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  • Jan 07 2019 15:05
    colindaven starred ewels/MegaQC
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  • Oct 10 2018 10:05

    ewels on FLASK_DEBUG

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Albert Vilella
@avilella
The custom _mqc.tsv seem to be loaded into MegaQC
It does give me though this message: Finished writing plot data (0 cfg, 164 data points) for report 22
which makes me think I need to add something to instruct how I want each field plotted. Any ideas how @ewels ?
Phil Ewels
@ewels
I'm not sure where that's being printed sorry
Albert Vilella
@avilella
Let's say I have a custom _mqc.tsv like the one below: foo name 1 sample1 2 sample2 3 sample3 4 sample4 5 sample5 6 sample6 7 sample7 8 sample8 9 sample9 10 sample10
foo     name
1       sample1
2       sample2
3       sample3
4       sample4
5       sample5
6       sample6
7       sample7
8       sample8
9       sample9
10      sample10
Do I need to add a config section somewhere so that foo becomes available to the list of metrics in MegaQC?
Ok, forgot what I said, it turns out the _mqc.tsv files are loaded into the .html report but are not found in the .json
So I will have to find a way to craft the .json file from the .tsv directly
Phil Ewels
@ewels
I'm a bit lost - the table renders in the MultiQC report correctly, but then isn't in the JSON?
I'm quite surprised if that's the case
I just doublechecked with some custom content files at my end and it worked ifne
{
    "report_general_stats_headers": [], 
    "config_version": "1.8.dev0 (ef579dc)", 
    "report_general_stats_data": [], 
    "config_creation_date": "2019-03-07, 17:42", 
    "config_title": null, 
    "config_report_comment": null, 
    "config_short_version": "1.8.dev0", 
    "config_intro_text": null, 
    "report_saved_raw_data": {
        "multiqc_my_section_with_a_table": {
            "samp_1": {
                "col1": 12.523, 
                "col2": 34.0
            }, 
            "samp_2": {
                "col1": 56.947, 
                "col2": 78.0
            }
        }
    }, 
    "report_data_sources": {}, 
    "report_multiqc_command": "/Users/ewels/miniconda2/envs/work/bin/multiqc -f table_headers_mqc.txt", 
    "config_analysis_dir": [
        "table_headers_mqc.txt"
    ], 
    "config_report_header_info": null, 
    "config_analysis_dir_abs": [
        "/Users/ewels/GitHub/MultiQC_TestData/data/custom_content/embedded_config/table_headers_mqc.txt"
    ], 
    "config_subtitle": null, 
    "report_plot_data": {}, 
    "config_script_path": "/Users/ewels/GitHub/MultiQC/multiqc/utils", 
    "config_git_hash": "ef579dcdcdb12a56ea516b2354472cb5f640353c"
}
Albert Vilella
@avilella
So in my case it produces a json with no data
avilella@avilellaM710t:~/multiqc/test$ find $PWD/ -name "*.json" | xargs cat
{
    "report_general_stats_headers": [], 
    "config_version": "1.5dev", 
    "report_general_stats_data": [], 
    "config_creation_date": "2019-03-07, 16:48", 
    "config_title": null, 
    "config_report_comment": null, 
    "config_short_version": "1.5dev", 
    "config_intro_text": null, 
    "report_saved_raw_data": {}, 
    "report_data_sources": {}, 
    "report_multiqc_command": "/usr/local/bin/multiqc --force --filename /home/avilella/multiqc/test/report__multiqc /home/avilella/multiqc/test", 
    "config_analysis_dir": [
        "/home/avilella/multiqc/test"
    ], 
    "config_report_header_info": null, 
    "config_analysis_dir_abs": [
        "/home/avilella/multiqc/test"
    ], 
    "config_subtitle": null, 
    "report_plot_data": {}, 
    "config_script_path": "/usr/local/lib/python2.7/dist-packages/multiqc/utils", 
    "config_git_hash": null
}
avilella@avilellaM710t:~/multiqc/test$ cat *.txt
# plot_type: 'table'
# section_name: 'My section with a table'
# description: 'a custom text introduction (a few sentences) for this section'
# pconfig:
#     namespace: 'Cust Data'
# headers:
#     col1:
#         title: 'My Column'
#         description: 'This is a longer hover text for my column'
#         format: '{:,.0f}'
#     col2:
#         title: 'Second Column'
#         description: 'Hover description text'
Sample            col1            col2
samp_1            12.523          34
samp_2            56.947          78
avilella@avilellaM710t:~/multiqc/test$ #/usr/local/bin/multiqc --force --filename /home/avilella/multiqc/test/report__multiqc /home/avilella/multiqc/test
Phil Ewels
@ewels
Hmm, MultiQC v1.5dev
that's pretty old
we're on 1.8dev now
My guess is that you need to update MultiQC for this to work with custom content then
Albert Vilella
@avilella
I updated to 1.7 and it worked, thanks.
Phil Ewels
@ewels
Ok great!
Sehrish Kanwal
@skanwal

Hi Phil,
I am testing the megaqc upload function (locally on my laptop) to get data into megaQC server.
I am getting Error - This function requires MultiQC to be installed..
Following this issue on github https://github.com/ewels/MegaQC/issues/66, I have multiqc installed on my laptop and I am running the upload command from the same environment where I used multiqc to generate the report/json file.
For context, I installed multiqc via conda. The multiqc conda environment is also active in my session. Trying from multiqc.utils import config as multiqc_config on python interpreter also works fine..

Any idea what could be the underlying issue?

Phil Ewels
@ewels
Hi Sehrish - that sounds very odd!
Are you super-sure that everything is definitely in the same environment? By checking which megaqc and which multiqc..?
Ah, and it’s definitely a recent version of MultiQC?
The code that triggers that message isn’t doing anything particularly special: https://github.com/ewels/MegaQC/blob/master/megaqc/commands.py#L173
Sehrish Kanwal
@skanwal

Ah, that’s going to be interesting.

which multiqc > /Users/kanwals/miniconda3/envs/multiqc/bin/multiqc
which megaqc > /Users/Kanwals/miniconda3/bin//megaqc

As you can tell, I installed both tools in separate conda environment. Aslo, used pip for megaqc installation.
Should I try installing megaqc in multiqc environment.?
Multiqc version is 1.7, so should definitely be not an issue.

Phil Ewels
@ewels
Yes they need to be installed in the same environment
Otherwise they are using different python installations, so they can’t see each other
Pip installs within a conda environment should be fine
which pip should show it in the conda env.
Sehrish Kanwal
@skanwal

Phil, tried reinstalling megaQC in the multiQC conda environment using pip. The installation went okay.
Both the tools are now installed in the same environment.
which megaqc > /Users/kanwals/miniconda3/envs/multiqc/bin/megaqc
which multiqc > /Users/kanwals/miniconda3/envs/multiqc/bin/multiqc

For testing, ran multiqc on a sample, and the report was successfully posted to megaqc server.
But upload is again throwing the same issue:

megaqc upload multiqc_data/multiqc_data.json
This is MegaQC v0.1.dev1

Env: test
 * Database type: sqlite
 * Database path: sqlite:////Users/kanwals/miniconda3/lib/python3.6/site-packages/test.db
Error - This function requires MultiQC to be installed
Phil Ewels
@ewels
Strange. Could you make an issue about this on the GitHub repo please?
I have no ideas as to how or why this could happen now though
It’s nothing special about MegaQC or MultiQC here - it’s just a simple python import.
Sehrish Kanwal
@skanwal
Thanks, Phil.
Sure, I'll open an issue on GitHub.
Michael Milton
@TMiguelT
I'd appreciate feedback from anyone on my Dash integration PR: ewels/MegaQC#81
Michael Milton
@TMiguelT
@ewels if you can get back to me about the dash PR and also the control chart thresholds, that would be great
I have an upcoming meeting at my work where I'll be talking about MegaQC, and if I can implement and then show off some of these features, there's a much better chance I'll be given time to work on MegaQC
Michael Milton
@TMiguelT
In particular I want to implement something for the alert thresholds that I can show, but I want to know if Dash is a reasonable direction to be taking
Phil Ewels
@ewels
I'll do my best :+1:
Michael Milton
@TMiguelT
Much appreciated
Michael Milton
@TMiguelT
Can you explain why the MegaQC API uses a token, rather than just the session cookies that normal requests use?
Phil Ewels
@ewels
Not sure I remember sorry.
I guess you don’t mean the key pair for uploads? Just regular API calls in-page?
That code was nearly all written by Denis (who changed jobs right after), so I don’t have a lot of insight into it sorry
Michael Milton
@TMiguelT
I mean the API token used for API calls from JavaScript
It's unusual because the application authenticates the user login, and then sets a session cookie. But then it also gives the user an API token which to me seems redundant
Phil Ewels
@ewels
Probably is then :+1: