run_from_cl.py

from lx.project import Project
from lx.spectraImport import getAMasterScan, doImport
from lx.mfql.runtimeExecution import TypeMFQL
from lx.mfql.mfqlParser import startParsing
import glob
import generateOptions

proy = r"test_res\test_res-project.lxp"
proy_xml = r"test_res\test_res-project_xml.lxp"
root_mfql_dir = r"test_res"
input_files_dir = r"test_res"


def getInputFiles(options):
    importDir = options["importDir"]
    extension = options["spectraFormat"]
    files = glob.glob(importDir + r"\*." + extension)
    return files


def direct(project_path):
    # lximport
    project = Project()
    project.load(project_path)
    project.testOptions()
    project.formatOptions()
    options_og = project.getOptions()
    options = generateOptions.fromFullOptions(options_og)
    # options = generateOptions.setOptions2likelyDefault(options)
    options = generateOptions.setOptions_fromImputPaths(input_files_dir, root_mfql_dir)

    # lxmain
    scan = doImport(  # note lpdxImportDEF_new is used when with gui
        spectraFormat=options["dataType"],
        scan=getAMasterScan(options),
        listFiles=getInputFiles(options),
        alignmentMS=options[
            "alignmentMethodMS"
        ],  # linear, hierarchical, heuristic o, only for mzXML
        alignmentMSMS=options["alignmentMethodMSMS"],
        scanAvg=options["scanAveragingMethod"],  # linear, heuristic
        importMSMS=options["importMSMS"],
    )  # Ii think oits always True?

    # lrRun
    mfqlFiles = generateOptions.getMfqlFiles(root_mfql_dir)

    # fronm lxmain startMFQL(options=options, queries=dictMFQL)
    mfqlObj = TypeMFQL(masterScan=scan)
    mfqlObj.options = options
    mfqlObj.outputSeperator = ","

    # parse input file k and save the result in mfqlObj.result
    startParsing(
        mfqlFiles,
        mfqlObj,
        isotopicCorrectionMS=options["isotopicCorrectionMS"],
        isotopicCorrectionMSMS=options["isotopicCorrectionMSMS"],
        complementSC=options["complementMasterScan"],
        generateStatistics=options["statistics"],
    )
    scan.dump(options_og["dumpMasterScanFile"])
    makeResultsFile(mfqlObj, options)  # this makes the -out files


def makeResultsFile(mfqlObj, options):
    result = mfqlObj.result
    # as in lxmain
    if result.mfqlOutput:
        strHead = ""
        if not options["noHead"]:
            for key in result.listHead:
                if key != result.listHead[-1]:
                    strHead += key + "%s" % mfqlObj.outputSeperator
                else:
                    strHead += key

            # generate whole string
            strResult = "%s\n" % strHead
        else:
            strResult = ""

        for k in result.dictQuery.values():
            strResult += "\n###,%s\n" % k.name
            strResult += k.strOutput
            strResult += "\n"

        # free 'k' because otherwise Python keeps all
        # the SurveyEntries. Don't ask me why...
        del k

        # put out
        f = open(options["resultFile"], "w")
        f.write(strResult)
        f.close()


if __name__ == "__main__":
    import timeit

    r = timeit.timeit("direct(proy)", setup="from __main__ import *", number=1)
    print(r)

    # Seconds from generate options
    # 9 options['timerange'] = (0.0, float("inf"))
    # 34  options['timerange'] = (0.0, float("inf")
    # 211 options['MSmassrange'] = (0.0, float("inf")); options['MSMSmassrange'] = (0.0, float("inf"))
    # print(r)
    # direct(proy)
    # direct(proy_xml)