How to re-host the website directly without building it once more?

[lijxug]

Hi, I've made some changes to the html folder manually, and want to re-host the website. I've noticed that if I use cbBuild to start the website, the files would be renewed. Just wondering if I can dirrectly start the manually-adjusted-server bypassing cbBuild.

[maximilianh]

Great question! You can use "cbUpgrade (directory) -p (port)" for this. Let me document this better now...

On Thu, Sep 9, 2021 at 10:54 AM StupidArcher @.***> wrote:

Hi, I've made some changes to the html folder manually, and want to re-host the website. I've noticed that if I use cbBuild to start the website, the files would be renewed. Just wondering if I can dirrectly start the manually-adjusted-server bypassing cbBuild.

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[maximilianh]

Actually, wait, there is no need to re-host the website. the webserver is independent from the building procedure. If you modify the html files, just reload the page in your internet browser, possibly holding "shift" to force a cache update.

If you need to force the cache update, probably I'm doing something wrong, because I thought I had addressed most caching problems now. But I think @mspeir has still an open bug ticket where if you modify the desc.conf or cellbrowser.conf, then one of the md5s is not updated and so you need to do the shift+reload yourself. I'd need to know more what exactly you changed.

On Thu, Sep 9, 2021 at 11:24 AM Maximilian Haeussler @.***> wrote:

Great question! You can use "cbUpgrade (directory) -p (port)" for this. Let me document this better now...

On Thu, Sep 9, 2021 at 10:54 AM StupidArcher @.***> wrote:

Hi, I've made some changes to the html folder manually, and want to re-host the website. I've noticed that if I use cbBuild to start the website, the files would be renewed. Just wondering if I can dirrectly start the manually-adjusted-server bypassing cbBuild.

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[lijxug]

@maximilianh Actually, your first suggestion might be what I want, because I already stopped the server and now I want it back on. I do need a command to re-host the website without rebuilding it. And.. cbUpgrade -p (port) (directory) doesn't seem to run. always got a manual output.

[maximilianh]

Hi, can you send me the error message? I don't understand what "always got a manual output" means, sorry.

On Thu, Sep 9, 2021 at 11:43 AM StupidArcher @.***> wrote:

@maximilianh https://github.com/maximilianh Actually, your first suggestion might be what I want, because I already stopped the server and now I want it back on. I do need a command to re-host the website without rebuilding it. And.. cbUpgrade -p (port) (directory) doesn't seem to run. always got a manual output.

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[lijxug]

@maximilianh My bad. What I tried to say is "cbUpgrade -p (port) (directory) doesn't seem to run. It always prints out the help message."

[maximilianh]

Yes, because, sorry I didn't specify the correct command, you also need to specify the directory of course, the command cannot guess your html directory:

cbUpgrade -p 8888 -o MYHTMLDIR

On Sun, Sep 12, 2021 at 9:19 AM StupidArcher @.***> wrote:

@maximilianh https://github.com/maximilianh My bad. What I tried to say is "cbUpgrade -p (port) (directory) doesn't seem to run. It always prints out the help message."

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[lijxug]

Great, thanks!

Yes, because, sorry I didn't specify the correct command, you also need to specify the directory of course, the command cannot guess your html directory: cbUpgrade -p 8888 -o MYHTMLDIR … On Sun, Sep 12, 2021 at 9:19 AM StupidArcher @.***> wrote: @maximilianh https://github.com/maximilianh My bad. What I tried to say is "cbUpgrade -p (port) (directory) doesn't seem to run. It always prints out the help message." — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#226 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TLY2MBF3J5XL5KAGW3UBRH67ANCNFSM5DWT5KOQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[zahoorhuma]

@maximilianh How can we run dataset hierarchies on windows machine via command and what will be the directory structure. I have read the documentation but confusion is still there.

[maximilianh]

OK, so the docs page is not clear... can you tell me what you understand from the docs page? This will help me extend it. Which part do you find confusing?

On Wed, Sep 14, 2022 at 5:41 PM zahoorhuma @.***> wrote:

@maximilianh https://github.com/maximilianh How can we run dataset hierarchies on windows machine via command and what will be the directory structure. I have read the documentation but confusion is still there.

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[zahoorhuma]

@maximilianh I am on windows machine. I am facing issues in running the cbBuild command for dataset hierarchies with -r option. So the folder structure is quite unclear to me. Not getting how to enable dataset hierarchies. Which cell browser file we have to set the dataRoot variable.

I am assuming the folder structure the way I am trying for dataset hierarchies be like:

---parent Folder ------Child Folder 1 i.e Data1 (has cellbrowser.conf file) ------Child Folder 2 i.e Data2 (has cellbrowser.conf file) ------cellbrowser.conf file ------dec.conf file

I am running the command like:

python cbBuild -i (the path of cell browser.conf file inside the parent Folder) -r (path of parent Folder (unzipped)) -o (path of output directory) -p (port number)

if I missed any option it throws me error like.. Did you forget to add -i etc.

Please guide me where I am wrong.

[maximilianh]

Here, the dataRoot is "parent Folder". Please do not use the -r option, just run cbBuild in "parent Folder". I am just adding documentation to -r and will need to change the docs page and fix something in the code to make sure that this is clearer.

Does this work for you?

Do you have a ~/.cellbrowser.conf file?

On Wed, Sep 14, 2022 at 7:09 PM zahoorhuma @.***> wrote:

I am on windows machine. I am facing issues in running the cbBuild command for dataset hierarchies with -r option. So the folder structure is quite unclear to me. Not getting how to enable dataset hierarchies. Which cell browser file we have to set the dataRoot variable.

I am assuming the folder structure the way I am trying for dataset hierarchies be like:

---parent Folder ------Child Folder 1 i.e Data1 ------Child Folder 2 i.e Data2 ------cellbrowser.conf file ------dec.conf file

I am running the command like:

python cbBuild -i -r -o -p

if I missed any option it throws me error like.. Did you forget to add -i etc.

Please guide me where I am wrong.

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[zahoorhuma]

@maximilianh Let me try this.

Yes every dataset has its cellbrowser.conf file.

As ~/.cellbrowser.conf is in Linux so don't know where to create that file in Windows.

Are we supposed to create that cellbrowser.conf file in the parent Folder?

[maximilianh]

Sorry, one problem here is my unfortunate naming of the files. the ~/.cellbrowser.conf file has nothing to do with the cellbrowser.conf files for the datasets.

The ~/.cellbrowser.conf file is a configuration file in your homedirectory. I don't know where that is but I think if you run cbBuild with -d, you can get an idea of where it is located on Windows. Also you can google for "python home directory windows" to get an idea where it is on Windows. Windows does have a homedirectory, just like Unix, it's just a little hidden. You can also use the CBDATAROOT environment variable.

On Thu, Sep 15, 2022 at 2:16 PM zahoorhuma @.***> wrote:

Let me try this.

Yes every dataset has its cellbrowser.conf file.

As ~/.cellbrowser.conf is in Linux so don't know where to create that file in Windows.

Are we supposed to create that cellbrowser.conf file in the parent Folder?

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[zahoorhuma]

Oh okay okay. let me try this and get back to you. Thank you so much @maximilianh .

[maximilianh]

Thank you for asking, because I'm realizing now where the problems are...

On Thu, Sep 15, 2022 at 2:35 PM zahoorhuma @.***> wrote:

Oh okay okay. let me try this and get back to you. Thank you so much @maximilianh https://github.com/maximilianh .

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[zahoorhuma]

@maximilianh I have tried the above solution but issue is still there.

I have set the environment variable CBDATAROOT with the value of parent folder.

Then, I run the command cbBuild it shows me the following error:

If I specified the -o option then it shows me the following error:

[maximilianh]

Yes, this problem looks unrelated to hierarchies... it just can't find the meta.tsv input file...? Is "src" a data directory?

On Thu, Sep 15, 2022 at 4:10 PM zahoorhuma @.***> wrote:

I have tried the above solution but issue is still there.

I have set the environment variable CBDATAROOT with the value of parent folder.

[image: image] https://user-images.githubusercontent.com/75778741/190424208-b419808a-53eb-4c7e-a617-932ffa6de9b7.png

Then, I run the command cbBuild it shows me the following error:

[image: image] https://user-images.githubusercontent.com/75778741/190424665-dc07021e-9aac-44d6-9781-7ac039bd27c7.png

If I specified the -o option then it shows me the following error:

[image: image] https://user-images.githubusercontent.com/75778741/190425293-ca138716-811f-43b0-99a1-4ed6e52bb3fc.png

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[zahoorhuma]

src is a directory coming from the cell browser github code clone. After running the above command it created a folder named sample in the output directory but no content inside. Meta.tsv file should be in the sample folder.

[maximilianh]

You cd into the "parent Folder", then run cbBuild. You cannot cd into the "src" folder and run cbBuild there, that cannot work in any way. You must be in your data directory to be able to run cbBuild and you specify the html output directory with the -o option.

On Thu, Sep 15, 2022 at 4:41 PM zahoorhuma @.***> wrote:

src is a directory coming from the cell browser github code clone. After running the above command it created a folder named sample in the output directory but no content inside. Meta.tsv file should be in the sample folder.

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[zahoorhuma]

@maximilianh let me try this as well.

[zahoorhuma]

@maximilianh Thank you. It has processed the data set. Thank you once again for the help.

[zahoorhuma]

@maximilianh could you please refer me where we can find the raw datasets if is there any?

[maximilianh]

hi sorry what do you mean, which "raw datasets" ?

On Fri, Sep 16, 2022 at 6:42 PM zahoorhuma @.***> wrote:

@maximilianh https://github.com/maximilianh could you please refer me where we can find the raw datasets if is there any?

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[zahoorhuma]

Means to say input dataset.. because I have seen cell browser images in that there is 3 collections 10 datasets kind of thing. How can we achieve that.

Please find the attached picture for your reference.

[maximilianh]

Hi, these are just the data hierarchy in action, we call them "collections". Did you see this part of the documentation? https://cellbrowser.readthedocs.io/en/develop/collections.html

On Sat, Sep 17, 2022 at 6:38 AM zahoorhuma @.***> wrote:

Means to say input dataset.. because I have seen cell browser images in that there is 3 collections 10 datasets kind of thing. How can we achieve that.

[image: cellbrowser-DatasetOverview converted] https://user-images.githubusercontent.com/75778741/190840640-6cebfe34-9e09-4fa7-9b88-f35e6c2b45b2.jpg

Please find the attached picture for your reference.

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[zahoorhuma]

@maximilianh yes I have tried but didn't get any fruitfull results

[maximilianh]

can you try "pip install cellbrowser --pre --upgrade" and see if that fixes the problem? You need a ~/.cellbrowser.conf file, the ~ character is the directory C:\Users\yourusername\ in Windows (replace username with your username)

The ~/.cellbrowser.conf must include a line dataRoot=<directory that includes all your data files> with double quotes around the directory

On Tue, Sep 20, 2022 at 2:40 PM zahoorhuma @.***> wrote:

@maximilianh https://github.com/maximilianh yes I have tried but didn't get any fruitfull results

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[zahoorhuma]

@maximilianh I have tried that. It does generate some files but while processing it gives me an error there is no meta data in cell browser.conf file.

[zahoorhuma]

Hey @maximilianh I want to restrict columns of meta.tsv file to some users. Any idea how can we do that. What is the role of meta.index file in it?

[maximilianh]

Sorry what do you mean with “users” and “restrict” ? I don’t understand the question.

On Fri 28 Oct 2022 at 17:55, zahoorhuma @.***> wrote:

Hey @maximilianh https://github.com/maximilianh I want to restrict columns of meta.tsv file to some users. Any idea how can we do that. What is the role of meta.index file in it?

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[zahoorhuma]

@maximilianh

This is the picture I want to restrict these metafields i.e Age,Area etc. I don't want Laminae metafield. How can we achieve that

[maximilianh]

If you want to remove a field from the meta data, just remove the field from meta.tsv and run cbBuild again.

I hope I understood your question correctly.

On Fri 28 Oct 2022 at 17:59, zahoorhuma @.***> wrote:

@maximilianh https://github.com/maximilianh [image: IMG-20221028-WA0035] https://user-images.githubusercontent.com/75778741/198681272-d0c11b98-5750-4b03-bc75-298526df8f7f.jpg

This is the picture I want to restrict these like I don't want Laminae metafield. How can we achieve it

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[zahoorhuma]

@maximilianh yeah you got my point.let me try this solution. Hope this works

[maximilianh]

No the cbImportXXC create the meta.tsv file in the data directory. In that data directory, you modify meta.tsv, then run cbBuild to create the html directory. This html directory contains a copy of the meta.tsv, yes, but is accompanied by a matching index file. You need to re-run cbBuild after each change to meta.tsv in the data directory to recopy the meta.tsv in the html folder and rebuild its index

On Fri 28 Oct 2022 at 18:08, zahoorhuma @.***> wrote:

But I have one question @maximilianh https://github.com/maximilianh this meta.tsv file build after we run cbBuild. Right? If we remove the field and on running the cbBuild again on the dataset isn't make the meta.tsv file again?

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[zahoorhuma]

@maximilianh let me try this solution

[zahoorhuma]

@maximilianh what is the purpose of meta.index file with meta.tsv? Is it contains the mapping of tsv file in it. Can we achieve it with meta.tsv file only. or meta.index file is necessary.

[maximilianh]

I’m not sure why you’re asking… You can only modify the data folder, not the html directory. the files in the html (htdocs) directory are not independent from each other: they go together. There is no need to change these files, as far as I know.

meta.index has the start and end coordinates of every line in meta.tsv. You cannot change meta.tsv in the html directory.

What you can do: change meta.tsv in the data directory, then run cbBuild which will copy over meta.tsv and rebuild meta.index

On Fri 28 Oct 2022 at 18:39, zahoorhuma @.***> wrote:

@maximilianh https://github.com/maximilianh what is the purpose of meta.index file with meta.tsv? Is it contains the mapping of tsv file in it. Can we achieve it with meta.tsv file only. or meta.index file is necessary.

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[zahoorhuma]

@maximilianh Thank you so much.