WIP: Initial draft for webservice implementation

[johandahlberg]

This doesn't have any tests yet, nor is it running asynchronously. I'll fix that next week.

For now this will make it possible to run checkqc as a webservice, and get something like this back:

$ curl -w'\n' localhost:9999/170726_D00118_0303_BCB1TVANXX | python -m json.tool
{
    "ClusterPFHandler": [
        {
            "data": {
                "lane": 1,
                "lane_pf": 117929896,
                "threshold": 180
            },
            "message": "Cluster PF was to low on lane 1, it was: 117.93 M",
            "type": "warning"
        },
        {
            "data": {
                "lane": 7,
                "lane_pf": 122263375,
                "threshold": 180
            },
            "message": "Cluster PF was to low on lane 7, it was: 122.26 M",
            "type": "warning"
        },
        {
            "data": {
                "lane": 8,
                "lane_pf": 177018999,
                "threshold": 180
            },
            "message": "Cluster PF was to low on lane 8, it was: 177.02 M",
            "type": "warning"
        }
    ],
    "ReadsPerSampleHandler": [
        {
            "data": {
                "lane": 7,
                "number_of_samples": 12,
                "sample_id": "Sample_pq-27",
                "sample_reads": 6.893002,
                "threshold": 90
            },
            "message": "Number of reads for sample Sample_pq-27 was too low on lane 7, it was: 6.893 M",
            "type": "warning"
        },
        {
            "data": {
                "lane": 7,
                "number_of_samples": 12,
                "sample_id": "Sample_pq-28",
                "sample_reads": 7.10447,
                "threshold": 90
            },
            "message": "Number of reads for sample Sample_pq-28 was too low on lane 7, it was: 7.104 M",
            "type": "warning"
        }
    ],
    "exit_status": 0
}

[codecov[bot]]

Codecov Report

Merging #29 into master will decrease coverage by 2.81%. The diff coverage is 72.15%.

@@            Coverage Diff             @@
##           master      #29      +/-   ##
==========================================
- Coverage   93.38%   90.56%   -2.82%     
==========================================
  Files          16       17       +1     
  Lines         544      615      +71     
==========================================
+ Hits          508      557      +49     
- Misses         36       58      +22

Impacted Files	Coverage Δ
checkQC/app.py	89.13% <100%> (+0.75%)	:arrow_up:
checkQC/qc_engine.py	100% <100%> (ø)	:arrow_up:
checkQC/web_app.py	66.66% <66.66%> (ø)
checkQC/config.py	88.7% <72.72%> (-3.6%)	:arrow_down:

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 9cbd398...b331507. Read the comment docs.