Commit 94e99ca9 authored by bue's avatar bue 🐮

@ annotTutorial : smoketest evolution first runset in

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[{"model": "appacaxis.sampleset", "pk": "cl-AU565-p0x3cpml1250000h72", "fields": {"annot_id": "cl-au565-p0x3cpml1250000h72", "acjson_file_overwrite": false, "acjson_file": "upload/acaxis/acpipe_acjson-cl-AU565-p0x3cpml1250000h72_ac.json", "set_display": "['AU565_CVCL1074-ATCCOwn_CRL2351_notavailable']", "available": true, "responsible": "Elmar__Bucher", "brick": ["human-AU565_CVCL1074-ATCCOwn_CRL2351_notavailable"]}}, {"model": "appacaxis.sampleset", "pk": "cl-HCC1954-p0x3cpml1250000h72", "fields": {"annot_id": "cl-hcc1954-p0x3cpml1250000h72", "acjson_file_overwrite": false, "acjson_file": "upload/acaxis/acpipe_acjson-cl-HCC1954-p0x3cpml1250000h72_ac.json", "set_display": "['HCC1954_CVCL1259-ATCCOwn_CRL2338_notavailable']", "available": true, "responsible": "Elmar__Bucher", "brick": ["human-HCC1954_CVCL1259-ATCCOwn_CRL2338_notavailable"]}}, {"model": "appacaxis.sampleset", "pk": "cl-HMEC122L-p4xNcpml5000h72", "fields": {"annot_id": "cl-hmec122l-p4xncpml5000h72", "acjson_file_overwrite": false, "acjson_file": "upload/acaxis/acpipe_acjson-cl-HMEC122L-p4xNcpml5000h72_ac.json", "set_display": "['HMEC122L_Own-LBNLOwn_AI333_MarkLaBarge']", "available": true, "responsible": "Elmar__Bucher", "brick": ["human-HMEC122L_Own-LBNLOwn_AI333_MarkLaBarge"]}}, {"model": "appacaxis.sampleset", "pk": "cl-HMEC240L-p4xNcpml5000h72", "fields": {"annot_id": "cl-hmec240l-p4xncpml5000h72", "acjson_file_overwrite": false, "acjson_file": "upload/acaxis/acpipe_acjson-cl-HMEC240L-p4xNcpml5000h72_ac.json", "set_display": "['HMEC240L_Own-LBNLOwn_AI619_MarkLaBarge']", "available": true, "responsible": "Elmar__Bucher", "brick": ["human-HMEC240L_Own-LBNLOwn_AI619_MarkLaBarge"]}}, {"model": "appacaxis.sampleset", "pk": "cl-MCF10A-p0xNcpml5000h72", "fields": {"annot_id": "cl-mcf10a-p0xncpml5000h72", "acjson_file_overwrite": false, "acjson_file": "upload/acaxis/acpipe_acjson-cl-MCF10A-p0xNcpml5000h72_ac.json", "set_display": "['MCF10A_CVCL0598-ATCCOwn_CRL10317_ICBP43']", "available": true, "responsible": "Elmar__Bucher", "brick": ["human-MCF10A_CVCL0598-ATCCOwn_CRL10317_ICBP43"]}}, {"model": "appacaxis.sampleset", "pk": "cl-MCF10A-p5x14cpml5000h72", "fields": {"annot_id": "cl-mcf10a-p5x14cpml5000h72", "acjson_file_overwrite": false, "acjson_file": "upload/acaxis/acpipe_acjson-cl-MCF10A-p5x14cpml5000h72_ac.json", "set_display": "['MCF10A_CVCL0598-ATCCOwn_CRL10317_ICBP43']", "available": true, "responsible": "Elmar__Bucher", "brick": ["human-MCF10A_CVCL0598-ATCCOwn_CRL10317_ICBP43"]}}]
[{"model": "appacaxis.sampleset", "pk": "cl-AU565-p0x3cpml1250000h72", "fields": {"annot_id": "cl-au565-p0x3cpml1250000h72", "acjson_file_overwrite": false, "acjson_file": "upload/acaxis/acpipe_acjson-cl-AU565-p0x3cpml1250000h72_ac.json", "set_display": "['AU565_CVCL1074-ATCCOwn_CRL2351_notavailable']", "available": true, "responsible": "Elmar__Bucher", "brick": ["human-AU565_CVCL1074-ATCCOwn_CRL2351_notavailable"]}}, {"model": "appacaxis.sampleset", "pk": "cl-HCC1954-p0x3cpml1250000h72", "fields": {"annot_id": "cl-hcc1954-p0x3cpml1250000h72", "acjson_file_overwrite": false, "acjson_file": "upload/acaxis/acpipe_acjson-cl-HCC1954-p0x3cpml1250000h72_ac.json", "set_display": "['HCC1954_CVCL1259-ATCCOwn_CRL2338_notavailable']", "available": true, "responsible": "Elmar__Bucher", "brick": ["human-HCC1954_CVCL1259-ATCCOwn_CRL2338_notavailable"]}}, {"model": "appacaxis.sampleset", "pk": "cl-HMEC122L-p4xNcpml5000h72", "fields": {"annot_id": "cl-hmec122l-p4xncpml5000h72", "acjson_file_overwrite": false, "acjson_file": "upload/acaxis/acpipe_acjson-cl-HMEC122L-p4xNcpml5000h72_ac.json", "set_display": "['HMEC122L_Own-LBNLOwn_AI333_MarkLaBarge']", "available": true, "responsible": "Elmar__Bucher", "brick": ["human-HMEC122L_Own-LBNLOwn_AI333_MarkLaBarge"]}}, {"model": "appacaxis.sampleset", "pk": "cl-HMEC240L-p4xNcpml5000h72", "fields": {"annot_id": "cl-hmec240l-p4xncpml5000h72", "acjson_file_overwrite": false, "acjson_file": "upload/acaxis/acpipe_acjson-cl-HMEC240L-p4xNcpml5000h72_ac.json", "set_display": "['HMEC240L_Own-LBNLOwn_AI619_MarkLaBarge']", "available": true, "responsible": "Elmar__Bucher", "brick": ["human-HMEC240L_Own-LBNLOwn_AI619_MarkLaBarge"]}}, {"model": "appacaxis.sampleset", "pk": "cl-MCF10A-p0xNcpml5000h72", "fields": {"annot_id": "cl-mcf10a-p0xncpml5000h72", "acjson_file_overwrite": false, "acjson_file": "upload/acaxis/acpipe_acjson-cl-MCF10A-p0xNcpml5000h72_ac.json", "set_display": "['MCF10A_CVCL0598-ATCCOwn_CRL10317_ICBP43']", "available": true, "responsible": "Elmar__Bucher", "brick": ["human-MCF10A_CVCL0598-ATCCOwn_CRL10317_ICBP43"]}}, {"model": "appacaxis.sampleset", "pk": "cl-MCF10A-p5x14cpml5000h72", "fields": {"annot_id": "cl-mcf10a-p5x14cpml5000h72", "acjson_file_overwrite": false, "acjson_file": "upload/acaxis/acpipe_acjson-cl-MCF10A-p5x14cpml5000h72_ac.json", "set_display": "['MCF10A_CVCL0598-ATCCOwn_CRL10317_ICBP43']", "available": true, "responsible": "Elmar__Bucher", "brick": ["human-MCF10A_CVCL0598-ATCCOwn_CRL10317_ICBP43"]}}]
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[{"model": "app3runset.runset", "pk": "mema-LI8C00201", "fields": {"annot_id": "mema-li8c00201", "acjson_file_overwrite": false, "acjson_file": "upload/runset/acpipe_acjson-mema-LI8C00201_ac.json", "endpointsetset_display": "[]", "perturbationsetset_display": "[]", "samplesetset_display": "[]", "supersetset_display": "[]", "study_display": "['hcc1954lapatinibss100']", "notes": "", "endpointsetset": [], "perturbationsetset": [], "samplesetset": [], "supersetset": [], "study": ["hcc1954lapatinibss100"]}}]
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[{"model": "app1study.study", "pk": "hcc1954lapatinibss100", "fields": {"study_name": "hcc1954_lapatinib_ss100", "date_submission": "1955-11-05", "url_experimentaldesigne": "https://not.yet.specified", "url_conclusion": "https://not.yet.specified", "investigation_display": "[]", "responsible_display": "[]", "notes": "", "investigation": [], "responsible": ["Jim__Korkola", "Spencer__Watson"]}}]
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[{"model": "app4superset.superset", "pk": "es8v005", "fields": {"annot_id": "es8v005", "notes": "", "acjson_file_overwrite": false, "acjson_file": "upload/superset/acpipe_aushon-es8v005_ac.json", "acpipemodule_display": "['acpipeaushon']", "endpointsetset_display": "", "perturbationsetset_display": "['es-1layout2v3', 'es-2layout2v3', 'es-3layout2v3']", "samplesetset_display": "[]", "supersetset_display": "[]", "supersetfile_display": "['gal20151215li8x005gal']", "responsible": "Elmar__Bucher", "acpipemodule": ["acpipe_aushon"], "endpointsetset": [], "perturbationsetset": ["es-1layout2v3", "es-2layout2v3", "es-3layout2v3"], "samplesetset": [], "supersetset": [], "supersetfile": ["gal20151215li8x005gal"]}}, {"model": "app4superset.superset", "pk": "es8v006", "fields": {"annot_id": "es8v006", "notes": "", "acjson_file_overwrite": false, "acjson_file": "upload/superset/acpipe_aushon-es8v006_ac.json", "acpipemodule_display": "['acpipeaushon']", "endpointsetset_display": "", "perturbationsetset_display": "['es-1layout2v3', 'es-2layout2v4', 'es-3layout2v4', 'es-4layout1v1']", "samplesetset_display": "[]", "supersetset_display": "[]", "supersetfile_display": "['gal20160419li8x006gal']", "responsible": "Elmar__Bucher", "acpipemodule": ["acpipe_aushon"], "endpointsetset": [], "perturbationsetset": ["es-1layout2v3", "es-2layout2v4", "es-3layout2v4", "es-4layout1v1"], "samplesetset": [], "supersetset": [], "supersetfile": ["gal20160419li8x006gal"]}}, {"model": "app4superset.superset", "pk": "es8v008", "fields": {"annot_id": "es8v008", "notes": "", "acjson_file_overwrite": false, "acjson_file": "upload/superset/acpipe_aushon-es8v008_ac.json", "acpipemodule_display": "['acpipeaushon']", "endpointsetset_display": "", "perturbationsetset_display": "['es-1layout3v6', 'es-2layout3v6', 'es-3layout2v6']", "samplesetset_display": "[]", "supersetset_display": "[]", "supersetfile_display": "['gal20161219li8x008gal']", "responsible": "Elmar__Bucher", "acpipemodule": ["acpipe_aushon"], "endpointsetset": [], "perturbationsetset": ["es-1layout3v6", "es-2layout3v6", "es-3layout2v6"], "samplesetset": [], "supersetset": [], "supersetfile": ["gal20161219li8x008gal"]}}]
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[{"model": "app4superset.superset", "pk": "es8C002", "fields": {"annot_id": "es8c002", "notes": "", "acjson_file_overwrite": false, "acjson_file": "upload/superset/acpipe_aushon-es8C002_ac.json", "acpipemodule_display": "['acpipeaushon']", "endpointsetset_display": "", "perturbationsetset_display": "['es-1layout2v3', 'es-2layout2v3', 'es-3layout2v3', 'escol-1v2']", "samplesetset_display": "[]", "supersetset_display": "[]", "supersetfile_display": "['gal20151215li8x005gal']", "responsible": "Elmar__Bucher", "acpipemodule": ["acpipe_aushon"], "endpointsetset": [], "perturbationsetset": ["es-1layout2v3", "es-2layout2v3", "es-3layout2v3", "esCol-1v2"], "samplesetset": [], "supersetset": [], "supersetfile": ["gal20151215li8x005gal"]}}, {"model": "app4superset.superset", "pk": "es8X005", "fields": {"annot_id": "es8x005", "notes": "", "acjson_file_overwrite": false, "acjson_file": "upload/superset/acpipe_aushon-es8X005_ac.json", "acpipemodule_display": "['acpipeaushon']", "endpointsetset_display": "", "perturbationsetset_display": "['es-1layout2v3', 'es-2layout2v3', 'es-3layout2v3', 'escol-1v2']", "samplesetset_display": "[]", "supersetset_display": "[]", "supersetfile_display": "['gal20151215li8x005gal']", "responsible": "Elmar__Bucher", "acpipemodule": ["acpipe_aushon"], "endpointsetset": [], "perturbationsetset": ["es-1layout2v3", "es-2layout2v3", "es-3layout2v3", "esCol-1v2"], "samplesetset": [], "supersetset": [], "supersetfile": ["gal20151215li8x005gal"]}}, {"model": "app4superset.superset", "pk": "es8X006", "fields": {"annot_id": "es8x006", "notes": "", "acjson_file_overwrite": false, "acjson_file": "upload/superset/acpipe_aushon-es8X006_ac.json", "acpipemodule_display": "['acpipeaushon']", "endpointsetset_display": "", "perturbationsetset_display": "['es-1layout2v3', 'es-2layout2v4', 'es-3layout2v4', 'es-4layout1v1', 'escol-1v2']", "samplesetset_display": "[]", "supersetset_display": "[]", "supersetfile_display": "['gal20160419li8x006gal']", "responsible": "Elmar__Bucher", "acpipemodule": ["acpipe_aushon"], "endpointsetset": [], "perturbationsetset": ["es-1layout2v3", "es-2layout2v4", "es-3layout2v4", "es-4layout1v1", "esCol-1v2"], "samplesetset": [], "supersetset": [], "supersetfile": ["gal20160419li8x006gal"]}}, {"model": "app4superset.superset", "pk": "es8X008", "fields": {"annot_id": "es8x008", "notes": "", "acjson_file_overwrite": false, "acjson_file": "upload/superset/acpipe_aushon-es8X008_ac.json", "acpipemodule_display": "['acpipeaushon']", "endpointsetset_display": "", "perturbationsetset_display": "['es-1layout3v6', 'es-2layout3v6', 'es-3layout2v6', 'escol-1v2']", "samplesetset_display": "[]", "supersetset_display": "[]", "supersetfile_display": "['gal20161219li8x008gal']", "responsible": "Elmar__Bucher", "acpipemodule": ["acpipe_aushon"], "endpointsetset": [], "perturbationsetset": ["es-1layout3v6", "es-2layout3v6", "es-3layout2v6", "esCol-1v2"], "samplesetset": [], "supersetset": [], "supersetfile": ["gal20161219li8x008gal"]}}]
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[{"model": "app4superset.supersetfile", "pk": "gal20151215li8x005gal", "fields": {"superset_file_overwrite": false, "superset_file": "upload/supersetfile/gal20151215LI8X005.gal", "code": "acgal.well8x35x20(\r\n s_runid = \"es8v005\",\r\n s_gal_txt = \"./gal20151215LI8X005.gal\",\r\n ld_sourceplate_acjson = [\r\n d_es1layout2v3,\r\n d_es2layout2v3,\r\n d_es3layout2v3,\r\n ],\r\n s_opath=\"./\",\r\n)"}}, {"model": "app4superset.supersetfile", "pk": "gal20160419li8x006gal", "fields": {"superset_file_overwrite": false, "superset_file": "upload/supersetfile/gal20160419LI8X006.gal", "code": "acgal.well8x35x20(\r\n s_runid = \"es8v006\",\r\n s_gal_txt = \"./gal20160419LI8X006.gal\",\r\n ld_sourceplate_acjson = [\r\n d_es1layout2v3,\r\n d_es2layout2v4,\r\n d_es3layout2v4,\r\n d_es4layout1v1,\r\n ],\r\n s_opath=\"./\",\r\n)"}}, {"model": "app4superset.supersetfile", "pk": "gal20161219li8x008gal", "fields": {"superset_file_overwrite": false, "superset_file": "upload/supersetfile/gal20161219LI8X008.gal", "code": "acgal.well8x35x20(\r\n s_runid = \"es8v008\",\r\n s_gal_txt = \"./gal20161219LI8X008.gal\",\r\n ld_sourceplate_acjson = [\r\n d_es1layout3v6,\r\n d_es2layout3v6,\r\n d_es3layout2v6,\r\n ],\r\n s_opath=\"./\",\r\n)"}}]
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[{"model": "app4superset.supersetfile", "pk": "gal20151215li8x005gal", "fields": {"superset_file_overwrite": false, "superset_file": "upload/supersetfile/gal20151215LI8X005.gal", "code": "acgal.well8x35x20(\r\n s_runid = \"es8X005\",\r\n s_gal_txt = \"./gal20151215LI8X005.gal\",\r\n ld_sourceplate_acjson = [\r\n d_es1layout2v3,\r\n d_es2layout2v3,\r\n d_es3layout2v3,\r\n ],\r\n s_opath=None,\r\n)"}}, {"model": "app4superset.supersetfile", "pk": "gal20160419li8x006gal", "fields": {"superset_file_overwrite": false, "superset_file": "upload/supersetfile/gal20160419LI8X006.gal", "code": "acgal.well8x35x20(\r\n s_runid = \"es8X006\",\r\n s_gal_txt = \"./gal20160419LI8X006.gal\",\r\n ld_sourceplate_acjson = [\r\n d_es1layout2v3,\r\n d_es2layout2v4,\r\n d_es3layout2v4,\r\n d_es4layout1v1,\r\n ],\r\n s_opath=None,\r\n)"}}, {"model": "app4superset.supersetfile", "pk": "gal20161219li8x008gal", "fields": {"superset_file_overwrite": false, "superset_file": "upload/supersetfile/gal20161219LI8X008.gal", "code": "acgal.well8x35x20(\r\n s_runid = \"es8X008\",\r\n s_gal_txt = \"./gal20161219LI8X008.gal\",\r\n ld_sourceplate_acjson = [\r\n d_es1layout3v6,\r\n d_es2layout3v6,\r\n d_es3layout2v6,\r\n ],\r\n s_opath=None,\r\n)"}}]
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[{"model": "app2track.memaassaytracking", "pk": "mema-li8c00201Day20160404", "fields": {"runset": "mema-LI8C00201", "plate_batch_id": "LI8C00201", "sample_addition_protocol": "Mema_step4-Cell_Plating_And_Treatment-v4", "sample_addition_dday": "2016-04-04", "sample_addition_operator": "Spencer__Watson", "drug_addition_day": "2016-04-05", "drug_addition_operator": "Spencer__Watson", "stain_addition_protocol": "Mema_step6-Cell_Fixing_And_Staining-v4", "fixing_day": "2016-04-08", "fixing_operator": "Spencer__Watson", "stain_addition_day": "2016-04-08", "stain_addition_operator": "Spencer__Watson", "image_acquisition_protocol": "Mema_step7-7_Image_Acquisition-v2", "image_acquisition_day": "2016-04-09", "image_acquisition_operator": "Spencer__Watson"}}]
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[{"model": "app2track.memasupersettracking", "pk": "es8v005Day20151216", "fields": {"superset": "es8v005", "protocol": "Mema_step2-Plate_Preparation-v3", "dday": "2015-12-16", "responsible": "Rebecca_and_Wally"}}, {"model": "app2track.memasupersettracking", "pk": "es8v006Day20160420", "fields": {"superset": "es8v006", "protocol": "Mema_step2-Plate_Preparation-v3", "dday": "2016-04-20", "responsible": "Wally__Thompson"}}, {"model": "app2track.memasupersettracking", "pk": "es8v008Day20161219", "fields": {"superset": "es8v008", "protocol": "Mema_step2-Plate_Preparation-v3", "dday": "2016-12-19", "responsible": "Rebecca_and_Wally"}}]
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[{"model": "app2track.memasupersettracking", "pk": "es8c002Day20160215", "fields": {"superset": "es8C002", "protocol": "Mema_step2-Plate_Preparation-v3", "dday": "2016-02-15", "responsible": "Rebecca_and_Wally"}}, {"model": "app2track.memasupersettracking", "pk": "es8X005Day20151216", "fields": {"superset": "es8X005", "protocol": "Mema_step2-Plate_Preparation-v3", "dday": "2015-12-16", "responsible": "Rebecca_and_Wally"}}, {"model": "app2track.memasupersettracking", "pk": "es8X006Day20160420", "fields": {"superset": "es8X006", "protocol": "Mema_step2-Plate_Preparation-v3", "dday": "2016-04-20", "responsible": "Wally__Thompson"}}, {"model": "app2track.memasupersettracking", "pk": "es8X008Day20161219", "fields": {"superset": "es8X008", "protocol": "Mema_step2-Plate_Preparation-v3", "dday": "2016-12-19", "responsible": "Rebecca_and_Wally"}}]
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###
# title: acpipeTemplateCode_mema-LI8C00201.py
#
# date: 2018-03-29
# license: GPL>=3
# author: bue
#
# description:
# acpipe script to generate a runset related acjson file.
# template automatically generated by annot softawre.
# check out: https://gitlab.com/biotransistor/annot
###
# python library
import json
# acpipe library
# check out: https://gitlab.com/biotransistor/acpipe_acjson
#import acpipe_acjson.acjson as ac
import acpipe_acjsonDev.acpipe_acjson.acjson as ac
# load samplesetsets
with open('../../experiment_acjson/acaxis/acpipe_acjson-cl-HCC1954-p0x3cpml1250000h72_ac.json') as f_json:
d_clhcc1954p0x3cpml1250000h72 = json.load(f_json)
# load perturbationsetsets
with open('../../experiment_acjson/acaxis/acpipe_acjson-ds-Lapatinib1v1_ac.json') as f_json:
d_dslapatinib1v1 = json.load(f_json)
with open('../../experiment_acjson/acaxis/acpipe_acjson-ls-1layout1v3_ac.json') as f_json:
d_ls1layout1v3 = json.load(f_json)
# load endpointsetsets
with open('../../experiment_acjson/acaxis/acpipe_acjson-ss-100v1_ac.json') as f_json:
d_ss100v1 = json.load(f_json)
# load supersetset
with open('../../experiment_acjson/superset/acpipe_aushon-es8C002_ac.json') as f_json:
d_es8c002 = json.load(f_json)
# fuse acaxis acjson files
# acfuseobject (0011)
d_memali8c00201 = ac.acfuseobject(
s_runid='mema-LI8C00201',
d_acjsonsample=d_clhcc1954p0x3cpml1250000h72,
d_acjsonperturbation=d_es8c002,
d_acjsonendpoint=d_ss100v1,
s_runtype='acpipe_acjson',
)
# acfuserepeat0011
ac.acfuserepeat0011(
d_acjsonmajor=d_memali8c00201,
d_acjsonminor=d_ls1layout1v3,
s_ambiguous='break',
b_deepcopy=False,
)
ac.acfuserepeat0011(
d_acjsonmajor=d_memali8c00201,
d_acjsonminor=d_dslapatinib1v1,
s_ambiguous='break',
b_deepcopy=False,
)
# update log
d_memali8c00201["log"] = "{} + {} + {} + {} + {}".format(
d_clhcc1954p0x3cpml1250000h72['acid'],
d_es8c002['acid'],
d_ls1layout1v3['acid'],
d_dslapatinib1v1['acid'],
d_ss100v1['acid'],
)
# write to json file
with open(d_memali8c00201['acid'], 'w') as f_acjson:
json.dump(d_memali8c00201, f_acjson, sort_keys=True)
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