expression loader

[kyrenya]

Hi there!
I'm trying to follow instructions, and I must be doing something wrong, because I get this message:

any idea of what is happening?

• I loaded biosamples file before
• The features in the expression column file are already in the database
• I created an analysis

Thanks a lot in advance! Cheers!

[bradfordcondon]

the importer supports two expression file formats- which were you using?

https://github.com/tripal/tripal_analysis_expression#expression-data-loader

Can you please share the first few lines of your expression file so I can confirm the format?

Thanks

[kyrenya]

hi there! thx for your reply
I'm trying to use a column file.
I already tried with the example included in this repo,

https://github.com/tripal/tripal_analysis_expression/blob/master/example_files/exampleExpressionData.rpkm

and now I'm trying with a file like this:
(minified, with just a couple of features, just to try the module).

LOC112032122 17.94043
LOC111982897 7.206919

[bradfordcondon]

Looks like that call of expression_create_biomaterial_structure was missing an argument. i sbmitted a patch.

I recommend using the matrix format instead, if you can. its better tested.

[kyrenya]

ok! the matrix worked! Thx! I'll try the patch anyway and let you know!

[bradfordcondon]

any problems @kyrenya ? or can i close this issue?

[kyrenya]

hi there! sorry I was away in a meeting and didnt come back to this yet! Matrix files worked, still didnt test the patch for the column ones, but I guess you can close! Thx!!

[kyrenya]

Hi there,
I'm trying to upload matrix files (new machine, fresh git clone of this module).
and I'm getting a window AJAX warning, with the following:

I'm trying to upload the sm125.xml example matrix file, to discard the fact that my files being not ok.

ANy help?
Thanks!

[bradfordcondon]

@kyrenya thats an example XML file, not an example matrix file.

<BioSampleSet>
    <BioSample access="public" publication_date="2016-05-06T08:50:02.560" last_update="2016-05-09T17:03:18.897"
               submission_date="2016-05-06T08:50:03.817" id="4958045" accession="SAMN04958045">
        <Ids>
            <Id db="BioSample" is_primary="1">SAMN04958045</Id>
            <Id db_label="Sample name">SM125</Id>
            <Id db="SRA">SRS1426053</Id>
        </Ids>
        <Description>
            <Title>Plant sample from Acer saccharum</Title>
            <Organism taxonomy_id="4024" taxonomy_name="Acer saccharum">
                <OrganismName>Acer saccharum</OrganismName>
            </Organism>
            <Comment>
                <Paragraph>Sugar Maple - pooled seedling leaf RNAs, 125 ppb ozone</Paragraph>
            </Comment>
        </Description>

The example biomaterial matrix file is here: https://github.com/tripal/tripal_analysis_expression/blob/master/example_files/3175-biomaterial.csv

this file does laod for me on my site. The "Check biosamples" button does NOT WORK for flat files, ONLY for XML.

That said, this issue is titled "expression loader" so thats confusing. If youre having problems wit hte biomaterial loader, please open a separate issue. Double check you are using the appropriate loader for the file.

[kyrenya]

sorry, I made a mess when explaining.
I try again:
I'm trying to upload a biosample example file
I'm assuming sm125.xml is one, and I managed to check biosamples with this file in my other machine, but when trying to do it in this new one, I get the message I showed before.

[bradfordcondon]

OK, im able to reproduce the error. at first I got a warning about the file being empty, but when i used the pre-existing file, I got the AJAX warning. Something has gone wrong with the biosample checker that lets you assign cvterms. However, the biomaterials still import fine if you run the importer. I created a ticket for this issue #284

[kyrenya]

uhm.. this is weird, I get the same message no matter if pre-existing file or with the importer :(

[bradfordcondon]

im working on it. i broke the property checker function trying to simplify the code unfortunately.

[kyrenya]

ok! sorry for that! I'll wait for your news then!
:) thanks a lot in advance!

[bradfordcondon]

this pr should resolve #285 . can you please update master and try again?

[kyrenya]

I think it works now! Thx! I will try now to upload my data!