def _do_syn_extract(self, spec, script, post_script):
        self.debug('Executing SynExtraction mode="{}"'.format(spec.mode))

        #modify the persister. the original persister for the automated run is saved at self.persister
        #arun.persister reset to original when syn extraction stops
        identifier=spec.identifier
        last_aq=self.arun.persister.get_last_aliquot(identifier)
        if last_aq is None:
            self.warning('invalid identifier "{}". Does not exist in database'.format(identifier))

        else:
            runid=make_runid(identifier, last_aq+1)
            self.arun.info('Starting SynExtraction run {}'.format(runid))
            self.arun.persister.trait_set(use_secondary_database=False,
                                          runid=runid,
                                          uuid=str(uuid.uuid4()))

            if self.arun.do_measurement(script=script, use_post_on_fail=False):
                if post_script:
                    self.debug('starting post measurement')
                    if not self.arun.do_post_measurement(script=post_script):
                        return

                self.debug('delay between syn extractions {}'.format(spec.delay_between))
                self.arun.wait(spec.delay_between)

                return True

    def _sync_meas_analysis_attributes(self, meas_analysis):
        # copy meas_analysis attrs
        nocast = lambda x: x

        attrs = [
            ('labnumber', 'labnumber', lambda x: x.identifier),
            ('aliquot', 'aliquot', int),
            ('step', 'step', str),
            #                  ('status', 'status', int),
            ('comment', 'comment', str),
            ('uuid', 'uuid', str),
            ('rundate', 'analysis_timestamp', nocast),
            ('timestamp', 'analysis_timestamp',
             lambda x: time.mktime(x.timetuple())
            ),
        ]
        for key, attr, cast in attrs:
            v = getattr(meas_analysis, attr)
            setattr(self, key, cast(v))

        self.record_id = make_runid(self.labnumber, self.aliquot, self.step)

        tag = meas_analysis.tag
        if tag:
            tag = meas_analysis.tag_item
            self.set_tag(tag)

    def _modify_secondary(self, ans, new_ans):
        self.info('modifying analyses in secondary db. dry={}'.format(self.dry))
        db = self.secondary_db
        if not db.connect():
            self.debug('Not connected to secondary db')
            return

        with db.session_ctx(commit=not self.dry):
            for ai, ni in zip(ans, new_ans):
                rid = ai.record_id
                dban = db.get_analysis_rid(rid)
                if dban:
                    ident = ni.identifier
                    dbirradpos = db.get_irradiation_position(ident)
                    if dbirradpos:
                        dban.RID = make_runid(ident, ni.aliquot, ni.step)
                        self.debug('setting {} to {}'.format(ident, dban.RID))
                        dban.Aliquot = '{:02d}'.format(int(ni.aliquot))
                        dban.Increment = ni.step
                        dban.Aliquot_pychron = ni.aliquot

                        dban.IrradPosition = ident
                        dban.RedundantSampleID = dbirradpos.SampleID
                    else:
                        self.unique_warning('Labnumber {} does not exist in Secondary DB'.format(ident))
                else:
                    self.warning('Analysis {} does not exist in Secondary DB'.format(rid))

    def __init__(self, dbrecord):
        self.uuid = dbrecord.uuid
        ln = dbrecord.labnumber
        labnumber = str(ln.identifier)
        aliquot = dbrecord.aliquot
        step = dbrecord.step
        self.record_id = make_runid(labnumber, aliquot, step)

        self.rundate = dbrecord.analysis_timestamp
        self.timestamp = time.mktime(self.rundate.timetuple())
        self.tag = dbrecord.tag or ''
        self.is_plateau_step = False

        meas = dbrecord.measurement
        if meas is not None:
            if meas.analysis_type:
                self.analysis_type = meas.analysis_type.name
            if meas.mass_spectrometer:
                self.mass_spectrometer = meas.mass_spectrometer.name

        sam = ln.sample
        if sam:
            self.sample = sam.name
            if sam.project:
                self.project = sam.project.name.lower()

    def _make(self, ep):
        project = "Minna Bluff"
        db = self.db
        with db.session_ctx():
            prj = db.get_project(project)
            Ar40, Ar39, Ar38, Ar37, Ar36 = [], [], [], [], []
            for dev in (("Eurotherm", "Furnace"), ("CO2")):
                for si in prj.samples:
                    for li in si.labnumbers:
                        self.debug("blanks for {},{}".format(si.name, li.identifier))
                        for ai in li.analyses:
                            if ai.extraction.extraction_device.name in dev:
                                bs = self._extract_blanks(ai)
                                if bs is not None:
                                    r = make_runid(li.identifier, ai.aliquot, ai.step)
                                    # self.debug('blanks for {} {}'.format(r,bs))
                                    Ar40.append(bs[0])
                                    Ar39.append(bs[1])
                                    Ar38.append(bs[2])
                                    Ar37.append(bs[3])
                                    Ar36.append(bs[4])

                reg = WeightedMeanRegressor()
                print "blanks for {}".format(dev)
                for iso in (Ar40, Ar39, Ar38, Ar37, Ar36):
                    ys, es = zip(*iso)

                    reg.trait_set(ys=ys, yserr=es)
                    print reg.predict()

    def _make_labnumber(self, li, root, options, prog):
        #make dir for labnumber
        ident = li.identifier
        ln_root = os.path.join(root, ident)
        r_mkdir(ln_root)

        prog.change_message('Making {} for {}'.format(self._tag, ident))

        #filter invalid analyses
        ans=filter(lambda x: not x.tag=='invalid', li.analyses)

        #group by stepheat vs fusion
        pred = lambda x: bool(x.step)

        ans = sorted(ans, key=pred)
        stepheat, fusion = map(list, partition(ans, pred))

        apred = lambda x: x.aliquot
        stepheat = sorted(stepheat, key=apred)
        project='Minna Bluff'

        li = li.identifier
        if stepheat:
            key=lambda x: x.aliquot
            stepheat=sorted(stepheat, key=key)
            for aliquot, ais in groupby(stepheat, key=key):
                name=make_runid(li, aliquot, '')
                self._make_editor(ais, 'step_heat', options, prog, False,
                                  (ln_root, name, name, project, (li,)))
        if fusion:
            self._make_editor(fusion, 'fusion', options, prog, False,
                              (ln_root, li, li, project, (li,)))

    def create(self, dbrecord, fast_load=False):
        # print 'asdfsadfsdaf', dbrecord, dbrecord.labnumber, dbrecord.uuid
        try:
            if dbrecord is None or not dbrecord.labnumber:
                return

            ln = dbrecord.labnumber

            self.labnumber = str(ln.identifier)
            self.identifier = self.labnumber

            self.aliquot = dbrecord.aliquot
            self.step = dbrecord.step
            self.record_id = make_runid(self.labnumber, self.aliquot, self.step)

            self.uuid = dbrecord.uuid
            self.tag = dbrecord.tag or ''
            self.rundate = dbrecord.analysis_timestamp

            sam = ln.sample
            if sam:
                self.sample = sam.name
                if sam.project:
                    if isinstance(sam.project, (str, unicode)):
                        self.project = sam.project.lower()
                    else:
                        self.project = sam.project.name.lower()

            irp = ln.irradiation_position
            if irp is not None:
                irl = irp.level
                ir = irl.irradiation
                self.irradiation_info = '{}{} {}'.format(ir.name, irl.name, irp.position)

            try:
                self.mass_spectrometer = dbrecord.mass_spectrometer
            except AttributeError:
                pass

            meas = dbrecord.measurement
            if meas:
                self.mass_spectrometer = meas.mass_spectrometer.name.lower()
                try:
                    self.analysis_type = meas.analysis_type.name
                except AttributeError, e:
                    pass
                    # print 'IsotopeRecord create meas 1 {}'.format(e)

            ext = dbrecord.extraction
            if ext:
                self.extract_value = ext.extract_value
                self.cleanup = ext.cleanup_duration
                self.duration = ext.extract_duration

                try:
                    if ext.extraction_device:
                        self.extract_device = ext.extraction_device.name
                except AttributeError, e:
                    pass

    def create(self, dbrecord):
    #        print 'asdfsadfsdaf', dbrecord, dbrecord.labnumber, dbrecord.uuid
        try:
            if dbrecord is None or not dbrecord.labnumber:
                return

            ln = dbrecord.labnumber

            self.labnumber = str(ln.identifier)
            self.identifier = self.labnumber

            self.aliquot = dbrecord.aliquot
            self.step = dbrecord.step
            self.uuid = dbrecord.uuid
            self.tag = dbrecord.tag or ''
            self.rundate = dbrecord.analysis_timestamp
            self.timestamp = time.mktime(self.rundate.timetuple())

            self.record_id = make_runid(self.labnumber, self.aliquot, self.step)
            #            print self.record_id, self.uuid

            if ln.sample:
                self.sample = ln.sample.name
            if dbrecord.labnumber.sample:
                self.sample = dbrecord.labnumber.sample.name

            irp = ln.irradiation_position
            if irp is not None:
                irl = irp.level
                ir = irl.irradiation
                self.irradiation_info = '{}{} {}'.format(ir.name, irl.name, irp.position)

            else:
                self.irradiation_info = ''

            meas = dbrecord.measurement
            if meas is not None:
                self.mass_spectrometer = meas.mass_spectrometer.name.lower()
                if meas.analysis_type:
                    self.analysis_type = meas.analysis_type.name
            ext = dbrecord.extraction
            if ext:
                if ext.extraction_device:
                    self.extract_device = ext.extraction_device.name

            self.flux_fit_status = self._get_flux_fit_status(dbrecord)
            self.blank_fit_status = self._get_selected_history_item(dbrecord, 'selected_blanks_id')
            self.ic_fit_status = self._get_selected_history_item(dbrecord, 'selected_det_intercal_id')
            self.iso_fit_status = self._get_selected_history_item(dbrecord, 'selected_fits_id')

            return True
        except Exception, e:
            import traceback

            traceback.print_exc()
            print e

    def make_summary(self):
        s = 'Pr'
        f = self.fit
        if f:
            if not f in INTERPOLATE_TYPES:
                f = f[:1].upper()

            s = '{}{}'.format(self.isotope, f)

        if self.preceding_id:
            p = self.preceding_analysis
            rid = make_runid(p.labnumber.identifier, p.aliquot, p.step)
            s = '{} ({})'.format(s, rid)

        return s

    def _construct_analysis(self, rec, prog, calculate_age=True, unpack=False, load_changes=False):
        atype = None
        if isinstance(rec, meas_AnalysisTable):
            rid = make_runid(rec.labnumber.identifier, rec.aliquot, rec.step)
            atype = rec.measurement.analysis_type.name
        elif hasattr(rec, 'record_id'):
            rid = rec.record_id
        else:
            rid = id(rec)

        graph_id = 0
        group_id = 0

        if hasattr(rec, 'group_id'):
            group_id = rec.group_id

        if hasattr(rec, 'graph_id'):
            graph_id = rec.graph_id

        if atype is None:
            atype = rec.analysis_type

        if prog:
            show_age = calculate_age and atype in ('unknown', 'cocktail')
            m = 'calculating age' if show_age else ''
            msg = 'loading {}. {}'.format(rid, m)
            prog.change_message(msg)

        meas_analysis = self.db.get_analysis_uuid(rec.uuid)

        klass=DBAnalysis if not self.use_vcs else VCSAnalysis
        ai = klass(group_id=group_id,
                   graph_id=graph_id)

        # if not self.use_vcs:
        synced=False
        if atype in ('unknown', 'cocktail'):
            if calculate_age:
                ai.sync(meas_analysis, load_changes=load_changes)
                ai.calculate_age(force=not self.use_vcs)
                synced=True

        if not synced:
            ai.sync(meas_analysis, unpack=unpack, load_changes=load_changes)

        return ai

    def add_analysis(self, spec, commit=True):
        db = self.db
        # for i in range(3):
        with db.session_ctx(use_parent_session=False) as session:
            irradpos = spec.irradpos
            rid = spec.runid
            trid = rid.lower()
            identifier = spec.labnumber

            if trid.startswith('b'):
                runtype = 'Blank'
                irradpos = -1
            elif trid.startswith('a'):
                runtype = 'Air'
                irradpos = -2
            elif trid.startswith('c'):
                runtype = 'Unknown'
                identifier = irradpos = self.get_identifier(spec)
            else:
                runtype = 'Unknown'

            rid = make_runid(identifier, spec.aliquot, spec.step)

            self._analysis = None
            db.reraise = True
            try:
                ret = self._add_analysis(session, spec, irradpos, rid, runtype)
                db.commit()
                return ret
            except Exception as e:
                import traceback
                self.debug('Mass Spec save exception. {}'.format(e))
                tb = traceback.format_exc()
                self.debug(tb)
                self.message('Could not save spec. runid={} rid={} to MassSpec DB.\n{}'.format(spec.runid, rid, tb))
                # if i == 2:
                #     self.message('Could not save spec.runid={} rid={} '
                #                  'to Mass Spec database.\n {}'.format(spec.runid, rid, tb))
                # else:
                #     self.debug('retry mass spec save')
                # # if commit:
                # db.rollback()
            finally:
                self.db.reraise = True

 def _set_device_sensitivity(self, s, e, mi, ed, pr, v, err,prog):
     """
         get all analyses between s, e
         where mass_spectrometer=mi, extract_device=ed, and project=pr
         set sensitivity to v +/-1s e
     """
     db=self.db
     with db.session_ctx():
         ans = db.get_analyses_date_range(s, e,
                                          mass_spectrometer=mi,
                                          extract_device=ed,
                                          project=pr)
         ans=filter(lambda x: not x.uuid in self._uuids, ans)
         self._uuids.extend([ai.uuid for ai in ans])
         self.debug('setting {} analyses'.format(len(ans)))
         prog.increase_max(len(ans))
         for ai in ans:
             r = make_runid(ai.labnumber.identifier,
                            ai.aliquot, ai.step)
             prog.change_message('Saving sensitivity for {}'.format(r))
             db.set_analysis_sensitivity(ai, v, err)

    def _sync(self, path, *args, **kw):
        self.path = path

        yd = self._load_yaml(path)
        attrs = ANALYSIS_ATTRS + ()
        for attr in attrs:
            if isinstance(attr, tuple):
                attr, ydattr = attr
            else:
                attr, ydattr = attr, attr
            setattr(self, attr, yd[ydattr])

        self.analysis_type = 'unknown'
        self.rundate = datetime.fromtimestamp(self.timestamp)
        self.set_j(yd['j'], yd['j_err'])
        self.record_id = make_runid(self.labnumber, self.aliquot, self.step)

        self.interference_corrections = yd['interference_corrections']
        self.production_ratios = yd['production_ratios']

        self._sync_isotopes(yd)

    def add_analysis(self, spec, commit=True):
        with self.db.session_ctx(commit=False) as sess:
            irradpos = spec.irradpos
            rid = spec.runid
            trid = rid.lower()
            identifier = spec.labnumber

            if trid.startswith("b"):
                runtype = "Blank"
                irradpos = -1
            elif trid.startswith("a"):
                runtype = "Air"
                irradpos = -2
            elif trid.startswith("c"):
                runtype = "Unknown"
                identifier = irradpos = self.get_identifier(spec)
            else:
                runtype = "Unknown"

            # paliquot = self.db.get_latest_analysis_aliquot(identifier)
            # if paliquot is None:
            #     paliquot=0
            #
            # rid = '{}-{:02n}'.format(identifier, spec.aliquot, spec.step)
            # self.info('Saving analysis {} to database as {}'.format(spec.rid, rid))
            rid = make_runid(identifier, spec.aliquot, spec.step)

            self._analysis = None
            try:
                return self._add_analysis(sess, spec, irradpos, rid, runtype)
            except Exception, e:
                import traceback

                tb = traceback.format_exc()
                self.message(
                    "Could not save spec.runid={} rid={} to Mass Spec database.\n {}".format(spec.runid, rid, tb)
                )
                if commit:
                    sess.rollback()

    def get_isotope_data(self, idx, k):
        v = self.get_isotope(idx, k)
        i = self.get_identifier(idx)
        a = self.get_aliquot(idx)
        s = self.get_step(idx)
        rid = make_runid(i, a, s)

        if isinstance(v, float):
            return [], []
        else:
            parser = self.parser
            sh = parser.sheet

            def g():
                parser.set_sheet(v, header_idx=0)
                cx, cy = parser.get_index('{}_xs'.format(k)), parser.get_index('{}_ys'.format(k))
                for row in parser.iterblock(0, rid):
                    yield row[cx].value, row[cy].value

            data = list(g())

            self.parser.set_sheet(sh)
            return map(list, zip(*data))

 def record_id(self):
     return make_runid(self.uuid, self.aliquot, self.step)

 def record_id(self):
     return make_runid(self.labnumber.identifier, self.aliquot, self.increment)

 def _get_record_id(self):
     record_id = self._record_id
     if not record_id:
         record_id = make_runid(self.labnumber, self.aliquot, self.step)
     return record_id

    def _construct_analysis(self, rec, group, prog, calculate_age=True, calculate_F=False,
                            unpack=False, load_aux=False):
        atype = None
        if isinstance(rec, meas_AnalysisTable):
            rid = make_runid(rec.labnumber.identifier, rec.aliquot, rec.step)
            atype = rec.measurement.analysis_type.name
        elif hasattr(rec, 'record_id'):
            rid = rec.record_id
        else:
            rid = id(rec)

        graph_id = 0
        group_id = 0

        if hasattr(rec, 'group_id'):
            group_id = rec.group_id

        if hasattr(rec, 'graph_id'):
            graph_id = rec.graph_id

        if atype is None:
            atype = rec.analysis_type

        if prog:
            m=''
            if calculate_age:
                show_age = atype in ('unknown', 'cocktail')
                m = 'calculating age' if show_age else ''
            elif calculate_F:
                m = 'calculating F'

            msg = 'loading {}. {}'.format(rid, m)
            prog.change_message(msg)

        if isinstance(rec, DBAnalysis):
            ai = rec
            if load_aux:
                ai.sync_aux(group)
            else:
                ai.sync(group, unpack=unpack, load_aux=load_aux)
        else:
            ai = DBAnalysis()  # if not self.use_vcs else VCSAnalysis
            # print ai
            ai.sync(group, unpack=unpack, load_aux=load_aux)
            # print ai, group

            # ai = klass(group_id=group_id,
            #        graph_id=graph_id)

        ai.trait_set(group_id=group_id,
                     graph_id=graph_id)

        # if not self.use_vcs:
        #
        # timethis(ai.sync, args=(group,),
        #          kwargs=dict(unpack=unpack, load_aux=load_aux))

        if atype in ('unknown', 'cocktail'):
            if calculate_age:
                # timethis(ai.sync, args=(meas_analysis, ),
                #          kwargs=dict(unpack=unpack, load_aux=load_aux))
                # timethis(ai.calculate_age, kwargs=dict(force=not self.use_vcs))
                ai.calculate_age()  #force=not self.use_vcs)
                # timethis(ai.sync, args=(meas_analysis,),
                #          kwargs=dict(unpack=unpack, load_aux=load_aux))
                # timethis(ai.calculate_age)

                # synced = True
        if calculate_F:
            ai.calculate_F()

        # if not synced:
        #     ai.sync(group, unpack=unpack, load_aux=load_aux)

        return ai

 def runid(self):
     if self._runid:
         return self._runid
     else:
         return make_runid(self.labnumber, self.aliquot, self.step)