daeh / zotero-markdb-connect Goto Github PK

Currently, matching via filename requires either @ at the beginning of the file or the citekey present in the yaml frontmatter. I'd like to match via filenames without @ and without a specific yaml frontmatter. Just via a filename in this format: citekey.md

Hi, is there a possibility to change the tag ObsCite attaches to the Zotero items?

Use case: I use the coloured tags in Zotero to indicate the status of the item. It moves from red="to read" or "to skim" to orange="read" and eventually green="finished notes" or violet="worth a second look".
It would be really nice if it was possible to integrate the ObsCite tag into that workflow smoothly :)

Thank you!

Re #3 . Would only work if

(1) the hidden BBT setting autoPinDelay turned on

OR

(2) all of the BBT citekeys in the MD notes are 'pinned' in Zotero.

So I linked the plugin to a folder in Obsidian "~/obsidian/cinema-project/1. Notes" but when I restart Zotero the message I get "no notes found." Is that because there is a space in the name of the folder? Thanks!

Hi,
I am writing to request a new feature for your plugin. I would like to suggest adding support for the markdown files exported from Readwise, so that the plugin can associate and tag the Readwise reading records in Zotero items.
As you may know, many users of Zotero also use Readwise to manage their highlights and notes. It would be very convenient if the plugin could automatically recognize and link the Readwise markdown files to the corresponding Zotero items, and tag them with relevant keywords or labels.
The exported markdown files from Readwise usually follow a specific naming convention, such as "Article Title(highlights).md". It would be great if the plugin could recognize this convention and use it to identify the associated Zotero items.
I believe that adding this feature would greatly enhance the functionality of your plugin and benefit many users who use both Zotero and Readwise. Thank you for your consideration!

My best,
qqyl

Dear @daeh,

for some reason the plugin won't work for me. The correct md files get picked up by the regex, and the corresponding citekeys are given to the plugin by bbt, but the don't get matched.
Am I doing something wrong or is this a bug?

MarkDBConnect-debug.txt

Kind regards
fruchtblase

Hello, I have a question, I have zotero installed on both devices, and the data has been synced, export a my library .JSON on one device, and create the corresponding MD notes, how do I do it on the other device What about syncing notes and annotations using my library exported on the first device?

Whenever I open zotero, I see this error from this plugin:

Everything seems to work ok, though. Just thought I'd report it in case there's some undefined behavior occurring.

Then the following popups:

This process takes a while, like 20-30 seconds or more, I guess, during which zotero freezes. Not sure if the freezing behavior can be eliminated.

I'm using the current settings:

Hi there!
Thanks for this plugin. I find, however, that when I right-click in Zotero on an Obsidian-Zotero synced item and point to "Open ObsidianMD Note" or "Show Markdown File" I only get a list that seems limited to 16 Obsidian notes although I may have many more notes with the relevant Zotero itemkey. I cannot seem to find any button to scroll down to see other notes or some other means to see them.
Is this perhaps by design, or is it a bug? Or am I doing something wrong?

I could not find any thread on this issue and decided to submit it as a new one. I am sorry if I missed an already-existing thread on it.
Thanks for your help

Running the sync can't match items or parse items even though yaml citekey is present and custom filter set to .+.md$
Any help would be immensely appreciated.

I get this in the report:

[
{
"citekey": null,
"citekey_metadata": null,
"citekey_title": null,
"zotkeys": [],
"zotids": [],
"name": "holbraad_ruptures_2019",
"path": "/Users/binou/switchdrive/Thèse/Thoughts/Research Annotations/holbraad_ruptures_2019.md"
},
{
"citekey": null,
"citekey_metadata": null,
"citekey_title": null,
"zotkeys": [],
"zotids": [],
"name": "powers_anthropology_2019",
"path": "/Users/binou/switchdrive/Thèse/Thoughts/Research Annotations/powers_anthropology_2019.md"
},
{
"citekey": null,
"citekey_metadata": null,
"citekey_title": null,
"zotkeys": [],
"zotids": [],
"name": "forbes_meaning_2007",
"path": "/Users/binou/switchdrive/Thèse/Thoughts/Research Annotations/forbes_meaning_2007.md"
},
{
"citekey": null,
"citekey_metadata": null,
"citekey_title": null,
"zotkeys": [],
"zotids": [],
"name": "irvine_deep_2014",
"path": "/Users/binou/switchdrive/Thèse/Thoughts/Research Annotations/irvine_deep_2014.md"
},
{
"citekey": null,
"citekey_metadata": null,
"citekey_title": null,
"zotkeys": [],
"zotids": [],
"name": "demossier_beyond_2011",
"path": "/Users/binou/switchdrive/Thèse/Thoughts/Research Annotations/demossier_beyond_2011.md"
},
{
"citekey": null,
"citekey_metadata": null,
"citekey_title": null,
"zotkeys": [],
"zotids": [],
"name": "janowski_reading_2012",
"path": "/Users/binou/switchdrive/Thèse/Thoughts/Research Annotations/janowski_reading_2012.md"
},
{
"citekey": null,
"citekey_metadata": null,
"citekey_title": null,
"zotkeys": [],
"zotids": [],
"name": "walter_uncertain_2006",
"path": "/Users/binou/switchdrive/Thèse/Thoughts/Research Annotations/walter_uncertain_2006.md"
},
{
"citekey": null,
"citekey_metadata": null,
"citekey_title": null,
"zotkeys": [],
"zotids": [],
"name": "fabian_if_2005",
"path": "/Users/binou/switchdrive/Thèse/Thoughts/Research Annotations/fabian_if_2005.md"
},
{
"citekey": null,
"citekey_metadata": null,
"citekey_title": null,
"zotkeys": [],
"zotids": [],
"name": "stensrud_climate_2019",
"path": "/Users/binou/switchdrive/Thèse/Thoughts/Research Annotations/stensrud_climate_2019.md"
}
]

I had this post also on obsidian-Forum as Reply:

I find your addon SUPER, even if it has not yet led to the goal or success with me.

I export Zotero items that I want to work with in Obsidian with the Zotero addon "mdnotes".
This creates Markdown files with the title
"@CITEKEY.md" (example: "@Akal_ea_2018_DistributedSensing.md").

These are located in the Obsidian Vault in a folder. The files also contain the additional Zotero link with the Zotero ID as the metadata field:

...
- title:: A Distributed Sensing Approach for Single Platform Image-Based Localization
- local:: [local zotero](zotero://select/items/1_4AYCPGBV)
- cloud:: http://zotero.org/users/4847583/items/4AYCPGBV
...

Example file: @Akal_ea_2018_DistributedSensing.md

The corresponding Zotero items should now get a tag "ObsCite".
In my case, there is NO exported JSON file of all Zotero items. Your addon aborts the sync with the error message "BBT JSON Library not found".
What is the purpose of the BBT JSON Library? Surely the information is directly accessible to the addon in Zotero?
My Zotero contains about 80000 entries. If I would set an auto-export, every time I make a change in Zotero, the whole database would be exported.

In my opinion, this file is not necessary:

• Search Obsidian folder
• each file starting with "@" is a citekey probably present in Zotero
• Search this citekey in the Zotero database
• if found, then assign tag "ObsCite
• if not found (e.g. because deleted in Zotero in the meantime but still present in Obsidian), then write to a "missing entry" list
• Write the list with the missing entries:
  • as a Zotero note or
  • write it as a Markdown file into the specified folder with the citekeys
  • Suggested name: "zotero-obsidian-citations missing-entries.md".

Is there a reason for needing the BBT JSON library that I'm just not seeing?

re #26

The connection doesn't seem to find the Group libraries I have inside my Zotero.

Is it not a feature or am I messing up a setting somewhere?

Thanks for the great plugins! On my side, the plugin appears to be incompatible with more than one citekey. I wonder if it's a bug? Namely, suppose we have a file like

---
citekey: [key1, key2, key3]
tags: [tag1, tag2, tag3]
---
content

On my computer the file MarkDBConnect-debug.json appears as:

{
   "citekey": null,
   "citekey_metadata": null,
   "citekey_title": null,
   "zotkeys": [],
   "zotids": [],
   "name": "filename",
   "path": "/[path-to-vault]/[filename].md"
  },

And my config is

Besides, I also test

---
citekey: 
  - key1
  - key2
  - key3
---
content

Unfortunately, it doesn't seem to work as well.

I hope the above information is useful and thanks again for the great plugin!

Hey, I tried to write the RegEx to macht md notes according to the Zotero-Item-Key just as suggested in the parantheses from the picture below. But the line failed to matching md notes with Zotero items.

This is what I was trying to match in metadata (in Logseq)

These are the lines that I tried:

• (?!(zotero:\/\/select\/library\/items\/))(\w{8})

• (?<=zotero:\/\/select\/library\/items\/)(\w{8}) (the positive lookbehind feature was reported to be not supported, so I changed to the above one, but failed again)

Thanks in advance 🥺🥺🥺

I'm not sure whether this window is caused by this plug-in, but I still want to ask how to close this window

Loving the concept behind this plugin, anything that gets the Zotero+Obsidian bond stronger is amazing. Thank you!

I'm not sure the feasibility of this request, but is it possible to remove the limitation of .md notes starting with a '@'? I'm sure it would allow this plug-in to integrate with a broader array of workflows.

Hi @daeh thank you so much for your support.

According to your request in the forum, I am attaching two MD files from my obsidian notes. One of them (the first one) is an old file, created from notes generated with Acrobat reader some months ago. The other is a newly created one with the latest beta version of Zotero (63).

@nimmoDielsAlderClick2011.md

@lindenmeyerSelfhealingBehaviourFuran2020.md

I am almost sure that this is probably a mistake from my side configuring the setup.

Thank you!

Please add support for Zotero 7. Thanks!

Hello, is there a way to create citations in APA style? The biggest issue is the way authors are shown ->

The basic format for a book citation requires listing the author's name, the title of the book, the publisher's name, and the date of publication.

Jakupcak, M., Luterek, J., Hunt, S., Conybeare, D., & McFall, M. (2008). Post-traumatic stress and its relationship to physical health functioning in a sample of Iraq and Afghanistan war veterans seeking post-deployment VA health care. Journal of Nervous and Mental Disease, 196, 425-428.

I have to use two separate Obsidian vaults (work and personal) but one Zotero Library (one account). The issue is that tags are removed from Zotero items when Obsidian Vault files are not found, which occurs when I switch between work and personal Vaults. This seems reasonable behavior to clean up tags, but of course causes problems across multiple vaults.

Perhaps a workaround could be, 1) option for tags be not removed at all, and/or 2) tags searched for items only in specific collections.

Zotero auto-updated the add-on, and after rebooting:

1. I can't enter into the Tools>Add-ons (no action!)
2. Looks like the BBT plugin is not working anymore
3. Your plugin does not update new notes from Obsidian

Zotero has no update, so it should not be a bug from their side.

EDIT: As the command menu "Add-ons" does not work, I can't even uninstall it.

Currently, you can specify a custom file filter, and the first capturing group will be taken as the BBT cite key. This fails when the filename and the YAML header title do not match, e.g. when there are escape characters in the filename.

For example, let's say I want to group all of my references under logseq namespaces, so I tell logseq to prefix imported citkeys with the string ref/. As the slash is escaped, these files are stored as refs%2FDoe23-UnderwaterBasketWeaving.md on the disk, but the title:: field inside the file's YAML header is title:: refs/Doe23-UnderwaterBasketWeaving.

This mismatch appears to cause MarkDB to choke. Using the file filter ^refs%2F.+\.md$ will cause the following errors upon a tag sync:

• There were 1 Markdown notes that could not be parsed.
• There were 1 citekeys in your Markdown notes that could not be matched to items in your Zotero library.
• There was an issue matching some of your Markdown notes (0 notes were matched successfully).

The error json produced by all of these is:

[
 {
  "citekey": null,
  "citekey_metadata": null,
  "citekey_title": null,
  "zotkeys": [],
  "zotids": [],
  "name": "refs%2FDoe23-UnderwaterBasketWeaving",
  "path": "/Users/grace/Library/Mobile Documents/iCloud~com~logseq~logseq/Documents/pages/refs%2FDoe23-UnderwaterBasketWeaving.md"
 }
]

Using the file filter ^refs/.+\.md$ will simply not match files.

I just updated MarkDBConnect to 0.0.21 (and BBT to 6.7.50) and every time I start MarkDBConnect reports all cited entries fail to be matched. Obsidian and BBT still work as expected. The only thing that is not working is that the MarkDBConnect option on the context menu does not show for items that are actually cited in Obsidian.

Looking at the MarkDBConnect-missing-entries.json it all looks fine to me. Here is the first of hundreds of entries:

{
"citekey": "allenInformationFlowResearch1969.md",
"citekey_metadata": null,
"citekey_title": "allenInformationFlowResearch1969.md",
"zotkeys": [],
"zotids": [],
"name": "@allenInformationFlowResearch1969",
"path": "path_to_file\\@allenInformationFlowResearch1969.md"
}

I created a couple of new citations in Obsidian, including one of a new entry in Zotero. MarkDBConnect reports these as additional ones that it fails to match and does not set the citation tag in Zotero.

add contextual menu item to open the associated MD note

Are there plans to support reading from multiple BBT or JSON library files? I work on several group libraries (one per project).

Hello and thank you for a very needed add-on!

I have been using this add-on for a while, and it has been working perfectly. But recently Zotero crashed every time I tried to open it, and through some debugging with the people at the Zotero forum we finally found that the bug was within this add-on. When i removed it, Zotero could open again. I'm no programmer so will not give any tips on what needs to be done, but in the forum thread there was an advice for a line that should be removed. For further explanation see the thread here: https://forums.zotero.org/discussion/comment/417064#Comment_417064

My naming rule is .+\.md$ ,and to put the citekey in the yaml area. But when the file name does not contain @citekey, it cannot match correctly. I tested it many times and did not achieve it. So can this plugin rely only on the citekey configuration in the yaml area? I don’t know where the problem is.

contextual menu item to reveal MD note in system explorer

this is a debugging log, and I have not used it for a long time. I donot konw how to fix it.

{
"version": "0.0.24",
"zoteroVersion": "6.0.26",
"isMac": true,
"isLinux": false,
"isWin": false,
"prefs": {
"matchstrategy": "zotitemkey",
"source_dir": "/Users/tsd/Library/Mobile Documents/iCloudmdobsidian/Documents/mac_tsd/zotero_note",
"filefilterstrategy": "default",
"filepattern": "{{citekey}}.md",
"zotkeyregex": "",
"metadatakeyword": ""
},
"config": {
"matchstrategy": "zotitemkey",
"source_dir": "/Users/tsd/Library/Mobile Documents/iCloudmdobsidian/Documents/mac_tsd/zotero_note",
"filefilterstrategy": "default",
"filepattern": "{{citekey}}.md",
"zotkeyregex": "",
"metadatakeyword": "",
"grouplibraries": "user",
"removetags": "keepsynced",
"tagstr": "ObsCite",
"vaultresolution": "path",
"vaultname": "",
"logseqgraphname": "",
"bbtinstalled": [
true
],
"checkSetting": false
}
}

Would it be possible implement "Show Markdown File" on Linux? At this time it just opens the parent directory (which is kind of useless as you would still have to look up the file).

showSelectedItemMarkdownInFilesystem: function (idx) {

        const entry_res = this._getSelectedEntry(idx);

        const file = new FileUtils.File(OS.Path.normalize(entry_res.path));
        if (file.exists()) {
            try {
                Zotero.debug("MarkDBconnect: Revealing " + file.path);
                file.reveal();
            } catch (e) {
                // On platforms that don't support nsIFile.reveal() (e.g. Linux),
                // launch the parent directory
                Zotero.launchFile(file.parent);
            }
        }
    },

I was thinking of running xdg-open with file.path as argument, but am not sure if/how this would be possible.

either internally or just expose the command to zutilo

Please add an option in the "MarkDBConnect Preferences" to open the MD files in Obsidian using the Obsidian Advanced URI instead of the default one. The main issue with using the default Obsidian URI is replacing the currently open tab instead of creating a new one.

Keep up the excellent work!

I have a few papers whose citekeys are pinned from inspirehep by betterbibtex. Those citekeys include colons. e.g. citekey: Co:2022jsn

I use the citekey as the title in Obsidian notes. Obsidian does not allow colon in the file title, and it changes ":" to "_".

In this case, how can I set the file filter? Of course, the following does not work.

related to #7

The Choose botton of Folder Containg Markdown Reading Note is not working. Nothing show up after I click the Choose botton.
And I copy the file path of md notes in the text box, but the pulug in still can not find md nites.

I've tried disabling/removing any other plugins, restarted both zotero and obsidian, looked at the debug logs.. [OSX Ventura, Zotero 6.0.29, Obsidian 1.4.16, MarkDBConnect 0.0.24]

When zotero starts it throws up:
[JavaScript Error: "TypeError: items is undefined" {file: "chrome://markdbconnect/content/scripts/mdbconnect.js" line: 782}]

When I try 'MarkDBConnect Sync Tags' the debug window show that it finds all the right .md files but doesn't add the tag to them? Immediately after the list of files it finds, the window shows:
(4)(+0000022): SELECT COALESCE(IA.parentItemID, itemID) AS itemID FROM items LEFT JOIN itemAnnotations IA USING (itemID) WHERE (itemID NOT IN (SELECT itemID FROM deletedItems UNION SELECT itemID FROM itemNotes WHERE parentItemID IS NOT NULL AND parentItemID IN (SELECT itemID FROM deletedItems) UNION SELECT itemID FROM itemAttachments WHERE parentItemID IS NOT NULL AND parentItemID IN (SELECT itemID FROM deletedItems)UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM deletedItems)UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM itemAttachments WHERE parentItemID IN (SELECT itemID FROM deletedItems)))) AND (itemID IN (SELECT itemID FROM items WHERE libraryID=?)) [1]

... and there it stops.

Any advice?

open logseq issue for global URI: logseq/logseq#2890 (comment)

related forum post: https://discuss.logseq.com/t/deep-linking-or-url-scheme-allow-linking-to-logseq-pages-from-outside-the-app/3146/20

original request for ZotObsCite support: https://twitter.com/DavidJaggi/status/1484130826635853825

Hi @daeh !
Just to report a minor bug. When launching Zotero, the following message appears:

After that, no other issue, the plugin continues to work fine

I'm having a similar issue as:
https://discuss.logseq.com/t/my-zotero-logseq-zettlr-word-workflow/8900/17?u=flan
Also, under Linux.

Here is an example Zotero item:

Here are my "Locating MD Files" settings:

Not shown in the screenshot above, I've also tried entering optional Metadata Keywords (multiple iterations—e.g., "extra," "Citation Key", etc.—all rejected due to special characters).

This is what the LogSeq YAML looks like:

Here is an example of a parsing error I get:

{
"citekey": null,
"citekey_metadata": null,
"citekey_title": null,
"zotkeys": [],
"zotids": [],
"name": "zt-zhangBayesianMixedHidden2014",
"path": "/home/onomat/GitProjects/FlogSeq3/pages/zt-zhangBayesianMixedHidden2014.md"
},

I'm not technical enough to find the parsing error very informative.

Thank you for developing this plugin. I'd appreciate any insight you might have.

either as an option that dictates the contextual menu action or as another contextual menu item

Hi - I just installed Zotero and the plug-in for use with Obsidian 1.1.9. I set everything up per instructions, specifying the file path and YAML keyword, and created a test note.

The plug-in works correctly when I include @citekey in the filename, but it is not working with I only have the citekey in YAML metadata.

Is it possible that something is broken? Please help!

Pete

The mdnotes plugin has an option to add the .md to the item in Zotero after it's created. Is there any chance of reproducing that feature in this beautiful plugin?

As far as I understand, most plugins are affected. Here are more details:

https://forums.zotero.org/discussion/94418/6-0-beta-plugins-cannot-be-installed

It seems the manifest should be updated to be compatible with the new v6.0-beta:

Citekeys in YAML frontmatter enclosed in quotation marks are not recognised. For example:

citekey: "somecitekey"
citekey: 'othercitekey'

Both of them are not recognized as correct citekeys, but they should - quoting strings in YAML is allowed.

a button in the preferences plane that stores all of the note data and the extra field, for any item that has an issue, and exports to a json that can be submitted for tech support

I'd love to use a status/HasMdNotes tag, but the plugin seems not to accept custom tags containing a slash. Can this be fixed?

Thanks :)

It would be very nice if the path to the Markdown notes would be searched including the subfolders.

To explain my reasons:
I collect the literature notes in a folder, but I divide them by project, because I have several hundred citations per project and in this way I can quickly find all the literature for the project without searching.