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Trinotate / Trinotate.github.io

web documentation for Trinotate
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Question about Trinotate.web #42

Open Genan-blur opened 3 years ago

Genan-blur commented 3 years ago

Hi all: I was luckily going to the final step that makes the localhost, but when I point my SQLite file to the website and click the submit icon, it says ''Error,cannot locate file://data/aureobasidium/Trinotate_database/Trinotate.sqlite' at home/ubuntu/miniconda3/envs/..../Trinotate-v3.2.1/TrinotateWeb/cgi-bin/index.cgi line 48''. I tried many times, redownloading the cgi model or the lighttpdp but failed. Please help!

brianjohnhaas commented 3 years ago

Hi,

If you try to list the file from a terminal like so:

ls -l /data/aureobasidium/Trinotate_database/Trinotate.sqlite

Does that work ok?

On Mon, Sep 28, 2020 at 4:12 AM Genan notifications@github.com wrote:

Hi all: I was luckily going to the final step that makes the localhost, but when I point my SQLite file to the website and click the submit icon, it says ''Error,cannot locate file://data/aureobasidium/Trinotate_database/Trinotate.sqlite' at home/ubuntu/miniconda3/envs/..../Trinotate-v3.2.1/TrinotateWeb/cgi-bin/index.cgi line 48''. I tried many times, redownloading the cgi model or the lighttpdp but failed. Please help!

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Genan-blur commented 3 years ago

Hi Thanks for your reply. it's ok. I can list it, and it shows:

-rwxrwxrwx 1 root root 558477312 Sep 28 10:59 /data/aureobasidium/Trinotate_database/Trinotate.sqlite

brianjohnhaas commented 3 years ago

Is the file system where that file is located on the same physical hardware that's running the TrinotateWeb webserver?

If so, are there error messages in the terminal where you launched TrinotateWeb?

On Mon, Sep 28, 2020 at 10:38 AM Genan notifications@github.com wrote:

Hi Thanks for your reply. it's ok. I can list it, and it shows:

-rwxrwxrwx 1 root root 558477312 Sep 28 10:59 /data/aureobasidium/Trinotate_database/Trinotate.sqlite

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Genan-blur commented 3 years ago

Hi: Sorry for the late reply. I found that it is because my path for the Trinotate.sqlite is wrong. But I encounter another problem, and now the error message in the webserver is: "error, cmd: mkdir -p tmp/tcache died with ret 256 at ~/miniconda3/envs/trinity/opt/Trinotate-Trinotate-v3.2.1/TrinotateWeb/cgi-bin/../../PerlLib/Textcache.pm line 78 TextCache::_ensure_cache_dir() called at ~/miniconda3/envs/trinity/opt/Trinotate-Trinotate-v3.2.1/TrinotateWeb/cgi-bin/../../PerlLib/Textcache.pm TextCache::cache_page".

And in the terminal is: CGI::Pretty is DEPRECATED and will be removed in a future release. Please see https://github.com/leejo/CGI.pm/issues/162 for more information at /home/ubuntu/miniconda3/envs/trinity/lib/site_perl/5.26.2/CGI/Pretty.pm line 20. mkdir: cannot create directory 'tmp': Permission denied.

Thanks a lot

brianjohnhaas commented 3 years ago

Hi,

Try doing this manually.

cd to your Trinotate/TrinotateWeb/cgi-bin/ directory.

Then: mkdir -p tmp/tcache

and: chmod -R 777 ./tmp

Let's see if that helps.

On Wed, Sep 30, 2020 at 1:23 PM Genan notifications@github.com wrote:

Hi: Sorry for the late reply. I found that it is because my path for the Trinotate.sqlite is wrong. But I encounter another problem, and now the error message in the webserver is: "error, cmd: mkdir -p tmp/tcache died with ret 256 at ~/miniconda3/envs/trinity/opt/Trinotate-Trinotate-v3.2.1/TrinotateWeb/cgi-bin/../../PerlLib/Textcache.pm line 78 TextCache::_ensure_cache_dir() called at ~/miniconda3/envs/trinity/opt/Trinotate-Trinotate-v3.2.1/TrinotateWeb/cgi-bin/../../PerlLib/Textcache.pm TextCache::cache_page".

And in the terminal is: CGI::Pretty is DEPRECATED and will be removed in a future release. Please see leejo/CGI.pm#162 for more information at /home/ubuntu/miniconda3/envs/trinity/lib/site_perl/5.26.2/CGI/Pretty.pm line 20. mkdir: cannot create directory 'tmp': Permission denied.

Thanks a lot

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Genan-blur commented 3 years ago

Thanks! It works.

brianjohnhaas commented 3 years ago

excellent!

On Wed, Sep 30, 2020 at 1:50 PM Genan notifications@github.com wrote:

Thanks! It's work.

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brianjohnhaas commented 2 years ago

hi,

not sure, but that warning is not usually fatal. Sometimes looking at the javascript debugging info in the browser gives hints. It might be trying to pull a resource that's no longer available.

If it's an old trinotate installation, you could try downloading the latest code and see if this part behaves better.

On Mon, Jul 26, 2021 at 11:15 AM giggu98 @.***> wrote:

I am encountering kind of similar problem. I want to use TrinotateWeb with my past Trinotate sqlite file (It used to work just fine!). But when I enter the path to the sqlite file on lighttpd local host page, nothing shows up on the webpage and the text box disappears. I checked my terminal and I found that there is the same warning message appears. I tried to check the github page you linked in the previous comment but I somehow could not access the page.

CGI::Pretty is DEPRECATED and will be removed in a future release. Please see https://github.com/leejo/CGI.pm/issues/162 for more information at /Users/gigabyte/opt/anaconda3/lib/site_perl/5.26.2/CGI/Pretty.pm line 21.

Thank you in advance.

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