We're now flagging the DB for repair on startup errors, so if that fixes
the problem (e.g., because of our undiagnosed skipped-schema-update-step
problem), we'd still like to know about it.
Show a popup if DB corruption is detected with a warning to avoid
storing the data directory in cloud storage, a link to a support page
with more information, and a button to restore from the last automatic
backup.
Also show the warning about cloud storage again after restoring from the
last automatic backup.
- Include file path
- Show separate message for linked files mentioning Linked Attachment
Base Directory
- Link to separate support page for linked files
Say "Use the [local|remote] version for all remaining conflicts" for
everything instead of saying "Use [local|remote] fields for all
remaining conflicts" for some conflicts.
This also fixes a test failure after 54343c49fb.
This changes the way item types, item fields, creator types, and CSL
mappings are defined and handled, in preparation for updated types and
fields.
Instead of being predefined in SQL files or code, type/field info is
read from a bundled JSON file shared with other parts of the Zotero
ecosystem [1], referred to as the "global schema". Updates to the
bundled schema file are automatically applied to the database at first
run, allowing changes to be made consistently across apps.
When syncing, invalid JSON properties are now rejected instead of being
ignored and processed later, which will allow for schema changes to be
made without causing problems in existing clients. We considered many
alternative approaches, but this approach is by far the simplest,
safest, and most transparent to the user.
For now, there are no actual changes to types and fields, since we'll
first need to do a sync cut-off for earlier versions that don't reject
invalid properties.
For third-party code, the main change is that type and field IDs should
no longer be hard-coded, since they may not be consistent in new
installs. For example, code should use `Zotero.ItemTypes.getID('note')`
instead of hard-coding `1`.
[1] https://github.com/zotero/zotero-schema
In particular, remove code related to opening/closing the Zotero pane,
which affects tests. The pane is now opened by default in Firefox, which
brings its behavior closer to the main version.
The menu includes all user interface options from the General
preferences (now removed from the preferences), toggles for the
collections pane, item pane, and tag selector, and, at long last, a
toggle for recursive collections ("Display Items from Subcollections").
The collections pane and item pane no longer reopen automatically when
restarting Zotero. People might still close them by mistake and not find
this menu, but we'll see how it goes.
Closes#1372
Without an accompanying "Restore from Online Library" option, which
doesn't currently exist, "Restore to Online Library" can be interpreted
two ways. It's clear if you read the text below or the confirmation
prompt, but if you don't you might accidentally do something very bad.
This was almost certainly also translated in misleading ways in other
locales.
- Fix don't-show-again checkbox for non-DB items
- Tweak warning text
- Don't show comma after year if year is missing (which it shouldn't be)
- Remove redundant try/catch
- Check for retracted items using data from Retraction Watch
- Show an X next to retracted items in the items list, and show a
scary message at the top of the item pane with more info and links.
- Lookup is done in a privacy-preserving manner using k-anonymity --
the server is unable to determine the specific items that exist in
the client, so people who don't sync don't need to share any library
data (though the server doesn't log the lookups anyway).
TODO:
- Pop up an alert when new items are found
- Show a confirmation prompt when citing a retracted item
- Support items without DOIs or PMIDs
- Add a proper PMID field and expand DOI to more item types so these
values don't need to be parsed out of Extra
- Clear the banner immediately when all possible fields are cleared
instead of waiting a few seconds
This should have been obvious, but we've been seeing Terminal when testing
because we're launching Zotero from the Terminal. Users with installed
Zotero version actually see 'Zotero' in instead of Terminal.
If there's no translated PDF or the translated PDF fails and the item
has a DOI, check Zotero's Unpaywall mirror for possible sources and try
to download one of those.
Unlike with "Add Item by Identifier" and "Find Available PDF" in the
item context menu, this does not try the DOI/URL page, since it would
result in more data leakage and most of the time you'd be saving from
the DOI page already. We could consider offering it as an option, but
for it to be useful, you'd have to have an institutional subscription,
be on-campus or connected via VPN (for now), and be saving from
somewhere other than the main page.
A new connector endpoint, sessionProgress, takes the place of
attachmentProgress. Unlike attachmentProgress, sessionProgress can show
new attachments that have been added to the save, and with a little more
work should also be able to show when a parent item has been recognized
for a directly saved PDF.
This also adds support for custom PDF resolvers, available to all PDF
retrieval methods. I'll document those separately.
Closes#1542
- Show a clearer message on a certificate error that includes the
underlying error, which should make debugging much simpler. (No more
checking in a browser and hoping it's the same connection.)
- Mention proxy server in message on startup proxy-check failure
- Include link to connection-error KB page on sync connection failure
Closes#1191Closes#1513
If a proxy is required and we can't connect to S3, show the (sync) error
icon. For SSL certificate errors, which are the most common cause of
this, the panel includes a link to the SSL cert troubleshooting page.
- Add the ability to extract a PDF URL from a given webpage using the
translation framework
- Add the ability to get open-access PDFs from landing pages from
Unpaywall data in addition to direct PDF URLs
- Use the above functionality to improve PDF retrieval for "Add Item by
Identifier"
- Add "Find Available PDFs" option to the item context menu to retrieve
PDFs for existing items from the DOI or URL page or using Unpaywall
data. The option appears for single items with a DOI or URL and no PDF,
and it always appears when selecting multiple top-level items (but
skips ineligible items).
PDF extraction from DOI/URL pages will currently only work with
unauthenticated access (i.e., on-campus or VPN, but not via a web-based
proxy).
Supersedes and closes#948
Use the new wizard for all imports (even if no Mendeley DB), and add a
page with a "Place imported collections and items into new collection"
option. If deselected, collections are added to the library root.
Accept Mendeley SQLite databases via File → Import… and perform a
direct import, including collections, timestamps, notes, attachments,
and extracted annotations.
When a Mendeley database is present, File → Import… shows a wizard that
lets you choose between a file and Mendeley for the source, and choosing
the latter shows a list of available databases in the Mendeley data
directory.
Known fields that aren't valid for a type are stored in Extra.
Files in the Mendeley 'Downloaded' folder are stored. Files elsewhere
are linked.
- Add a File Handling section to the General pane of the preferences,
and move several prefs from Miscellaneous to there
- Add a UI to that section for choosing the PDF handler
- Update Zotero.launchFileWithApplication() to use /usr/bin/open on
macOS if the handler is an .app (which it will be if set through the
chooser, since it's limited to Mac applications, though an executable
can still be set via the hidden pref if desired for some reason)
- Move prefs for style/translator updates and translator error reporting
(which isn't particularly relevant anymore in the client) to Advanced
By default the PDF handler chooser says "System Default", which isn't
the nicest thing, and there's probably a way to get/guess the system
default, since Firefox seems to know it (at least on macOS), but I
couldn't quickly find a way to do it.
Addresses #1450
Applies to dragging to the collections pane or the items pane, adding
via New Item menu, or saving via the connector server
If the renaming pref is enabled, the PDF is renamed after recognition.
Can be disabled in the preferences
Closes#917
Automatic renaming is now done for dragging of an external file onto an
item (as added in 7cb95f41) as well as dragging as a linked file,
dragging a non-native (not text or HTML) URL, "Attach Link to File…",
"Attach Stored Copy of File…", and "Retrieve Metadata for PDF". It only
applies if a single file is being added and if the parent item has no
non-HTML attachments. By default, the renaming only applies to PDFs, but
this can be changed with the renameAttachmentFiles.automatic.fileTypes
hidden pref.
A new General pref, "Automatically rename attachment files using parent
metadata", controls whether the renaming happens.
Files saved via web translators are renamed regardless of this pref,
because they would often be gibberish otherwise.
Closes#113
purgeDataObjects(), which runs at the beginning of the sync process,
uses transactions, and those can fail after the default wait timeout if
there's another active transaction. Instead, check explicitly for
another transaction and, if there is one, display a nice message and
wait for it to finish. This isn't foolproof, but it should reduce the
frequency of "operation timed out" sync errors. (Avoiding all long
transactions would be a better solution.)
"Delay citation updates until manual refresh" would be fine in the doc
prefs, but "until manual refresh" is a bit too awkward for the prompt.
Instead, go with @rmzelle's suggestion from #1242 of referring to
"automatic citation updates", and invert the checkbox.
- When a child note is opened in a separate window, the parent window is
selected. (This used to work but was broken in 5.0.)
- When a top-level note is opened (via double-click), the right-hand pane
changes to show "Editing in separate window".
- If a note that's currently open in a separate window is clicked on,
the right-hand pane shows "Editing in a separate window".
- If a note window is closed and the item is selected, the note editor
reappears in the right-hand pane after the note is saved.
This will avoid unnecessary UI updates and data loss bugs from the two
notes getting out of sync (and is just generally cleaner).
Also:
- General cleanup of note display code
Restores the "Restore to Zotero Server" functionality, now using the
API:
1. Get all remote keys and send `DELETE` for any that don't exist
locally.
2. Upload all local objects in full (non-patch) mode using only library
version so that the remotes are overwritten.
3. Reset file sync history, causing all files to be uploaded (or, more
likely, reassociated with existing remote files).
Since these are treated as regular updates on the server, they'll sync
down to other clients normally. Unsynced changes by other clients might
still trigger conflicts.
This and Reset File Sync History can also now be run on group libraries,
with a library selector in the Reset pane (which I forgot to do with
React).
The full sync option is now removed from the Reset pane, since there
wasn't ever really a reason to run it manually.
We should be able to reimplement Restore from Online Library (#1386)
using the inverse of this approach.
Closes#914
Can be an absolute path or 'profile' to use 'zotero' subdirectory of
profile directory as in earlier versions (but which won't be treated as
a legacy location eligible for migration)
Closes#1305
With the new system, it wasn't possible through the UI to generate debug
output for another action that happened after a restart, since it just
restarted immediately. This adds a prompt after selecting the menu
option that allows for restarting now, restarting later, or cancelling.
Better instructions and behavior if the data directory is inaccessible
or missing, including automatically detecting a directory at the default
location if the configured directory is missing and offering to use the
default instead. Together, this means that if, say, security software
prevents Zotero from accessing the data directory within the Firefox
profile, it will suggest that the user move it to ~/Zotero and then
prompt to use that directory.
Show "Copy Citation" and "Copy Bibliography" when a bib format is
selected and "Copy as BibTeX", etc., when an export is selected. If a
site-specific setting is in effect from the last active URL, use that
instead.
If no regular items are selected in bib mode, the menu options are
disabled.
This also now filters non-regular items out when in bib mode -- before
if you selected a combination it would include a bunch of 'n.d.' lines.
Closes#1155, Disable Copy Citation menu option when a translator is
selected for Quick Copy
Adds a submenu for quickly generating and submitting debug output, with
a button to copy the Debug ID to the clipboard and a one-click option to
restart with logging enabled. Debug output can also now be viewed in
real-time using the new debug output viewer window (previously available
only via a command-line flag).
The locale switcher has moved to the top of the Advanced prefpane (where
Debug Output Logging used to go) in a Miscellaneous section, and there's
a new "Advanced Configuration" section (mirroring Thunderbird) at the
bottom for "Config Editor".
Closes#1108
- Move csledit and cslpreview to a Tools section of the Cite pane as
Style Editor and Style Preview
- Rename "Open about:config" to "Config Editor"
- Hide about:memory unless devtools.errorconsole.enabled is enabled,
which isn't particularly appropriate and maybe we can find something
better, but about:memory doesn't really need to be visible by default
Closes#1264
It was previously set from general.useragent.locale, but that's not used
by default, meaning that date interpretation and some other things might
have been incorrect for everyone who didn't set a locale explicitly and
toggle matchOS...
"Report Errors" menu item was in Actions (gear) menu, which has been
hidden in 5.0 (cf. 82292eef77). It is now
accessible from the Help menu.
Adjust Report Error instructions accordingly.
Closes#1022
Could try to explain site-specific settings, but it's somewhat
complicated (requires the Zotero Connector, uses the last active tab
regardless of drag destination), so maybe enough to explain on the
linked documentation page.
- Replace Developers section with text that links to RRCHNM, the credits
page, and Get Involved.
- Remove dedicated zotero.org link
- Only show link underlines on hover
I think it might be worth having a tag management window that lets you
view tags as a grid, sort by column (e.g., type), select ranges, delete,
consolidate, etc., but until then, this fulfills a popular request.
Instead of My Publications being a separate library, have it be a
special collection inside My Library. Top-level items can be dragged
into it as before, and child items can be toggled off and on with a
button in the item pane. Newly added child items won't be shown by
default.
For upgraders, items in the My Publications library will be moved into
My Library, which might result in their being duplicated if the items
weren't removed from My Library. The client will then upload those new
items into My Library.
The API endpoint will continue to show items in the separate My
Publications library until My Publications items are added to My
Library, so the profile page will continue to show them.
This allows for imported items to be saved individually instead of being
saved in a batch after processing the entire imported file (which for
large imports would hang the UI, even if the actual saving was
asynchronous). This also fixes the progress meter during asynchronous
saves.
To take advantage of this, import translators will need to return a
promise when available (using the native Promise object) from doImport()
and wait for optional promises from item.complete().
The logic here can probably be streamlined further. (E.g., we might be
able to say that item.complete() always returns a promise.) It's
complicated by the fact that, at the moment, Promise isn't available in
child sandboxes, though this can probably be fixed.
Tests forthcoming, but they require a translator that supports this,
which needs to be committed separately.
View with -w for a cleaner diff.
- Add Cmd/Ctrl-Shift-I for "Import…"
- Cmd/Ctrl-Shift-V apparently pastes without formatting, so don't override it.
Instead, add a shortcut key to the menu option, defaulting to
Cmd-Option-Shift-I/Ctrl-Alt-Shift-I
- The I in both is now localizable
- Make version copyable
- Include "What's new" link to changelog
- Update some links and descriptions
To-do:
- Replace dev credits with a nice statement like in the Firefox About pane
And change "Changes take effect in new windows" to "Changes take effect
after restart"
(The note font size still requires a restart, as do the shortcut keys in
the Advaned pane.)
And treat an existing non-empty directory as a failure during the
migration, since it should now never happen
Also suggest manually moving on Windows if more than 100 attachments
* Mark feedItems read in a single batch SQL update
* Automatically remove old feed items
* User-facing preference globally and per-feed for feed item expiration
- Don't block the UI with a progress meter during imports. Instead, show
a popup in the bottom right when the import is done that shows how
many items were saved.
- Fix hang when importing some files
- Fix various problems with asynchronous operations/transactions
- Use the save queue for imports instead of creating concurrent
transactions that can time out
- Wait for the save to finish before returning from the translate()
promise. All save modes now use the save queue, so code that
handled the non-save-queue process can probably be removed.
- Serialize child attachments instead of running them concurrently.
This might make multi-attachment saves a little slower, since they
can't download at the same time, but it avoids problems with
concurrent transactions. We might be able to improve this to allow
concurrent downloads, or allow concurrent saves for a limited
number of items (e.g., from web saving) if not for larger imports.
- Change collection handling during import, since UI is now active
- Select the root collection at the beginning of the import
- Assign items and collections to the root during the import instead
of at the end
- Don't select other collections
- Change a few ItemSaver functions to use promises and remove
unnecessary callbacks. (This includes some connector code that needs
to be tested.)
- Change some `parentID` variables in ItemSaver to `parentItemID` for
clarity, since collections are now handled in more places
To-do:
- Save items in smaller batches instead of doing all in the same
transaction
- Show progress meter in a bottom-right popup during the import
It would be good for people not to kill the process indiscriminately, but the
migration will theoretically pick up where it left off, so it shouldn't be too
big a deal.
Would be nice to have a determinate progress meter on Windows, but that
will require enumerating all files, which maybe would just make things
slower. Might be safer, though, by discouraging people from
force-quitting.
This adds a new button to the Advanced prefs to migrate the data directory to
$HOME/Zotero. The button only appears if the data directory is set to the
default location within a profile directory (including the other program from
the one running, even though that's technically stored as a custom data
directory).
On Mac/Linux, directories within the data directory are moved with /bin/mv. On
Windows, or if that fails, they're copied recursively using OS.File.move()
(which annoyingly doesn't reliably support directory moving). The former should
be instantaneous on most systems (unless the data directory or 'storage' were
on a different filesystem from $HOME).
If the database fails to transfer, migration fails and the data directory
setting remains on the old directory. If the database transfers but other files
fail, the data directory setting is updated. In both cases, the user is
encouraged to migrate remaining files manually with a button that reveals the
directories and quits the program.
This isn't yet tested on Linux or Windows, and migration isn't yet suggested
automatically.
Adds Zotero.File.reveal(), Zotero.File.directoryIsEmpty(), and
Zotero.File.moveDirectory().
- Use $HOME/Zotero if zotero.sqlite exists, and set it as a custom data
directory so that 4.0 uses it if loaded (resulting in a
newer-db-version error instead of an empty database)
- Don't prompt whether to use data directory from the other version's
profile directory (i.e., Firefox or Standalone) -- just do it
This could be extended to address #118/#145, but for now it makes some of the
more common search conditions (Creator, Collection, etc.) more prominent.
Clicking it cancels the current window, opens the Cite pane of the
prefs, and selects the Styles tab. (This will be more useful once we
have inline style installation from that pane.)
On reset, items are overwritten with pristine versions if available and deleted
otherwise, and then the library is marked for a full sync. Unsynced/changed
files are deleted and marked for download.
Closes#1002
Todo:
- Handle API key access change (#953, in part)
- Handle 403 from data/file upload for existing users (#1041)
This is necessary because you can copy a database synced with a
different account into the data directory without affecting the stored
pref.
Also tweak the text to use proper quotes and remove quaint references to
"the server".
- Only show first pane (without Sharing pane) if no files or files
aren't included
- Update authorship checkbox to reflect file include setting to avoid
confusion
- Clarify in intro text that license applies to files, not notes --
notes here are no different than notes in any public library, so it's
sort of up to the user to clarify those if they're substantial enough
for it to matter
- Adjust alignment of authorship checkbox if more than one line
The on-change auto-sync now syncs only the modified library, and does so
quite efficiently (and should be able to be made more efficient), so we
might be able to reduce the timeout below 15 seconds.
- Hide notes, tags and related for feed items in itembox
- Add feed support for <enclosure> elements
- Add feed syncing methods for synced settings (additional work is
needed on the sync architecture to download synced settings from the
server)
- Change feed item clear policy to be less aggressive
- Adjust for deasyncification
- Disable translate-on-select
- Closeadomasven/zotero#7, Remove context menu items from feeds
Fixes the incompatible-version dialog and adds info on the version used
to upgrade the database, which may be helpful for troubleshooting.
Also fixes showing of the Zotero toolbar icons even in case of a startup
error.
Also:
- Remove last-sync-time mechanism for both WebDAV and ZFS, since it can
be determined by storage properties (mtime/md5) in data sync
- Add option to include synced storage properties in item toJSON()
instead of local file properties
- Set "Fake-Server-Match" header in setHTTPResponse() test support
function, which can be used for request count assertions -- see
resetRequestCount() and assertRequestCount() in webdavTest.js
- Allow string (e.g., 'to_download') instead of constant in
Zotero.Sync.Data.Local.setSyncState()
- Misc storage tweaks
Improves UX of sync authentication.
The account is now linked and unlinked and an API key related to
the client is generated transparently in the background.
The API key is deleted on unlinking.
No sync options are allowed before linking an account.
Display a warning when choosing data directory
Or on opening Zotero Pane for existing users with data dir in dropbox
Also:
Fix a bug where it won't use custom path if "Choose..." button is
pressed instead of radio button.
Change filepicker to show current data directory on display
Disallow everything other than adding a child note in My Publications,
since the wizard only shows on drag (currently, at least). Need to
disable translation separately.
Also show "Delete Item[s]..." in the trash context menu, and hide rather
than disable various menu options.
Addresses #703 -- still need to disable saved search saving
This mostly gets ZFS file syncing and file conflict resolution working
with the API sync process. WebDAV will need to be updated separately.
Known issues:
- File sync progress is temporarily gone
- File uploads can result in an unnecessary 412 loop on the next data
sync
- This causes Firefox to crash on one of my computers during tests,
which would be easier to debug if it produced a crash log.
Also:
- Adds httpd.js for use in tests when FakeXMLHttpRequest can't be used
(e.g., saveURI()).
- Adds some additional test data files for attachment tests
Also:
* _finalizeErase in Zotero.DataObject is now inheritable
* Call _initErase before starting a DB transaction
* removes Zotero.Libraries.add and Zotero.Libraries.remove (doesn't seem like this is used any more)
This will appear much less frequently, since non-conflicting field changes on
both sides can be resolved automatically, but genuine field conflicts still
require manual conflict resolution.
The merge pane is no longer editable, since the itembox code to do that is
async and can't run in a modal window, but it's not really necessary,
particularly with conflicts happening less frequently.
TODO:
- Remote item deletions
- File conflicts
- Maybe handle some edge cases where the conflicted items fail to save
There's a lot more to do, and this isn't ready for actual usage, but the
basic functionality is mostly in place and has decent test coverage. It
can successfully upgrade a library last used with classic syncing and
pull down changes via the API. Uploading mostly works but is currently
disabled for safety until it has better test coverage.
Downloaded JSON is first saved to a cache table, which is then used to
populate other tables and later for generating PATCH requests and
automatically resolving conflicts (since it shows what was changed
locally and what was changed remotely). Objects with unmet dependencies
or unknown fields are skipped for now but don't block the rest of the
sync.
Some of the bigger remaining to-dos:
- Tests for uploading
- Re-do the preferences to get an API key
- File sync integration
- Full-text syncing integration
- Manual conflict resolution (though this already includes much smarter
conflict handling that automatically resolves many conflicts)
Since modal windows (e.g., the Create Bib window and the Quick Copy site
editor window) can't use yield, style retrieval
(Zotero.Styles.getVisible()/getAll()) is now synchronous, depending on a
previous async Zotero.Styles.init(). The translator list is generated in
the prefs window and passed into the Quick Copy site editor, but it's
possible the translators API should be changed to make getTranslators()
synchronous with a prior init() as well.
For new installations, a panel will show for the Z icon with a ">"
button to go to a second panel for the save icon. For existing
installations, a panel will show just for the save icon. In both cases,
the panels are non-auto-hiding but are dismissed if clicked on or when a
new content page is loaded.
There's also a new close button, but it's not enabled currently. Might
be useful for panels with embedded links where an accidental click on
the panel alone shouldn't close the panel (like the Firefox customize
mode wizard).
- When relinking a missing stored file, copy it into the attachment's
storage directory automatically
- Previously, selecting a file outside the attachment subdir would
just result in a missing attachment, since it only looks for stored
files within the subdir
- Display an error message if a Windows shortcut (.lnk) is added via
drag-and-drop or via a file dialog on non-Windows systems, until we
can figure out how to determine the original file
- Shortcuts can cause errors during syncing, for unclear reasons
- Neither nsIFile::copyToFollowingLinks() nor nsIFile::target work for
me to get the original file, even when nsIFile::isSymlink() returns
true
- Windows file dialogs seem to automatically resolve shortcuts, so
it's only an issue there for drag-and-drop
- Disallow hidden files from being selected in relink dialog
- I think some people on Windows with hidden files shown relink the
.zotero* files that show up when they click Locate, which causes
file sync errors. Which brings us to...
- Fix file sync errors for *.lnk and .zotero* files
- Ignore existing .zotero* attachment files, treating the files as
missing instead to encourage relinking
- Strip leading period in getValidFileName() to prevent added files from
being hidden
- This allows hidden files to be added explicitly; they just won't
stay that way in the storage directory
(These things should have tests, but that will have to happen on the 5.0
branch.)
- Simplified schema
- Tags are now added without reloading entire tag selector
- On my system, adding 400 tags to an item (separately, with the tag
selector updating each time) went from 59 seconds to 42. (Given that
it takes only 13 seconds with the tag selector closed, though,
there's clearly more work to be done.)
- Tag selector now uses HTML flexbox (in identical fashion, for now, but
with the possibility of fancier changes later, and with streamlined
logic thanks to the flexbox 'order' property)
- Various async fixes
- Tests
