Trying to open aibe:link content on Brain Explorer 2

[Slutship99]

Hello everyone. I'm new to this forum, glad to met ya. I need help with the following:

Brain Explorer 2 (for short BE2) is a free software used to "browse" around the brain, from basic anatomy to genome data. It's freely available here: http://human.brain-map.org/static/brainexplorer

There is a function that open certain kind of links on a browser, with the format aibe:link (aibe is for Allen Institute Brain Explorer). Here an example: aibe://human.brain-map.org/mri_viewer/data/heatmap/probe_values?atlas=351&resolu‌​tion=samples&probes=1036443&selectedDonor=9861&well=2569&colormap=redgreen&exprRa‌​nge=-6,6

For example, you browse the BE2 website, then open certain aibe:link (clicking on "Launch Brain Explorer 2), so this launch BE2 and also download certain kind of data. In the first 30 sec of this video you can see what I mean https://youtu.be/7aUWdKvSIG0

On Ubuntu, there is no way to make browser to open a wine program by default unless you config xdg-open and create a .desktop file. I asked for this on askubuntu.com, and the first answer was fine in order to solve this part of the problem --> http://askubuntu.com/questions/627469/h ... is-on-wine

But also, and this is the very intriguing issue, program doesn't donwload aibe:link content as it does on windows. I was told on askubuntu that on registry there was this key

HKEY_CLASSES_ROOT\aibe\shell\open\command

with the following content

"C:\Program files\Allen Institute\Brain Explorer 2\BrainExplorer2.exe" /url "%1"

Which supposedly handles the aibe:link and tell the program "this is your stuff" (with the /url "%1" part). I found this key on a windows install I did, but not in my Ubuntu install. Curiously I cannot create the key, because when attempt doing it throws me the message "key file already exists", but there isn't such key on that path. My guess is that the program would do its work if I were able to create that key.

I'm very confused. Also I ask this because I'm doing a bit of research in home, since this is a very useful tool, so would be very appreciated someone could help me here

[Slutship99]

Oh and the full key content on windows is this:

Code: Select all

Windows Registry Editor Version 5.00

[HKEY_CLASSES_ROOT\aibe]
@="URL:Brain Explorer 2"
"URL Protocol"=""

[HKEY_CLASSES_ROOT\aibe\DefaultIcon]
@="\"C:\\Program Files (x86)\\Allen Institute\\Brain Explorer 2\\BrainExplorer2.exe\",1"

[HKEY_CLASSES_ROOT\aibe\shell]

[HKEY_CLASSES_ROOT\aibe\shell\open]

[HKEY_CLASSES_ROOT\aibe\shell\open\command]
@="\"C:\\Program Files (x86)\\Allen Institute\\Brain Explorer 2\\BrainExplorer2.exe\" /url \"%1\""

[dimesio]

I've been playing around with this, and haven't been able to get it to work. However, I think you are incorrect about the program being supposed to download data when you click the link in a browser. The first time you run the app, it prompts you to download 4 atlases; both the video you linked to and the app's documentation give me the impression that clicking the link in your browser is merely supposed to open Brain Explorer with the appropriate section of the atlas loaded from your already-downloaded copy. That's the part that's not working.

[Slutship99]

I've been playing around with this, and haven't been able to get it to work. However, I think you are incorrect about the program being supposed to download data when you click the link in a browser. The first time you run the app, it prompts you to download 4 atlases; both the video you linked to and the app's documentation give me the impression that clicking the link in your browser is merely supposed to open Brain Explorer with the appropriate section of the atlas loaded from your already-downloaded copy. That's the part that's not working.

Mmm well the program it really downloads and opens data from aibe:links, and this is what is opened on Brain Explorer 2. This data contains expression of particular genes you have looked for on website (like in this example). There is thousands of different genes, so you download data for one or more genes of your choose to visualize on previously downloaded Brain maps (mouse or human). The same data can be downloaded in a zip package (below on image), in order to be analyzed on excel or statistic software. This data is a few kilobytes on size, so my guess is that is downloaded each time you click on the aibe link if that is your question.



I was sugested that aibe links could be opened following HKEY_CLASSES_ROOT key syntax menctioned above. So, typing on wine, for example:

Code: Select all

wine "path-to-BrainExplorer2.exe" /url "aibe://human.brain-map.org/mri_viewer/data/heatmap/probe_values?atlas=351&resolution=samples&probes=1036443&selectedDonor=10021&well=7312&colormap=redgreen&exprRange=-3.3000000000000003,3.299999999999999"

Should result on BE2 downloading the data and showing it on the 3d atlas. But isn't working, and my suspect is because that key is missing and cannot add it by editing with regedit.

[Slutship99]

P.D: I realized that sometimes when using it on windows you must open the atlas first (human atlas for the above case), after that you click on aibe link, or else it doesn't download/open anything. Well, just sometimes, but is a little meaningless bug.

P.D2: hope explaining myself clearly since english is not my native language.

[dimesio]

P.D: I realized that sometimes when using it on windows you must open the atlas first (human atlas for the above case), after that you click on aibe link, or else it doesn't download/open anything. Well, just sometimes, but is a little meaningless bug.

It's hardly meaningless; not downloading is the exact problem you're having. Wine aims for "bug for bug compatibility," so if it's a problem in Windows, it will be a problem in Wine, too. It's been my experience that bugs that exist "sometimes" in Windows tend to be triggered much more often in Wine.

Regarding the registry, everything you listed as being on Windows was added by the app's installer on my system, except for

Code: Select all

[HKEY_CLASSES_ROOT\aibe]
@="URL:Brain Explorer 2"
"URL Protocol"=""

(I added that one manually, but it didn't help.) So I think the message you are getting from regedit is probably correct, and you just overlooked it. I can also tell you that having it doesn't fix the problem.

You should try installing Firefox and Flash in the same wineprefix and seeing if it works from that.

[Slutship99]

(I added that one manually, but it didn't help.) So I think the message you are getting from regedit is probably correct, and you just overlooked it. I can also tell you that having it doesn't fix the problem.

You should try installing Firefox and Flash in the same wineprefix and seeing if it works from that.

Well I did that just this afternoon, installed BrainExplorer 2, Flash and Firefox on same prefix. Firefox still cannot redirect aibe links content to BE2, it says that there isn't an app able to handle that. This is very strange :/

I will try to open an aibe link on a windows console following the same syntax I menctioned ("c:/path/BE2.exe" /url "aibe:link")

Should I post my registry content on HKEY_CLASSES_ROOT to see if there is something missing?

[Slutship99]

By the way, I just though that I could try edit the windows Firefox default apps to manage aibe links. First, I need to make appear the aibe on the list of recognized extensions (I don't know how). But even if it works (I hope so), I wanna know how to make this work from Ubuntu native browsers as I been trying.

[Slutship99]

Well I was trying to edit with gedit the file called mimeTypes.rdf (which apparently contains the recognized extensions of firefox and the instructions to follow in the case) in order to make windows firefox recognize the aibe links or at least put it in the list of extensions managed by firefox. But I'm not so good at this kind of things. Help

https://support.mozilla.org/en-US/kb/ap ... dles-files