Question: Bioblend download bed/interval file : HistoryDatasetAssociation not accessible
0
gravatar for christophe.habib
2.2 years ago by
France
christophe.habib340 wrote:

Hello everyone,

I need to download a large amount of files from histories of different users. These files are named the same way so I can easily get their IDs with histories.show_matching_datasets with a regular expression. The code looks like this :

hl = gi.histories.get_histories()
for h in hl:
    histID=h['id']
    todl = gi.histories.show_matching_datasets(histID,name_filter=".*_thing.vcf")[0]['id']
    gi.datasets.download_dataset(todl, file_path="./")

It works fine with VCF files, but when I try to do it with a bed files it doesn't work. I will try to give you all the details.

When I try to do it on the bed file I want to download, in a python terminal I have this error :

If I copy/paste the link in my browser it downloads the file (and the file is OK).

If I look into the uwsgi log I can read HistoryDatasetAssociation error (not accessible):

If I try to download the file with Galaxy interface and then use "Get Data" to have it in another history, and then try to download it with bioblend, I have the exact same error.

Here is the file :

Can you reproduce this error ?

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by christophe.habib340

I just tested this on another instance, in another server, and it works. The instance where it doesn't works is located in a hospital where everything go through a proxy. I have already configurated the proxy in supervisor for uwsgi and handler.

When I try to get the file with wget I have this error :

So I guess something is missing in my configuration... Maybe NGINX needs to be configured as well for the hospital proxy ?

ADD REPLYlink written 2.2 years ago by christophe.habib340

In my nginx config file I have add these lines as suggested here : https://wiki.galaxyproject.org/Admin/Config/nginxProxy to send files with Nginx

location /_x_accel_redirect/ {
    internal;
    alias /;
}

Do I need to add something related to the hospital proxy ? What I don't understand is why I have no problem for VCF files, and I have this error for this type of file only.

PS : i tried to remove these lines and restart nginx, it does not change anything

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by christophe.habib340
2
gravatar for christophe.habib
2.2 years ago by
France
christophe.habib340 wrote:

Ok the problem was solved by upgrading Bioblend... pip install --upgrade bioblend

It's ridiculous, but i'll leave this post, if someone meets the same issue ...

ADD COMMENTlink written 2.2 years ago by christophe.habib340
0
gravatar for christophe.habib
2.2 years ago by
France
christophe.habib340 wrote:

Well actually it works only for a bed file that I have imported with get data. Not with the existing one, generated with my workflow. So the problem is not solved.

I tried to compare the dataset, I see something strange, the display_type is empty in the dataset that I can download :

ADD COMMENTlink written 2.2 years ago by christophe.habib340

So I wonder if the module that download the file is using the display type in any way ? I would like to try to modify the display types, but I can't manage to do it with bioblend. Any advice ?

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by christophe.habib340

I just tried a minimal workflow, imported the 2 input that create the bed file. It create a file with display_type not null. So this lead is wrong it is not the reason of this behaviour.

ADD REPLYlink written 2.2 years ago by christophe.habib340
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