I also wonder if it would change any of the workings of this great plugin to move groups and texts folders manually to a new database, and the annotations in the groups folder to external folders. Keeping them in another database, separated from the long pdfs they link to, might be better for DT’s See also. And keeping them externally, they’ll be accessible to Spotlight
Also, and only it doesn’t change its workings either, if it would it be easy to change the Annotation Pane’s script for the groups folders to get the name from the pdf they refer to, instead of their DT’s hyperlink.
I played around a bit with Scrivener’s reference pane and I can’t find a good solution. The problem is that when the file name changes Scrivener will not be able to find the file and hence a link to the original annotation in the text will be of no use. The best I can suggest is adopting a strategy of flagging or labelling any files whose links are put in Scrivener to alert you not to change the name.
This would not work for a number of reasons. Thanks for the input though, the point you raise is very valid. For this reason v303 turns off the classification and indexing of the annotations in the groups folder. They are effectively invisible to DT’s indexing and classification. The groups folders take almost no space at all because they contain only replicants.
Turn on “create spotlight index” in the database properties to make the database searchable by spotlight.
Maybe I have missed a use case but the groups folder in intended to be effectively invisible. There is no good reason to get a source document’s group folder by going to annotations/group. The way to get to a source document’s group folder is through the source document’s url link.
Thanks for taking the time to give input jmm (and those of others in this thread and who have emailed me). It has been invaluable in tracking down bugs and in producing a help file which should hopefully be in a future version.
I have some observations to make, not as a negative viewpoint but as a contribution to improve this great tool.
1. v303 - some problems 1.1 - “side panel”
First, the number of selected words is limited. Some of the text is missed and not appear on side panel.
Secondly, some of the characters not appear. Not only special characters as " or # but all the punctuation. 1.2 - annotation/notes field
Remains the problem with the paragraphs: unlike the version v2, the result is a continuous phrase with the expression “[return]” in the paragraphs’ place.
2. a useful extra field
In some cases we work with a reference manager. These references have some important information. Thence, I ask if is easy add a new field in the Annotation Pane (optional) to introduce the link to the reference. For example, Bookends or Papers (Endnote no) have the feature that allows create a “link” to access to the reference.
3. Keystroke
Once you said:
I’m a newbie not only in DT but also in the mac world… and in System Preferences>Keyboard I didn’t find any reference to this script! How to create this keystroke?
Hi, Paulo. I can reply to the above question. You first open the Automator app, choose Service and put the script into a Run AppleScript action. Later, open System Preferences, choose Keyboard settings, go to the Shortcuts tab and in Application shortcuts, assign the hotkeys, as it is graphically explained here.
Alternatively, you can use any launcher that supports executing AppleScripts and setting global hot keys, such as FastScripts.
Thank you, Frederiko. Points taken. I’m now tagging some annotations to indicate their name should not be changed. I have also turned Spotlight on in the DT database properties, which I think it allows searches in ~/Library/Caches/Metadata/ The problem with this is that files there are devoid of tags -my main organization criteria in DT.
Just in case it works for Paulo as well, I will mention that I tag all annotations with their Citation ID from my reference manager. When I select the citation tag I get a view in which it is possible to browse, read and write in the annotations without many clicks. The same view I would get from the annotations’ group folder (as Three Panes, Widescreen). I find this view more confortable to work with than the icons’ view reachable from the annotations’s source documents’ link. I include an image.
Since I don’t know much about DT’s AI, I wonder if it makes a real difference to restrict pdf file names to their short citation ID, although I always forget which title Author Year stand for. The thing is that when searching, annotations will come up due to the wordings of the descriptive pdf titles they include in their text content, although particular annotations may not focus on the searched topic at all.
For the same reason, I also wonder if long pdfs and short annotations should be kept in different databases.
I didn’t realise this but I tested it and you are correct. The alternative might be to put annotations in an indexed file which would make the keywords available to spotlight.
A newly created group inherits its window style (icon, column split, three panes) and the viewable columns from it parent folder (when opened as a separate folder). This makes it very important to set up the folder structure carefully before you start, if like me, you use different views for different folders. So instead of the icon view that you are seeing when you select the annotation group from the source link, I have the folder set up to show me a split view with only the relevant columns open that I need. This is done by setting up the correct view in the annotation/groups folder.
It is probably because I am not following your methodology properly but your system seem on first glance to be quite clumsy and not conducive to easily finding information.
I would set it up a little differently :-
The title would be the name of the pdf document
The author and the year would be tags, or parent folders
The annotations title would reference something relevant to the annotations, such as the first few words of the selected text. This would help in search and AI to identify the relevance of a searched document
The full citation should appeal in the annotation text so there is no need to reference this information from the source document
I use my folder structure to automatically generate the citations while I am writing in OmniOutliner using variation of this script: [url]Cite&Write with OmniOutliner]
Just a suggestion because when I was in academics reference managers hadn’t been invented yet.
Reference back to the citation manager
Paulo mentioned that a reference back to the citations manager (such as Endnotes, or Bookends) would be useful. I don’t have any experience with citation reference managers so I am going to experiment and see how best to create a link back to the citation manager. This would seem to be the best answer to jmm’s problem too.
@ Frederico: I was also in academics before citation managers had been invented, churning out bibliographies and course suyllabi that were funded and distributed by the National Science Foundation.
But at least we had advanced from clay tablets to shoeboxes of index cards containing handwritten information.
I’m also an enthusiast of Annotation Pane. To the point of convincing me to come back to DT. I’m slowly moving my data from good but inflexible Atlas.ti and MaxQDA, so I still have a tendency to rely more on structured organization than on freer search.
The problem I had of getting the icons’ view was due to not searching from the top most folder, i.e. Inbox, but from the annotations’ groups or text folder. I record my mistake here in case another user experiences the same.
Another convenient way to quickly browse annotations is Cover Flow, but DT doesn’t seem to focus rtfs as immediately as Path Finder.
As for the reference manager, thank you for your consideration. All I need from it is the citation ID, which I already have in DT, both as a tag and at the beginning of the pdf’s title. Therefore, even if I ever want to have a look at a record, I don’t see it as a significant part of my workflow.
Thank you as well for sharing your methodology, Frederiko. What you have described is not too different from mine, what may not be clear because of the language. The main difference might be that I include a good number of keywords in the annotation title, so that I can search in Spanish as well if the source document is in English. As a side note, I think it would make a big difference to newcomers if DT made available a few videos not only about the functions but about real power uses of the app.
I have moved externally the text folder to have it indexed. And back again inside the database when I’ve realised I shouldn’t risk loosing the hyperlinks among annotations I include in some of them.
Maybe as a result of the above, now the new annotations I make have their properties set to be excluded from Classification, Search and See also. I’ve checked that both the annotations’ texts and concerned group folders are not set to exclude. Any idea about how I could change this behavior?
I understand why you got an icon view. One of the placeholders in the rtf is %annotationGroupLink%. This places a link in the rtf called ‘Source Document annotations’. Clicking ‘Source document annotations’ will display an icon view of the annotations tag group which is not very helpful in this context. Instead try right clicking on ‘Source Document annotations’ and selecting open link. This will open the annotation tag group in a new window and respect the layout settings of the group. The way devonthink layouts interact can be complex because of all the permutations.
You should not lose the hyperlinks if you move the rtfs into an indexed folder but I haven’t tested it extensively so I can’t recommend it.
No, it wasn’t anything you did. There was a bug in the code which I have fixed in v305. To fix the exclusion simply select all the annotation texts and and choose ‘show info’ from the right click menu. From there you can reset the properties of all the selected files at once.
As for the automatic exclusion of annotations from search… in v305 it seems to be still there. I recall that you mentioned that v303 turned off the classification and indexing of the annotations in the groups folder. For what I have tested manually, when I change this setting in an annotation in the groups folder, it also changes in its replicate in the text folder. Could this be the issue?
Whatever the case, this is not much of a problem to keep using Annotation Pane, as the setting can be changed manually for the time being.
This is a short script which will work with the documents produced by the Annotation Pane and the Document Review Pane to produce a sheet of all the selected source documents, annotations and their related metadata such as the extra groups defined in config.scpt.
It will produce a sheet that looks something like this:
Sheets are easily exported to Excel, Numbers or a variety of other formats
The Sheet has the following columns: Item no. A sequential number incrementing for each row Running PDF page Number The page number of the pdf if all the pdfs in the sheet were numbered sequentially. Other file types are ignored. Useful for producing indexes. Date The creation date of the document. Document name The name of the document. Spotlight comment The spotlight comment of the file. Page Number The page number that the document references if its an annotation OR the Bates number if such a number is detected in the the spotlight comment. Source Document The name of the source document if the document is an annotation. …Tag columns… The tags of the file for each of the specialGroup1, specialGroup2 and extraGroups tag groups as defined in the config.scpt file.
Not possible. Nothing on iOS works with AppleScript or the other tools used in Frederiko’s tool. There are plenty of annotation tools on iOS that work with DTTG2. Or, you could learn Python or Swift and write your own
Follow up question… Are you saying that there are other annotation tools on iOS outside of DTTP that one could use w/in DTTP – to compliment (or enhance) DTTP annotation? Or are you just saying that DTTP has good annotation tools?
Just wondering if there’s any way to add tags from DTTP-annotated documents that would transfer into the OS X version of DTP.
Ooops! Just realized that I didn’t properly articulate that idea. What I meant to say (or ask) was …
Just wondering if there’s any way to add tags from DTTP-annotated documents and include annotations to those tags (in the way that this script provides) that would translate from iOS / DTTP to the DTP / OSX app.
Any ideas or suggestions? Happy to even consider a hack solution.
Once again I’m here to appeal to your generous help.
In my case I use this script as a tool for my literature review: read and annotate documents - notes, ideas, etc…
First I have two main groups/folders called “Primary Sources” and “Secondary Sources”. Inside these groups I place/index each Document in one sub-folder/group (for example: “Leach 1997”).
When working with one document, I’m interested to place all related annotations inside the same document folder (or in a group inside that folder).
For me this is the better way to organize my work.
Considering the script I ask:
--DEFAULT LOCATIONS -----------------------
-- The default location where document groups and annotations are stored
property groupLocations : "Inbox/annotations/groups"
property annotationLocations : "Inbox/annotations/text"
1. It’s possible change the “default locations” to the same path of the document?
2. Why the script create two folders (“groups” and “text”)? Are both necessary? Can the script work only with one (“group” for each document)?
The two folders serve different purposes but contain replicants of each other. The “groups” is intended to be a “hidden” folder. You should never need to go into it. It contains a groups that are unique to every annotated document. When you click the URL link of an annotated document, it takes you to this “hidden folder” which contains replicants of every annotation to that document, no matter where those annotations are actually kept. This hidden group is already replicating to some extent the functionality you want by linking the document to the annotations. You find it by clicking the URL link at the top of a document.
The “text” group is the default location for text annotations - that is an easy place to find all annotations. Checking the “Set annotation location checkbox” in the annotation pane brings up a standard group selector panel which allows you to choose any location to save your text annotation. You could check the “Set annotation location” checkbox and choose to store your annotation in the same group as the document. I can see however if you wanted that as the default location that it could be tedious.
No by default you cant do this. I have however produced a modified version of the script which will do what you want. You can download it here. (This is not intended for general use but only for Paulo’s specific request)
Many, many thanks for the ‘exclusivity’
Deeply grateful.
If I’m not wrong, the difference is: instead the annotations go to the default “text” group they remain on the same group/folder of the document. Right?
Considering the implicit process, when finished the review of document the result is a folder with the document and the annotations (single annotations). In my workflow the logic of ‘single’ annotations is important: tagging, comments, etc. But at the end I feel the missing of a general view, a kind of “scrivening mode” (Scrivener) to view all the ‘single’ annotations together but keeping all the singular metadata (links, tags, etc.) - just a more practical view mode (different from the “Merge”). Maybe a feature to one future DTP version
I support the request of a Scrivener-like contiguous view of documents in DT. But by now Annotation Pane has become such a central part of my work in DT that I’m worried it may not work in the next version!
I have a question as well: So far, all the created annotations are excluded from search, classification and see also. I have tried changing the permissions to the general text folder which contains all replicates. To no avail, so I carry on changing this setting manually to several notes from time to time. Is there a way I can change this automatic behaviour in the script?
