Commit 74e9b7db authored by elmbeech@zoho.com's avatar elmbeech@zoho.com
Browse files

@ an2ome : smoketest bugfix

parent 95072cca

web/apptoomero/an2ome.py

+6 −4
Original line number Diff line number Diff line
@@ -431,7 +431,7 @@ def runjson2csv(): 
                    s_endpoint5concunit = ""

                    s_endpoint5timereact = None

                    s_endpoint5timeunit = ""

                    # handle primary secondary antibody link

                    # handle compound stains and primary secondary antibody link

                    d_endpoint2micchannel = {}

                    d_channel2gent = {}

                    for s_endpoint in list(d_json[s_spot]["content"]["endpoint"].keys()):
@@ -441,12 +441,14 @@ def runjson2csv(): 
                        s_anendpoint = "-".join(ls_annotid)

                        try:

                            i_channel = d_brickwall[s_anendpoint]["microscopy_channel"]

                            if ("-" in s_endpoint):

                                s_endpoint = s_endpoint.split("-")[1]

                            if not ("-" in s_endpoint):

                                d_endpoint2micchannel.update({s_endpoint : i_channel})  # compound stain

                            else:

                                s_endpoint = s_endpoint.split("-")[1]  # secondary antibody

                                d_endpoint2micchannel.update({s_endpoint : i_channel})

                                d_channel2gent.update({i_channel : s_endpoint})

                        except KeyError:

                            s_hostorganism = d_brickwall[s_anendpoint]["host_organism"]

                            s_hostorganism = d_brickwall[s_anendpoint]["host_organism"]  # primary antibody

                            d_channel2gent.update({s_hostorganism : s_endpoint})

                    for o_channel, s_gent in d_channel2gent.items():

                        if not (type(o_channel) is int):