Need some help re my Annotation workflow-DTTG<>Goodreader

Hello all,

Some months ago, popped this ([url]'Open in GoodReader' messes up the name of the PDF]) up in response to a query, and I’ve since been playing around with some options.
I’ve now reached the final part of the process, but am concerned I might be missing something far more simple, to try and finally “join up” my PDF article, and its annotated notes.

I would appreciate some suggestions from anyone who might have some ideas!

To summarise:

1.) Replicate PDF’s I want to annotate into my Sync folder, in DTPO;

2.) Label them all Green: “Currently Being Looked At”;

3.) Sync to DTTG;

4.) Identify PDF I want to annotate in Goodreader - label it Purple: “Being Collected” - open in Goodreader;

5.) In Goodreader, tap on Toolkit icon next to filename [Note: Goodreader has now automatically allocated a new, unique filename to the PDF (e.g. BFC29FE1-76FB-4F33-81AB-520FC3036AC0)] - tap on “LINK”;

6.) The following pop-up menu appears: “Link Copied to Clipboard: Now you can paste it to any application that can open URL links for automatic opening of this file in GoodReader”;

7.) Back to DTTG - tap on INFO icon of the article that has just been sent to GR, tap on COMMENT, tap & hold to paste - clean up the few lines of URL coding before and after the GR unique filename - maybe insert something like “GR code:” before the unique filename, although this shouldn’t be necessary, strictly speaking - tap SAVE;

7a.) This step is crucial - it’s now pasted the GR Unique Code into the Spotlights Comment section of the article in DTTG, which when synched back to DTPO, will serve as the ‘link’ between the Annotation to be made, and the relevant PDF article that was annotated;

8.) Back to Goodreader - annotate the document;

9.) Where I insert an annotated/“sticky” note, with a comment for myself - I FIRST type “GR@N”, [for GoodReader Annotation - obviously others could type anything here that would make for a uniquely identifiable term, that is only likely to appear in Goodreader annotations], hit ENTER, and then insert my comment in between two <> symbols. I’m hoping this latter step might help my in future, should I come up with some sort of Applescript, to parse only that text immediately following “GR@N” and to be found between <> - although, I’m not sure if this is possible;

10.) Finish annotating document - call up document contextual menu in Goodreader, tap on the ‘book icon’ in the middle, at the bottom, and open the Bookmarks/Outlines/Annotations pop-up menu. Tap on EMAIL SUMMARY - email it to myself;

11.) Tap “OPEN IN” button - “Send PDF as is” - open PDF in DTTG;

12.) Change label of PDF that has just been annotated in GR from Purple (“Being Collected”) - to Red (New - To Read) – again, not strictly necessary, but this way, I can keep track of all pdfs that are currently being annotated in GR, those that have been annotated already, and those that still must be annotated;

13.) RINSE AND REPEAT - repeat Steps 4-12 above, with each of the PDF’s in DTTG, until all have been annotated in GR and then returned to DTTG - and all have had their Annotation summaries emailed;

14.) Sync back to DTPO – check that annotations made on all the PDFs in my Sync folder, that are now all labeled Red “New - To Read”, are duly reflected on the original files, wherever they may be (hence my replicating the files into the sync folder initially) – if changes are reflected [and they always are, it’s merely a precautionary check that I perform each time] - DELETE all files in the sync folder.

14a.) With the sync files deleted, the originally-replicated files become the sole instances of the files again - but all annotations made in GR via DTTP are now reflected on them, without my having had to move any files anywhere.

15.) Open MAIL – got to “GR Annotation” Smart Mailbox, which looks for “Annotation Summary for File” in the subject line of the emails so sent from GR;

16.) (Here be a clunky part - suggestions welcome!) Select body of email, copy into Textedit, save RTF file with name of Unique Code copied from first line of body of email, place in Folder being watched/indexed by DTPO;

17.) Open DTPO - paste same Unique Code (that I have just copied in Step 16 - therefore still in my clipboard) into the search field – this calls up the Annotation Summary rtf file that has now been indexed in, AND the PDF article that has the same Unique Code within the Spotlights comment section - as placed there by Step 7;

18.) I then see the image below:

DEVONthink Academics (Active) Database — %22BFC29FE1-76FB-4F33-81AB-520FC3036AC0%22 at 13.16.10.png

Here be the top corner of the RTF summary, as showing the initial information placed therein automatically, by the Email Annotation Summary process. Note the link I created, to link the RTF annotation summary to the PDF in question (Bogg_Death of Statutory Recognition…")

DEVONthink Pro Office at 13.17.31.png

What I would appreciate some guidance in:

What would be the easiest, most meaningful manner to “link” the RTF of the annotation summary, and the PDF of the actual article?

Obviously, having the two linked, would allow me to conduct searches with “GR@N”, for whatever annotated note I can remember having made somewhere… I could then find the annotated text, and link back to the original PDF. Since the RTF remains editable, I could add additional commentary, that I might choose to add after the annotation process via GR was completed, inside the RTF document.

I have become an avid fan of the “New from Template-Annotation” - since this automatically generates the live link between PDF and any notes I make, which is brilliant. I would prefer to be able to either replicate this process with my Annotation summary RTF’s, or somehow simply incorporate them into that existing Template-Annotation process…

I’m really open to suggestions about all of the above - so far I’ve only done about 15 odd summaries, and want to try and settle on the correct approach, before continuing.

Last point I could make, is that seeing all my steps set-out above like that, I can imagine that it looks like a laborious and time-consuming process. Happily, it’s not at all… Most of that really involves a few taps here and there, and is done in seconds. Were I to have to do batches and batches of them at once, then yes - it could get tedious - but doing it as I finish an annotation really doesn’t take me all that long, before moving on to the next one…

There’s a lot to parse here, and a lot of work on your part to share it with all of use. That’s very generous of you, @Cassady – thanks!!! :smiley:

Without addressing the entire rubric, I wonder if there’s a simpler way.

  1. Do your annotations in GR as noted, roundtrip the document back to DTTG, and sync back to the desktop.
  2. Back in GR, email the annotations to yourself as before.
  3. Back on the desktop, just import that email to DEVONthink, copy its item link, then add that link as the URL for the annotated PDF (see Tools > Show Info…)
  • It would be very easy to write a script and assign it to a keystroke to automate this step #3
  • Optionally: you could convert the .eml to RTF beforehand.
  • Or optionally you could merge the original PDF and the .eml into a new RTF

If you happen to sync the annotated PDF and that email back to DTTG some time, then the link to the .eml annotation will be active on the iPad.

The process I’m suggesting eliminates the need to fiddle with GR’s URLs.

korm - appreciate the feedback!

Unfortunately, you’ve just brought home how much I still have to learn about DTPO… :blush:

I followed your post, right up and till #3 - i.e., the moment it got complicated! :wink:
If you don’t mind explaining a bit more…

I considered importing the email - but as you mention, it doesn’t allow for editing(??) - which is why I sent it through Textedit to convert into a RTF. Is this what you mean by “Optionally: you could convert the .eml to RTF beforehand” - or is there some easier trick within Mail that I am missing?

Then, I think I’m misunderstanding your terminology:

What/where is the “item link” of the imported email that you mention?

I presume you’re suggesting I add this ‘item-link’ to the URL field inside the Tools>Show Info menu, of the PDF I want to link back to?

THIS >> …“If you happen to sync the annotated PDF and that email back to DTTG some time, then the link to the .eml annotation will be active on the iPad”… I did not know!
Wow. That could be pretty darn useful…

If you could maybe help clarify the ‘item-link’, I would be very grateful. Would be sweet to get the above working!

Your 3rd bullet – Or optionally you could merge the original PDF and the .eml into a new RTF – again, think I know what you mean - just want to be sure. Is this where I use the New From Template>Annotation, to create a RTF that links automatically back to the PDF - and then can “drag and drop” the PDF and .eml into the RTF, for both to be active/scrollable and searchable?

If I understand that correctly - also toyed with this as an option… But didn’t like the duplication that ended up occurring - since I would now presumably have an ‘original/initial’ .eml, the PDF article, and a RTF annotation containing both again… I was concerned that calling up a search would show duplicated results, since Search would surley find the term within the .eml file, and the RTF containing it?

Thanks again for the suggestions.

Good to know that things are slowly falling into place. Cannot believe how much my ‘system’ has come along - when it feels like just the other day, I was staring at my database, after having just done my first import thinking: Is that it??? :laughing:

… assuming that DEVONthink Pro Office is installed … and that an email has been sent from GR that is accessible thru Mail on the desktop …

  1. Click the annotation email in Mail and chooseMessage > Add to DEVONthink Pro Office
  2. Depending on your settings in DEVONthink > Preferences > Import you’ll be prompted for a destination for the email, or it will appear in your Inbox
  3. Switch to DEVONthink and select the annotation .eml document that you just imported in steps 1 & 2
  4. OPTION: control-click the .eml message and choose Convert > … to select among the list of possible formats to which you can convert the .eml document – RTF is one of these; there are others. (The commands at Data > Convert can be used instead of the contextual menu.)
  5. Control-click either the .eml message or the document to which you converted the .eml message
  6. Choose Copy Item Link from the contextual menu (or Edit > Copy Item Link).
  7. Click the .pdf document that you annotated in GR and then synced back to the desktop
  8. Open the panel at Tools > Show Info…
  9. In the URL field of the Show Info panel press command-v to paste the Item Link
  10. Close the Show Info panel

Now, it you look at the link bar (just above the document preview panel in three-pane view) for the annotated PDF you will see a clickable link – that is the link that will open the copy of the annotation email that is stored in DEVONthink.

Ignore the rest of my comments – no time to explain and they are not important

Live & learn.

Thanks korm! :smiley:

It would have taken me forever to think of your Step 4’s Data>Convert to RTF – this alone will save much effort, as it bypasses Textedit. Big Thanks!

Ditto your Step 6 Edit>Copy Item Link!

It works a charm - which, as you pointed out, saves my having to play around with the URL links between DTTG and Goodreader.

Having said that - the one benefit to inserting the GR unique code into the Comments field of the pdf whilst it’s still in DTTG, is that it makes the search-to-link easier when back in DTPO.
Reason being that when the Annotation Summary is emailed to me from GR - I have no way of knowing which PDF article it relates to, since nowhere in that file, is mention made of the identifiers I would usually make use of - i.e. Author/Title/Year etc.

Again - unless I’m missing something (highly likely) - were I not to insert the Unique Code into the Comments field in DTTG, when I send the email from Mail to DTPO, and convert to RTF - I would still need a way to know what PDF that Annotation Summary is for… Were I to only be annotating a handful of PDF’s at a time, this wouldn’t be too difficult - but where 40/50 are being done in a batch - the Unique Code comes into play… [I think! :wink: :question: ]

Thanks for helping me to understand how the Copy Item Link works. I would have continued plodding along with the ‘insert link’ via Alias route. This works too - but again, involves quite a bit of user input.

One thing I have noticed - is where I ‘create’ a link via the suggested URL to the RTF file, with the contents of the converted .eml - if I then click on Data>New From Template>Annotation - it takes me directly to the top of that already-created RTF file, as opposed to creating a ‘separate’ RTF…

I still need to play around with what would happen where a PDF already has a wiki-linked RTF, with miscellaneous notes/commentary/pdf-clippings therein - and then try and establish a new URL link between that PDF and a Annotation Summary .eml converted RTF file…

Once I’ve done that - I will pop back, and edit my original post/workflow, as needed!

Figured I would update this a bit…

Getting a bit closer to a workable solution.
In fact - I’m rather pleased with how things are working currently.

Yes, it’s still clunky - and can no doubt use some Applescript** love/genius - BUT – I’ve become a huge fan of ActionsApp for iPad - and with some sweet FLOWs, I’ve ‘automated’ plenty of steps, which allows me to accomplish all of the below, with a few taps on my iPad! :smiley:

Despite korm’s excellent suggestions above - I’ve bypassed going directly to DTPO with the GoodReader’s annotation summary.

Why? I did some searching, and worked out how to use TextWrangler (& GREP), to get to what I was hoping for.

By parsing the text file, I can generate a new RTF, that only includes my comments that were popped into the sticky-note-annotations in GoodReader.

Import these into DTPO - and I’m golden, so to speak… 8)

Here’s where I’m at:

1.) Annotate away - use an iOS shortcut to generate my specific search term (so that it can be used in DTPO’s search). Place the text in between <GR@N…>, as shown in the pic.

GR 004 annotation example.png
2.) Email the annotation summary to myself.

3.) Copy the email text - import into TextWrangler, using “New (With Clipboard)”

3a) Run “Process Lines Containing” - and run the GREP search, as shown in pic.

Grep function.png
3b) Use ActionsApp to insert text snippets, to place the first few lines into the RTF file - to be used in DTPO. Included herein, is inserting “File: XXX-XXX-XXX.pdf” - the XXX being the unique GoodReader identifier, as mentioned in steps 5 & 7 in my original post.

3c) Still using ActionsApp, save the newly generated RTF [that now contains only my parsed Annotation notes], with the same XXX as the filename. Save this in a folder being indexed by DTPO.

4.) In DTPO - use the same XXX identifier, that’s still in my clipboard, to call up a DTPO search - what is thrown back is only the newly indexed RTF, with my parsed annotation notes – and the PDF it’s applicable to, that is called up due to the same XXX identifier having been placed inside the Comment Field, in DTTG (in step 7, in my original post).

5.) Use “Copy Item Link” of the PDF - insert into the RTF at “Wik-link to PDF” - and I’m done. :slight_smile:

What I now have, is the ability to call up a search using “GR@N” AND “[search term]” - which will pull up any hits, but only in annotation notes’ RTF’s - and I then have a wiki-link in place, back to the original PDF that the annotation notes refers to.

As mentioned - clunky. But workable.

Hope this might help someone else, who has ZERO scripting knowledge, but is prepared to spend a bit of time, fashioning a workaround.

The parse ‘step’ really makes the above worthwhile. I basically reduce a 20/30/40 page text file, containing EVERY annotation (underlines; highlights; squiggly-lines and corrupt OCR text - especially in older pdf’s) - into 10/20 lines of only my notes to self. This now allows me to annotate freely on my iPad (leaving the heavy-duty notes for DTPO, and the New>>From Template>>Annotation), without worrying about some important comment, being virtually lost amongst the hundreds/thousands.

Last point - this may seem like plenty of work - but all the above, honestly involves about a minute or two, and a few taps on the iPad in ActionsApp… Given that I only do this process periodically, and then - only with 30-40 files at a time, it takes about 10 minutes, and is well worth it, in my opinion!

**[Note-to-self: Start that “Teach myself Applescript Project”]

Here be a snapshot of a 17 page RTF Annotation file, prior to the parse in TextWrangler:

Here be the end-result, after the parse:

At risk of necromancing my own thread – and without wanting to flog a dead-horse/bang a silly drum ad nauseum, I am a happy camper today! :smiley:

I have been steadily plugging away with my workflow above, over the course of the last year – whilst every-so-often wondering if it might not turn into something that I’m spending hours on, only to never use…

Well, writing up this afternoon, and I needed to find a particular point I just knew I had seen in an article on my iPad somewhere along the line… several minutes searching yielded too many hits to wave through – until it occurred to me, that a point as NB as this, would no doubt have seen me ‘make a note for myself’ inside Goodreader.

Ran a search only inside my Goodreader annotation notes, and seconds later – bingo! :smiley:

Figured I would pop something up here to simply supply proof of the fact that, occasionally, spending time devising workflows actually pay off, as opposed to only fulfilling the geek-need inside of one! :wink:

When LiquidText is available, you’ll want to reconsider and simplify your workflow. Get the beta and see what you think.

Done. Wow. Hope it delivers as suggested in the promo! Thanks.

Thanks for the LiquidText mention, korm. Cassady, I hope you were able to get setup with the beta. If either of you have questions or would like to share feedback (which we would love to hear!), please email me at
LiquidText user and employee

I have, thanks Tina - and will take you up on that offer as soon as I’ve spent enough time on it. Looks very promising so far.