note, or a collection.",8000);
}
};

So, it turns out that the moveTo nsIFile method might be broken on linux because, although it moves the file it fails to update its path information in the object. Then when you make the call to Zotero.Attachments.importFromFile the filename information is incorrect and it can't attach it.

I changed the moveFile code to look like this:

moveFile: function(file, destination, filename){
// create a nslFile Object of the destination folder
var dir = Components.classes["@mozilla.org/file/local;1"].
createInstance(Components.interfaces.nsILocalFile);
dir.initWithPath(destination);

// move file to new location
file.moveTo(dir, filename);
var newfile = Components.classes["@mozilla.org/file/local;1"].
createInstance(Components.interfaces.nsILocalFile);

// HACK (is there a better way to set the path?)
newfile.initWithPath(destination+'/'+filename);

return(newfile);
},

and now instead of all the stuph with the newfile_path in zotfileAction, I just make this call:

var newfile=this.moveFile(lastfile, this.prefs.getCharPref("dest_dir"), filename);

With that hack in place, where we create a new file handle to the newly renamed file, it seems to work. The old workaround failed for the same reason because moveFile was returning the file.path, which hadn't been updated properly.

I wonder if this is a full on Mozilla bug...

Also, does anyone know the proper way to join a directory and file in javascript that will be cross-platform? In python I would use os.path.join, but I don't know what to do here, so I just concatenated the strings, but it will clearly not work on windows.

Best,
Per

Hi. I've seen in the website
and Zotfile works on linux. (ubuntu 10.04 beta2+updates) firefox 3.6.3 zotero 2.0.2.
Tnx

Just a thank you. Zotfile has really improved my satisfaction with Zotero! Perhaps it should be worked into the main Zotero package. Anyway, keep up the good work!

It would not be difficult to make Zotfile do this, but it would apply to only files imported by Zotfile.

There is some discussion about this in the forums. Probably the best way to do this would be either a standalone script that reads Zotero database and copies files (or links in operating systems that support this) to a folder structure or a plugin that does this. Not particularly difficult to code, but this far no-one has done it.

Here is my take on the problem. This perl script creates a folder structure that contains links to the Zotero data directory to approriate files in the form of JournalName/Year/filename. If you take this script and schedule it to run daily, it currently does or can be easily modified to most of the things in the post above. Currently only works for items stored inside Zotero because it was not immediately apparent from the Zotero database how paths to linked items are encoded.

Tested on OS X 10.6 and should work without modifications with other unixes too.



#!/usr/bin/perl

use DBI;

my $zoterostorage="/Users/mronkko/Documents/Research/Zotero Data";
my $target="/Users/mronkko/Documents/Research/Articles";

my $dbh = DBI->connect("dbi:SQLite:dbname=$zoterostorage/zotero.sqlite","","");

# Query all PDF attachments

my $sth = $dbh->prepare('SELECT idv1.value, idv2.value, i2.key, ia.path FROM itemDataValues idv1, itemDataValues idv2, itemData id1, itemData id2, items i, items i2, itemAttachments ia WHERE i.itemID=id1.itemID AND i.itemID=id2.itemID AND idv1.valueID=id1.valueID AND id1.fieldID=14 AND idv2.valueID=id2.valueID AND id2.fieldID=12 AND ia.sourceItemID=i.itemID AND ia.linkMode=1 AND ia.mimeType="application/pdf" AND i2.itemID=ia.itemID' ) or die "Couldn't prepare statement: " . $dbh->errstr;

$sth->execute() or die "Couldn't execute statement: " . $sth->errstr;

print "Building links\n";

while (@data = $sth->fetchrow_array()) {
# date, journal, key, path
my $year=substr($data[0],0,4);
my $file=substr($data[3],8);
my $itempath="$zoterostorage/storage/$data[2]/$file";
my $linkpath="$target/$data[1]/$year/$file";
print "\nLinking item\n$itempath\n--> $linkpath\n\n";

#Create the link, but only if the file exists
if(-e $itempath){

#And if the same file is not already linked
if(-e $linkpath){
print "Skipping because link already exists";
}
else{
#Ensure that the path exists

unless(-d "$target/$data[1]"){
mkdir "$target/$data[1]" or die "Unable to create path $target/$data[1]";
}
unless(-d "$target/$data[1]/$year"){
mkdir "$target/$data[1]/$year" or die "Unable to create path $target/$data[1]/$year";
}

symlink($itempath,$linkpath) or die "Unable to create link";
}
}
else{
print "Skipping non-existingfile";
}
}


Hi,

http://www.columbia.edu/~jpl2136/zotfile_150b.xpi

here is a new version of zotfile for testing. The new version can also (batch) rename and move existing attachments which I think a lot of people would like to do. Please be careful with the batch renaming at this point! You can basically select all the items in your library, start the zotfile function 'ZotFile - Rename Existing Attachments' and all attachments are moved and renamed (+ changed back and forth between imported to linked) according to the logic defined in the zotfile options.

It would be good to hear whether the new version works for you or not and what system you are using (Is there anyone using FF4 on Lunix?).

Here is a list of changes:
- FF4 compatible
- Rename Existing Attachments. It's now also possible to (batch) rename and move existing attachments. Specifically, there are now two functions: 1) add new attachments items ('ZotFile - Attach New File') and 2) rename and move existing attachments. You can now select one or multiple items, right click and select 'ZotFile - Rename Existing Attachments'. The attachments from these items will be renamed and moved according to the zotfile logic. So in principle, you can seamlessly move between linked or imported attachments or different naming conventions. Currently, items with multiple attachments are skipped, though, but I plan to change that.
- I have removed the zotfile button. Currently you can only start the two function by right clicking on items and selecting them from the context menu. What do you think about that? Should there be a button? I would like to add zotfile to the drop-down menu from zotero's paper-clip button but I don't know how to do that right now. Any ideas?

And here is what I am still planing for 1.5:
- make the whole thing work for items with multiple attachments
- hopefully solve the bugs (not working in second window, linux compatible)

Maybe I will also look into the folder thing but I am not sure yet. I agree with those who wrote that it's not difficult at all but I just have to make sure that I am not spending too much time with this. Also, I am pretty much only doing statistical programming so that I didn't had any javascript background when I started this but was able to learn things quickly. So I can only encourage people to try things out as long as you have some programming background. I am also happy to help if you are looking at the zotfile code. I think that the biggest hurdle right now is the bad documentation of the Zotero API.


Joscha

ps: Does any one know how to a) add the zotfile functions to zotero's paperclip drop-down menu and b) how I can make the zotfile options in the right click menu only appear for certain item types?

ps2: For those who have already looked at the zotfile code: zotfileAction is not called AttachNewFile.

@ Joscha

Thank you very much for both updates. I tested b2 briefly and it seems it perfectly works with Windows (with \ for folders).

I just noticed that the functions appears twice in the context-menu. Maybe it is a problem from the modifications I previously did. However, it shouldn't, since I desinstalled the previous, modified version of Zotfile before installing the new one.

Is there a special reason for sometimes repeating an if statement with the opposite expression rather than using something like "else" ?

For what concerns the removed button: to my opinion, this is not mandatory, but might be useful to "remind" the user that Zotfile is installed :D.
However, what may be more useful, but certainly more difficult to program, is the possibility to have keyboard shortcut(s).

I had a quick look at your code and, indeed, it's far more elegant than my tentative. I will look at it in further detail to see what and how it might be improved (regarding e.g. your questions).

Thanks again!

Thierry

P.-S.: Is the preference ".import" a new one, too?