#!/opt/conda/conda-bld/influx_si_1614334837027/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/python
"""Parse _res.kvh file from stdin or from first parameter
and write the measurment section of ftbl file in file(s) suffixed with '_simN.ftbl'
Where N is an integer corresponding to parallel experiment number.
In case of instationary labeling, label kinetics are written in file(s)
suffixed with '_cinlabN.txt'
usage: res2ftbl_meas.py [network_res[.kvh]] # produce network_simN.ftbl where N is parallel experiment number.

"""
if __name__ == "__main__" or __name__ == "influx_si.cli":
    import sys, os, getopt
    import re
    import datetime as dt
    
    import influx_si
    import tools_ssg
    import kvh
    #import pprint # for debuging only
    def usage():
        print(__doc__)
    me="res2ftbl_meas"
    secdef={
        "m": """MASS_SPECTROMETRY
	META_NAME	FRAGMENT	WEIGHT	VALUE	DEVIATION""",
        "p": """PEAK_MEASUREMENTS
	META_NAME	PEAK_NO	VALUE_S	VALUE_D-	VALUE_D+	VALUE_DD	VALUE_T	DEVIATION_S	DEVIATION_D-	DEVIATION_D+	DEVIATION_DD/T""",
        "l": """LABEL_MEASUREMENTS
	META_NAME	CUM_GROUP	VALUE	DEVIATION	CUM_CONSTRAINTS""",
    }
    pfield="META_NAME	PEAK_NO	VALUE_S	VALUE_D-	VALUE_D+	VALUE_DD	VALUE_T	DEVIATION_S	DEVIATION_D-	DEVIATION_D+	DEVIATION_DD/T".split("\t")
    sdfield={
        "S": "DEVIATION_S",
        "D-": "DEVIATION_D-",
        "D+": "DEVIATION_D+",
        "DD": "DEVIATION_DD/T",
        "T": "DEVIATION_DD/T",
    }
    try:
        opts,args=getopt.getopt(sys.argv[1:], "h", ["help", "DEBUG"])
    except getopt.GetoptError as err:
        print(str(err))
        usage()
        sys.exit(1)
    DEBUG=False
    for o,a in opts:
        if o in ("-h", "--help"):
            usage()
            sys.exit(0)
        elif o=="--DEBUG":
            DEBUG=True
        else:
            assert False, "unhandled option"
    fkvh=args[0] if len(args) else ""
    if fkvh and fkvh[-4:] != ".kvh":
        fkvh+=".kvh"
    if fkvh and not os.path.exists(fkvh):
        sys.stderr.write(me+": file '"+fkvh+"' does not exist.\n")
        sys.exit(1)
    fkvh=open(fkvh, "r") if fkvh else sys.stdin

    d=kvh.kvh2tlist(fkvh, strip=True) # all kvh data
    #pprint.pprint(d)
    ivers=[int(v) if re.match("^\d+$", v) else -1 for v in d[0][1][0][1].split(".")]
    if ivers[0] < 4:
        raise Exception("This software is designed to work with kvh files produced by influx_si v4.0 and higher. Found version '%s'."%d[0][1][0][1]) 
    case_i=d[0][1][1] == ("labeling", "instationary")
    
    # base of output names
    bout=fkvh.name[:-8] if fkvh.name[-4:] == ".kvh" else "stdin"
    
    # get all measurement SD
    sdev=[]
    try:
        sdev=[ v for (k,v) in d if k == "measurement SD" ].pop()
    except:
        pass
    if not sdev:
        raise Exception("No section 'measurement SD' in '%s'"%fkvh.name)
    sdev=dict((k,v) for (k,v) in sdev)
    # get all simulated measurements
    meas=[]
    try:
        meas=[ v for (k,v) in d if k == "simulated measurements" ].pop()
    except:
        pass
    if not meas:
        raise Exception("No section 'simulated measurements' in '%s'"%fkvh.name)
    meas=dict((k,v) for (k,v) in meas)
    
    
    f_ftbl=open("%s_sim1.ftbl"%bout, "w")
    # flux measurements
    if "measured fluxes" in meas:
        f_ftbl.write("""FLUX_MEASUREMENTS
	FLUX_NAME	VALUE	DEVIATION\n""")
        for (i, (k,v)) in enumerate(meas["measured fluxes"]):
            f_ftbl.write("\t%s\t%s\t%s\n"%(k[4:], v, sdev["flux"][i][1]))
    # pool measurements
    if "measured pools" in meas:
        f_ftbl.write("""METAB_MEASUREMENTS
	META_NAME	VALUE	DEVIATION\n""")
        for (i,(k,v)) in enumerate(meas["measured pools"]):
            f_ftbl.write("\t%s\t%s\t%s\n"%(k[3:], v, sdev["pool"][i][1]))
    f_ftbl.close()
    # labeled measurements (for parallel experiments)
    mlab=meas.get("labeled data", meas.get("labeled data (scaled)"))
    if not mlab:
        sys.exit(0)
    nb_exp=len(mlab)
    for iexp in range(nb_exp):
        if not mlab[iexp]:
            continue
        f_ftbl=open("%s_sim%d.ftbl"%(bout, iexp+1), "w" if iexp else "a")
        meas=mlab[iexp][1]
        if case_i:
            # write all kinetic data
            f=open("%s_cinlab%d.txt"%(bout, iexp+1), "w")
            f.write("# simulated measurement from %s\n"%mlab[iexp][0])
            f.write("# generated by %s at %s\n"%(me, dt.datetime.strftime(dt.datetime.now(), "%Y-%m-%d %H:%M:%S")))
            f.write("%s\t%s\n"%meas[0])
            for (nm,row) in meas[1:]:
                f.write("%s\t%s\n"%(nm, row)) # skip iexp number in rowid
            f.close()
            meas=[(k,v.split("\t")[0]) for (k,v) in meas[1:]] # skip first row with row_col
        mtype=""
        dpeak={}
        for (i,m) in enumerate(meas):
            sd=sdev["labeled"][iexp][1][i][1]
            # split id
            sid=m[0].split(":")
            if mtype != sid[0]:
                # new measurement type starts here
                mtype=sid[0]
                f_ftbl.write(secdef[mtype]+"\n")
                oldmetab=""
                oldfrag=""
                oldweight=-1
                oldrid=""
                oldc_no=0
                # flush previous peak dict
                if dpeak:
                    f_ftbl.write("\t".join([""] + [dpeak.get(f, "") for f in pfield])+"\n")
                    dpeak={}
            if mtype=="m":
                ## mass measurement
                metab, frag, weight, rid = sid[1:]
                if metab != oldmetab or frag != oldfrag or int(weight) <= oldweight:
                    # new metab starts here
                    oldmetab, oldfrag, oldweight = (metab, frag, int(weight))
                    f_ftbl.write("\t%s\t%s\t%d\t%s\t%s\n"%(metab, frag, int(weight), m[1], sd))
                else:
                    f_ftbl.write("\t%s\t%s\t%d\t%s\t%s\n"%("", "", int(weight), m[1], sd))
            elif mtype=="p":
                ## peak measurement
                metab, c_no, ptype, rid = sid[2:]
                val=m[1]
                if oldmetab != metab:
                    ## new metab starts here
                    oldmetab=metab
                    oldrid=""
                    # flush previous dict
                    if dpeak:
                        f_ftbl.write("\t".join([""] + [dpeak.get(f, "") for f in pfield])+"\n")
                        dpeak={}
                    dpeak["META_NAME"]=metab
                if oldrid != rid:
                    # new peak for a given metab starts here
                    oldrid=rid
                    # flush previous dict
                    if "PEAK_NO" in dpeak:
                        f_ftbl.write("\t".join([""] + [dpeak.get(f, "") for f in pfield])+"\n")
                        dpeak={}
                    dpeak["PEAK_NO"]=c_no
                dpeak["VALUE_"+ptype]=val
                dpeak[sdfield[ptype]]=sd
            elif mtype=="l":
                ## label measurements
                metab, constr, rid = sid[1:]
                if metab != oldmetab:
                    # new metab starts here
                    oldmetab=metab
                    f_ftbl.write("\t%s\t1\t%s\t%s\t%s\n"%(metab, m[1], sd, constr))
                else:
                    f_ftbl.write("\t%s\t1\t%s\t%s\t%s\n"%("", m[1], sd, constr))
        # flush last peak dict
        if dpeak:
            f_ftbl.write("\t".join([""] + [dpeak.get(f, "") for f in pfield])+"\n")
            dpeak={}
        f_ftbl.close()
    sys.exit(0)
