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test_populate.py

Source:test_populate.py

1#!/usr/bin/env python32# -*- coding: utf-8 -*-3# Copyright (c) 2018 Bhojpur Consulting Private Limited, India. All rights reserved.4#5# Permission is hereby granted, free of charge, to any person obtaining a copy6# of this software and associated documentation files (the "Software"), to deal7# in the Software without restriction, including without limitation the rights8# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell9# copies of the Software, and to permit persons to whom the Software is10# furnished to do so, subject to the following conditions:11#12# The above copyright notice and this permission notice shall be included in13# all copies or substantial portions of the Software.14#15# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR16# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,17# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE18# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER19# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,20# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN21# THE SOFTWARE.22"""23   Test of the Tables service with the populate_metadata.py24   and populate_roi.py scripts.25"""26from ode.testlib import ITest27import string28import csv29import gzip30import os.path31import re32import shutil33import sys34from ode.api import RoiOptions35from ode.grid import ImageColumn36from ode.grid import RoiColumn37from ode.grid import StringColumn38from ode.model import OriginalFileI39from ode.model import FileAnnotationI, MapAnnotationI, PlateAnnotationLinkI40from ode.model import RoiAnnotationLinkI41from ode.model import RoiI, PointI, ProjectI, ScreenI42from ode.rtypes import rdouble, rlist, rstring, unwrap43from ode.sys import ParametersI44from ode.util.populate_metadata import (45    get_config,46    ParsingContext,47    BulkToMapAnnotationContext,48    DeleteMapAnnotationContext,49)50from ode.util.populate_roi import AbstractMeasurementCtx51from ode.util.populate_roi import AbstractPlateAnalysisCtx52from ode.util.populate_roi import MeasurementParsingResult53from ode.util.populate_roi import PlateAnalysisCtxFactory54from ode.constants.namespaces import NSBULKANNOTATIONS55from ode.constants.namespaces import NSMEASUREMENT56from ode.util.temp_files import create_path57from ode.util.metadata_mapannotations import MapAnnotationPrimaryKeyException58from ode.util.metadata_utils import NSBULKANNOTATIONSCONFIG59from pytest import mark60from pytest import raises61MAPR_NS_GENE = 'bhojpur.net/mapr/gene'62pythonminver = mark.skipif(sys.version_info < (2, 7),63                           reason="requires python2.7")64def coord2offset(coord):65    """66    Convert a coordinate of the form AB12 into 0-based row-column indices67    TODO: This should go into a utils file somewhere68    """69    ALPHA = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'70    m = re.match('([A-Z]+)([0-9]+)$', coord.upper())71    assert m72    ra, ca = m.groups()73    r = 074    for a in ra:75        r = r * 26 + ALPHA.find(a) + 176    c = int(ca)77    return r - 1, c - 178class Fixture(object):79    def init(self, test):80        self.test = test81    def setName(self, obj, name):82        q = self.test.client.sf.getQueryService()83        up = self.test.client.sf.getUpdateService()84        obj = q.get(obj.__class__.__name__, obj.id.val)85        obj.setName(rstring(name))86        return up.saveAndReturnObject(obj)87    def createCsv(88        self,89        colNames="Well,Well Type,Concentration",90        rowData=("A1,Control,0", "A2,Treatment,10")91    ):92        csvFileName = create_path("test", ".csv")93        csvFile = open(csvFileName, 'w')94        try:95            csvFile.write(colNames)96            csvFile.write("\n")97            csvFile.write("\n".join(rowData))98        finally:99            csvFile.close()100        return str(csvFileName)101    def createProject(self, name, datasets=("D001", "D002"),102                      images=("A1", "A2")):103        prj = ProjectI()104        prj.setName(rstring(name))105        for x in datasets:106            ds = self.createDataset(names=images)107            ds = self.setName(ds, x)108            prj.linkDataset(ds.proxy())109        return self.test.client.sf.getUpdateService().saveAndReturnObject(prj)110    def createDataset(self, names=("A1", "A2")):111        ds = self.test.make_dataset()112        imgs = self.test.import_fake_file(113            images_count=len(names))114        for i, name in enumerate(names):115            # Name must match exactly. No ".fake"116            img = imgs[i]117            img = self.setName(img, name)118            self.test.link(ds, img)119        return ds.proxy()120    def createScreen(self, rowCount, colCount):121        plate1 = self.test.import_plates(plate_rows=rowCount,122                                         plate_cols=colCount)[0]123        plate2 = self.test.import_plates(plate_rows=rowCount,124                                         plate_cols=colCount)[0]125        plate1 = self.setName(plate1, "P001")126        plate2 = self.setName(plate2, "P002")127        screen = ScreenI()128        screen.name = rstring("Screen")129        screen.linkPlate(plate1.proxy())130        screen.linkPlate(plate2.proxy())131        return self.test.client.sf.getUpdateService().\132            saveAndReturnObject(screen)133    def createPlate(self, rowCount, colCount):134        plates = self.test.import_plates(plate_rows=rowCount,135                                         plate_cols=colCount)136        return plates[0]137    def get_csv(self):138        return self.csv139    def get_cfg(self):140        return os.path.join(141            os.path.dirname(__file__), 'bulk_to_map_annotation_context.yml')142    def get_namespaces(self):143        return [NSBULKANNOTATIONS]144    def assert_rows(self, rows):145        assert rows == self.rowCount * self.colCount146    def assert_child_annotations(self, oas):147        for ma, wid, wr, wc in oas:148            assert isinstance(ma, MapAnnotationI)149            assert unwrap(ma.getNs()) == NSBULKANNOTATIONS150            mv = ma.getMapValueAsMap()151            assert mv['Well'] == str(wid)152            assert coord2offset(mv['Well Name']) == (wr, wc)153            if (wr, wc) == (0, 0):154                assert mv['Well Type'] == 'Control'155                assert mv['Concentration'] == '0'156            else:157                assert mv['Well Type'] == 'Treatment'158                assert mv['Concentration'] == '10'159    def get_all_map_annotations(self):160        qs = self.test.client.sf.getQueryService()161        q = "FROM MapAnnotation WHERE ns in (:nss)"162        p = ParametersI()163        p.map['nss'] = rlist(rstring(ns) for ns in self.get_namespaces())164        r = qs.findAllByQuery(q, p)165        return r166class Screen2Plates(Fixture):167    def __init__(self):168        self.count = 6169        self.annCount = 4170        self.rowCount = 1171        self.colCount = 2172        self.csv = self.createCsv(173            colNames="Plate,Well,Well Type,Concentration",174            rowData=("P001,A1,Control,0", "P001,A2,Treatment,10",175                     "P002,A1,Control,0", "P002,A2,Treatment,10"))176        self.screen = None177    def assert_rows(self, rows):178        """179        Double the number of rows due to 2 plates.180        """181        assert rows == 2 * self.rowCount * self.colCount182    def get_target(self):183        if not self.screen:184            self.screen = self.createScreen(self.rowCount, self.colCount)185        return self.screen186    def get_annotations(self):187        query = """select s from Screen s188            left outer join fetch s.annotationLinks links189            left outer join fetch links.child190            where s.id=%s""" % self.screen.id.val191        qs = self.test.client.sf.getQueryService()192        screen = qs.findByQuery(query, None)193        anns = screen.linkedAnnotationList()194        return anns195    def get_child_annotations(self):196        query = """197            SELECT wal.child,wal.parent.id,wal.parent.row,wal.parent.column198            FROM WellAnnotationLink wal join wal.parent well199                    join well.plate p join p.screenLinks l join l.parent s200            WHERE s.id=%d""" % self.screen.id.val201        qs = self.test.client.sf.getQueryService()202        was = unwrap(qs.projection(query, None))203        return was204class Plate2Wells(Fixture):205    def __init__(self):206        self.count = 4207        self.annCount = 2208        self.rowCount = 1209        self.colCount = 2210        self.csv = self.createCsv()211        self.plate = None212    def get_target(self):213        if not self.plate:214            self.plate = self.createPlate(self.rowCount, self.colCount)215        return self.plate216    def get_annotations(self):217        query = """select p from Plate p218            left outer join fetch p.annotationLinks links219            left outer join fetch links.child220            where p.id=%s""" % self.plate.id.val221        qs = self.test.client.sf.getQueryService()222        plate = qs.findByQuery(query, None)223        anns = plate.linkedAnnotationList()224        return anns225    def get_child_annotations(self, ns=None):226        query = """227            SELECT wal.child,wal.parent.id,wal.parent.row,wal.parent.column228            FROM WellAnnotationLink wal229            WHERE wal.parent.plate.id=%d""" % self.plate.id.val230        if ns is not None:231            query += (" AND wal.child.ns='%s'" % ns)232        qs = self.test.client.sf.getQueryService()233        was = unwrap(qs.projection(query, None))234        return was235class Plate2WellsNs(Plate2Wells):236    # For this test use explicit files instead of generating them as an237    # additional safeguard against changes in the test code238    def __init__(self):239        self.count = 8240        self.annCount = 8 * 2  # Two namespaces241        self.rowCount = 2242        self.colCount = 4243        d = os.path.dirname(__file__)244        self.csv = os.path.join(d, 'bulk_to_map_annotation_context_ns.csv')245        self.plate = None246    def get_cfg(self):247        return os.path.join(os.path.dirname(__file__),248                            'bulk_to_map_annotation_context_ns.yml')249    def get_namespaces(self):250        return [NSBULKANNOTATIONS, MAPR_NS_GENE]251    def assert_row_values(self, rowvalues):252        # First column is the WellID253        assert rowvalues[0][1:] == (254            "FBgn0004644", "hh", "hedgehog;bar-3;CG4637", "a1")255        assert rowvalues[1][1:] == (256            "FBgn0003656", "sws", "swiss cheese;olfE;CG2212", "a2")257        assert rowvalues[2][1:] == (258            "FBgn0011236", "ken", "ken and barbie;CG5575", "a3")259        assert rowvalues[3][1:] == (260            "FBgn0086378", "", "Alg-2", "a4")261        assert rowvalues[4][1:] == (262            "", "hh",263            "DHH;IHH;SHH;Desert hedgehog;Indian hedgehog;Sonic hedgehog", "b1")264        assert rowvalues[5][1:] == (265            "", "sws",266            "PNPLA6;patatin like phospholipase domain containing 6", "b2")267        assert rowvalues[6][1:] == (268            "", "ken", "BCL6;B-cell lymphoma 6 protein", "b3")269        assert rowvalues[7][1:] == (270            "", "", "Alg-2", "b4")271    def assert_child_annotations(self, oas):272        wellrcs = [coord2offset(c) for c in (273            'a1', 'a2', 'a3', 'a4', 'b1', 'b2', 'b3', 'b4')]274        nss = [NSBULKANNOTATIONS, MAPR_NS_GENE]275        wellrc_ns = [(wrc, ns) for wrc in wellrcs for ns in nss]276        check = dict((k, None) for k in wellrc_ns)277        annids = []278        for ma, wid, wr, wc in oas:279            assert isinstance(ma, MapAnnotationI)280            annids.append(unwrap(ma.getId()))281            ns = unwrap(ma.getNs())282            wrc = (wr, wc)283            # Well names/ids aren't included in this test, because this also284            # test that annotations are combined by primary key285            assert (wrc, ns) in check, 'Unexpected well/namespace'286            assert check[(wrc, ns)] is None, 'Duplicate annotation'287            # Use getMapValue to check ordering and duplicates288            check[(wrc, ns)] = [(p.name, p.value) for p in ma.getMapValue()]289        # Row a290        assert check[(wellrcs[0], nss[0])] == [291            ('Gene', 'hh'),292            ('FlyBase URL', 'http://flybase.org/reports/FBgn0004644.html'),293        ]294        assert check[(wellrcs[0], nss[1])] == [295            ('Gene', 'hh'),296            ('Gene name', 'hedgehog'),297            ('Gene name', 'bar-3'),298            ('Gene name', 'CG4637'),299        ]300        assert check[(wellrcs[1], nss[0])] == [301            ('Gene', 'sws'),302            ('FlyBase URL', 'http://flybase.org/reports/FBgn0003656.html'),303        ]304        assert check[(wellrcs[1], nss[1])] == [305            ('Gene', 'sws'),306            ('Gene name', 'swiss cheese'),307            ('Gene name', 'olfE'),308            ('Gene name', 'CG2212'),309        ]310        assert check[(wellrcs[2], nss[0])] == [311            ('Gene', 'ken'),312            ('FlyBase URL', 'http://flybase.org/reports/FBgn0011236.html'),313        ]314        assert check[(wellrcs[2], nss[1])] == [315            ('Gene', 'ken'),316            ('Gene name', 'ken and barbie'),317            ('Gene name', 'CG5575'),318        ]319        assert check[(wellrcs[3], nss[0])] == [320            ('Gene', ''),321            ('FlyBase URL', 'http://flybase.org/reports/FBgn0086378.html'),322        ]323        assert check[(wellrcs[3], nss[1])] == [324            ('Gene', ''),325            ('Gene name', 'Alg-2'),326        ]327        # Row b328        assert check[(wellrcs[4], nss[0])] == [329            ('Gene', 'hh'),330        ]331        assert check[(wellrcs[4], nss[1])] == [332            ('Gene', 'hh'),333            ('Gene name', 'DHH'),334            ('Gene name', 'IHH'),335            ('Gene name', 'SHH'),336            ('Gene name', 'Desert hedgehog'),337            ('Gene name', 'Indian hedgehog'),338            ('Gene name', 'Sonic hedgehog'),339        ]340        assert check[(wellrcs[5], nss[0])] == [341            ('Gene', 'sws'),342        ]343        assert check[(wellrcs[5], nss[1])] == [344            ('Gene', 'sws'),345            ('Gene name', 'PNPLA6'),346            ('Gene name', 'patatin like phospholipase domain containing 6'),347        ]348        assert check[(wellrcs[6], nss[0])] == [349            ('Gene', 'ken'),350        ]351        assert check[(wellrcs[6], nss[1])] == [352            ('Gene', 'ken'),353            ('Gene name', 'BCL6'),354            ('Gene name', 'B-cell lymphoma 6 protein'),355        ]356        assert check[(wellrcs[7], nss[0])] == [357            ('Gene', ''),358        ]359        assert check[(wellrcs[7], nss[1])] == [360            ('Gene', ''),361            ('Gene name', 'Alg-2'),362        ]363        assert len(annids) == 16364        assert len(set(annids)) == 16365class Plate2WellsNs2(Plate2WellsNs):366    # For this test use explicit files instead of generating them as an367    # additional safeguard against changes in the test code368    def __init__(self):369        super(Plate2WellsNs2, self).__init__()370    def get_cfg(self):371        return os.path.join(os.path.dirname(__file__),372                            'bulk_to_map_annotation_context_ns2.yml')373    def assert_child_annotations(self, oas, onlyns=None):374        """375        Pass onlyns to check that only annotations in that namespace exist376        """377        wellrcs = [coord2offset(c) for c in (378            'a1', 'a2', 'a3', 'a4', 'b1', 'b2', 'b3', 'b4')]379        nss = [NSBULKANNOTATIONS, MAPR_NS_GENE]380        if onlyns:381            nss = [onlyns]382        wellrc_ns = [(wrc, ns) for wrc in wellrcs for ns in nss]383        check = dict((k, None) for k in wellrc_ns)384        annids = []385        for ma, wid, wr, wc in oas:386            assert isinstance(ma, MapAnnotationI)387            annids.append(unwrap(ma.getId()))388            ns = unwrap(ma.getNs())389            wrc = (wr, wc)390            # Well names/ids aren't included in this test, because this also391            # test that annotations are combined by primary key392            assert (wrc, ns) in check, 'Unexpected well/namespace'393            assert check[(wrc, ns)] is None, 'Duplicate annotation'394            # Use getMapValue to check ordering and duplicates395            check[(wrc, ns)] = [(p.name, p.value) for p in ma.getMapValue()]396        if onlyns == NSBULKANNOTATIONS:397            self._assert_nsbulkann(check, wellrcs)398            assert len(annids) == 8399            assert len(set(annids)) == 8400        if onlyns == MAPR_NS_GENE:401            self._assert_nsgeneann(check, wellrcs)402            assert len(annids) == 8403            assert len(set(annids)) == 4404        if not onlyns:405            self._assert_nsgeneann(check, wellrcs)406            assert len(annids) == 16407            assert len(set(annids)) == 12408    def _assert_nsbulkann(self, check, wellrcs):409        # Row a410        assert check[(wellrcs[0], NSBULKANNOTATIONS)] == [411            ('Gene', 'hh'),412            ('FlyBase URL', 'http://flybase.org/reports/FBgn0004644.html'),413        ]414        assert check[(wellrcs[1], NSBULKANNOTATIONS)] == [415            ('Gene', 'sws'),416            ('FlyBase URL', 'http://flybase.org/reports/FBgn0003656.html'),417        ]418        assert check[(wellrcs[2], NSBULKANNOTATIONS)] == [419            ('Gene', 'ken'),420            ('FlyBase URL', 'http://flybase.org/reports/FBgn0011236.html'),421        ]422        assert check[(wellrcs[3], NSBULKANNOTATIONS)] == [423            ('Gene', ''),424            ('FlyBase URL', 'http://flybase.org/reports/FBgn0086378.html'),425        ]426        # Row b427        assert check[(wellrcs[4], NSBULKANNOTATIONS)] == [428            ('Gene', 'hh'),429        ]430        assert check[(wellrcs[5], NSBULKANNOTATIONS)] == [431            ('Gene', 'sws'),432        ]433        assert check[(wellrcs[6], NSBULKANNOTATIONS)] == [434            ('Gene', 'ken'),435        ]436        assert check[(wellrcs[7], NSBULKANNOTATIONS)] == [437            ('Gene', ''),438        ]439    def _assert_nsgeneann(self, check, wellrcs):440        # Row a441        assert check[(wellrcs[0], MAPR_NS_GENE)] == [442            ('Gene', 'hh'),443            ('Gene name', 'hedgehog'),444            ('Gene name', 'bar-3'),445            ('Gene name', 'CG4637'),446            ('Gene name', 'DHH'),447            ('Gene name', 'IHH'),448            ('Gene name', 'SHH'),449            ('Gene name', 'Desert hedgehog'),450            ('Gene name', 'Indian hedgehog'),451            ('Gene name', 'Sonic hedgehog'),452        ]453        assert check[(wellrcs[1], MAPR_NS_GENE)] == [454            ('Gene', 'sws'),455            ('Gene name', 'swiss cheese'),456            ('Gene name', 'olfE'),457            ('Gene name', 'CG2212'),458            ('Gene name', 'PNPLA6'),459            ('Gene name', 'patatin like phospholipase domain containing 6'),460        ]461        assert check[(wellrcs[2], MAPR_NS_GENE)] == [462            ('Gene', 'ken'),463            ('Gene name', 'ken and barbie'),464            ('Gene name', 'CG5575'),465            ('Gene name', 'BCL6'),466            ('Gene name', 'B-cell lymphoma 6 protein'),467        ]468        assert check[(wellrcs[3], MAPR_NS_GENE)] == [469            ('Gene', ''),470            ('Gene name', 'Alg-2'),471        ]472        # Row b473        assert check[(wellrcs[4], MAPR_NS_GENE)] == check[474            (wellrcs[0], MAPR_NS_GENE)]475        assert check[(wellrcs[5], MAPR_NS_GENE)] == check[476            (wellrcs[1], MAPR_NS_GENE)]477        assert check[(wellrcs[6], MAPR_NS_GENE)] == check[478            (wellrcs[2], MAPR_NS_GENE)]479        assert check[(wellrcs[7], MAPR_NS_GENE)] == [480            ('Gene', ''),481            ('Gene name', 'Alg-2'),482        ]483class Plate2WellsNs2UnavailableHeader(Plate2WellsNs2):484    # For this test use explicit files instead of generating them as an485    # additional safeguard against changes in the test code486    def __init__(self):487        self.count = 4488        self.annCount = 4*2489        self.rowCount = 2490        self.colCount = 2491        self.csv = self.createCsv(492            colNames="Well,Gene,Gene Names",493            rowData=("a1,gene-a1,a1-name", "a2,gene-a2,a2-name",494                     "b1,gene-a1,a1-name", "b2,gene-a2,a2-name")495        )496        self.plate = None497    def get_cfg(self):498        return os.path.join(os.path.dirname(__file__),499                            'bulk_to_map_annotation_context_ns2_empty.yml')500    def assert_child_annotations(self, oas):501        wellrcs = [coord2offset(c) for c in (502            'a1', 'a2', 'b1', 'b2')]503        nss = [NSBULKANNOTATIONS, MAPR_NS_GENE]504        wellrc_ns = [(wrc, ns) for wrc in wellrcs for ns in nss]505        check = dict((k, None) for k in wellrc_ns)506        annids = []507        for ma, wid, wr, wc in oas:508            assert isinstance(ma, MapAnnotationI)509            annids.append(unwrap(ma.getId()))510            ns = unwrap(ma.getNs())511            wrc = (wr, wc)512            # Well names/ids aren't included in this test, because this also513            # test that annotations are combined by primary key514            assert (wrc, ns) in check, 'Unexpected well/namespace'515            assert check[(wrc, ns)] is None, 'Duplicate annotation'516            # Use getMapValue to check ordering and duplicates517            check[(wrc, ns)] = [(p.name, p.value) for p in ma.getMapValue()]518        # Row a519        assert check[(wellrcs[0], nss[0])] == [520            ('Gene', 'gene-a1'),521            ('Gene name', 'a1-name'),522            ('Gene ID', '')523        ]524        assert check[(wellrcs[1], nss[0])] == [525            ('Gene', 'gene-a2'),526            ('Gene name', 'a2-name'),527            ('Gene ID', '')528        ]529        assert check[(wellrcs[0], nss[1])] == [530            ('Gene', 'gene-a1'),531            ('Gene name', 'a1-name'),532            ('Gene ID', '')533        ]534class Plate2WellsNs2Fail(Plate2WellsNs2):535    # For this test use explicit files instead of generating them as an536    # additional safeguard against changes in the test code537    def __init__(self):538        self.count = 4539        self.annCount = 2540        self.rowCount = 1541        self.colCount = 2542        self.csv = self.createCsv(543            colNames="Well,Gene,Gene Names",544            rowData=("a1,,ABC", "A2,,ABC")545        )546        self.plate = None547    def get_cfg(self):548        return os.path.join(os.path.dirname(__file__),549                            'bulk_to_map_annotation_context_ns2_fail.yml')550    def get_namespaces(self):551        return 'bhojpur.net/mapr/gene_fail'552class Dataset2Images(Fixture):553    def __init__(self):554        self.count = 4555        self.annCount = 2556        self.csv = self.createCsv(557            colNames="Image Name,Type,Concentration",558        )559        self.dataset = None560        self.images = None561        self.names = ("A1", "A2")562    def assert_rows(self, rows):563        # Hard-coded in createCsv's arguments564        assert rows == 2565    def get_target(self):566        if not self.dataset:567            self.dataset = self.createDataset(self.names)568            self.images = self.get_dataset_images()569        return self.dataset570    def get_dataset_images(self):571        if not self.dataset:572            return []573        query = """select i from Image i574            left outer join fetch i.datasetLinks links575            left outer join fetch links.parent d576            where d.id=%s""" % self.dataset.id.val577        qs = self.test.client.sf.getQueryService()578        return qs.findAllByQuery(query, None)579    def get_annotations(self):580        query = """select d from Dataset d581            left outer join fetch d.annotationLinks links582            left outer join fetch links.child583            where d.id=%s""" % self.dataset.id.val584        qs = self.test.client.sf.getQueryService()585        ds = qs.findByQuery(query, None)586        anns = ds.linkedAnnotationList()587        return anns588    def get_child_annotations(self):589        if not self.images:590            return []591        params = ParametersI()592        params.addIds([x.id for x in self.images])593        query = """ select a, i.id, 'NA', 'NA'594            from Image i595            left outer join i.annotationLinks links596            left outer join links.child as a597            where i.id in (:ids) and a <> null"""598        qs = self.test.client.sf.getQueryService()599        return unwrap(qs.projection(query, params))600    def assert_child_annotations(self, oas):601        for ma, iid, na1, na2 in oas:602            assert isinstance(ma, MapAnnotationI)603            assert unwrap(ma.getNs()) == NSBULKANNOTATIONS604            mv = ma.getMapValueAsMap()605            img = mv['Image Name']606            con = mv['Concentration']607            typ = mv['Type']608            assert img[0] in ("A", "a")609            which = long(img[1:])610            if which % 2 == 1:611                assert con == '0'612                assert typ == 'Control'613            elif which % 2 == 0:614                assert con == '10'615                assert typ == 'Treatment'616class Dataset2Images1Missing(Dataset2Images):617    def __init__(self):618        super(Dataset2Images1Missing, self).__init__()619        self.annCount = 1620    def get_target(self):621        """622        Temporarily alter self.names so that the super623        invocation creates fewer images than are expected.624        """625        old = self.names626        try:627            self.names = old[0:-1]  # Skip last628            return super(Dataset2Images1Missing, self).get_target()629        finally:630            self.names = old631class Dataset101Images(Dataset2Images):632    def __init__(self):633        self.count = 4634        self.annCount = 102635        self.names = []636        rowData = []637        for x in range(0, 101, 2):638            name = "A%s" % (x+1)639            self.names.append(name)640            rowData.append("%s,Control,0" % name)641            name = "A%s" % (x+2)642            self.names.append(name)643            rowData.append("A%s,Treatment,10" % (x+2))644        self.csv = self.createCsv(645            colNames="Image Name,Type,Concentration",646            rowData=rowData,647        )648        self.dataset = None649        self.images = None650    def assert_rows(self, rows):651        assert rows == 102652class GZIP(Dataset2Images):653    def createCsv(self, *args, **kwargs):654        csvFileName = super(GZIP, self).createCsv(*args, **kwargs)655        gzipFileName = "%s.gz" % csvFileName656        # failing on python 2.6657        # the following workaround can be reverted once py26 is dropped658        # with open(csvFileName, 'rb') as f_in:659        #      with gzip.open(gzipFileName, 'wb') as f_out:660        #          shutil.copyfileobj(f_in, f_out)661        f_in = open(csvFileName, 'rb')662        try:663            try:664                try:665                    f_out = gzip.open(gzipFileName, 'wb')666                except:667                    f_out = gzip(gzipFileName, 'wb')668                shutil.copyfileobj(f_in, f_out)669            finally:670                f_out.close()671        finally:672            f_in.close()673        return gzipFileName674class Project2Datasets(Fixture):675    def __init__(self):676        self.count = 5677        self.annCount = 4678        self.csv = self.createCsv(679            colNames="Dataset Name,Image Name,Type,Concentration",680            rowData=("D001,A1,Control,0", "D001,A2,Treatment,10",681                     "D002,A1,Control,0", "D002,A2,Treatment,10"))682        self.project = None683    def assert_rows(self, rows):684        # Hard-coded in createCsv's arguments685        assert rows == 4686    def get_target(self):687        if not self.project:688            self.project = self.createProject("P123")689            self.images = self.get_project_images()690        return self.project691    def get_project_images(self):692        if not self.project:693            return []694        query = """select i from Image i695            left outer join fetch i.datasetLinks dil696            left outer join fetch dil.parent d697            left outer join fetch d.projectLinks pdl698            left outer join fetch pdl.parent p699            where p.id=%s""" % self.project.id.val700        qs = self.test.client.sf.getQueryService()701        return qs.findAllByQuery(query, None)702    def get_annotations(self):703        query = """select p from Project p704            left outer join fetch p.annotationLinks links705            left outer join fetch links.child706            where p.id=%s""" % self.project.id.val707        qs = self.test.client.sf.getQueryService()708        ds = qs.findByQuery(query, None)709        anns = ds.linkedAnnotationList()710        return anns711    def get_child_annotations(self):712        if not self.images:713            return []714        params = ParametersI()715        params.addIds([x.id for x in self.images])716        query = """ select a, i.id, 'NA', 'NA'717            from Image i718            left outer join i.annotationLinks links719            left outer join links.child as a720            where i.id in (:ids) and a <> null"""721        qs = self.test.client.sf.getQueryService()722        return unwrap(qs.projection(query, params))723    def assert_child_annotations(self, oas):724        for ma, iid, na1, na2 in oas:725            assert isinstance(ma, MapAnnotationI)726            assert unwrap(ma.getNs()) == NSBULKANNOTATIONS727            mv = ma.getMapValueAsMap()728            ds = mv['Dataset Name']729            img = mv['Image Name']730            con = mv['Concentration']731            typ = mv['Type']732            if ds == 'D001' or ds == 'D002':733                if img == "A1":734                    assert con == '0'735                    assert typ == 'Control'736                elif img == "A2":737                    assert con == '10'738                    assert typ == 'Treatment'739                else:740                    raise Exception("Unknown img: %s" % img)741            else:742                raise Exception("Unknown dataset: %s" % ds)743@pythonminver744class TestPopulateMetadataConfigLoad(ITest):745    def get_cfg_filepath(self):746        return os.path.join(os.path.dirname(__file__),747                            'bulk_to_map_annotation_context.yml')748    def _assert_configs(self, default_cfg, column_cfgs, advanced_cfgs):749        assert default_cfg == {"include": True}750        assert column_cfgs is None751        assert advanced_cfgs == {}752    def test_get_config_local(self):753        default_cfg, column_cfgs, advanced_cfgs = get_config(754            None, cfg=self.get_cfg_filepath())755        self._assert_configs(default_cfg, column_cfgs, advanced_cfgs)756    def test_get_config_remote(self):757        ofile = self.client.upload(self.get_cfg_filepath()).proxy()758        cfgid = unwrap(ofile.getId())759        default_cfg, column_cfgs, advanced_cfgs = get_config(760            self.client.getSession(), cfgid=cfgid)761        self._assert_configs(default_cfg, column_cfgs, advanced_cfgs)762@pythonminver763class TestPopulateMetadataHelper(ITest):764    def _test_parsing_context(self, fixture, batch_size):765        """766            Create a small csv file, use populate_metadata.py to parse and767            attach to Plate. Then query to check table has expected content.768        """769        target = fixture.get_target()770        # Deleting anns so that we can re-use the same user771        self.delete(fixture.get_annotations())772        child_anns = fixture.get_child_annotations()773        child_anns = [x[0] for x in child_anns]774        self.delete(child_anns)775        csv = fixture.get_csv()776        ctx = ParsingContext(self.client, target, file=csv)777        ctx.parse()778        if batch_size is None:779            ctx.write_to_ode()780        else:781            ctx.write_to_ode(batch_size=batch_size, loops=10, ms=250)782        # Get file annotations783        anns = fixture.get_annotations()784        # Only expect a single annotation which is a 'bulk annotation'785        assert len(anns) == 1786        tableFileAnn = anns[0]787        assert unwrap(tableFileAnn.getNs()) == NSBULKANNOTATIONS788        fileid = tableFileAnn.file.id.val789        # Open table to check contents790        r = self.client.sf.sharedResources()791        t = r.openTable(OriginalFileI(fileid), None)792        return t793    def _assert_parsing_context_values(self, t, fixture):794        cols = t.getHeaders()795        rows = t.getNumberOfRows()796        fixture.assert_rows(rows)797        for hit in range(rows):798            rowValues = [col.values[0] for col in t.read(range(len(cols)),799                                                         hit, hit+1).columns]800            assert len(rowValues) == fixture.count801            # Unsure where the lower-casing is happening802            if "A1" in rowValues or "a1" in rowValues:803                assert "Control" in rowValues804            elif "A2" in rowValues or "a2" in rowValues:805                assert "Treatment" in rowValues806    def _test_bulk_to_map_annotation_context(self, fixture, batch_size):807        # self._testPopulateMetadataPlate()808        assert len(fixture.get_all_map_annotations()) == 0809        assert len(fixture.get_child_annotations()) == 0810        cfg = fixture.get_cfg()811        target = fixture.get_target()812        anns = fixture.get_annotations()813        fileid = anns[0].file.id.val814        ctx = BulkToMapAnnotationContext(815            self.client, target, fileid=fileid, cfg=cfg)816        ctx.parse()817        assert len(fixture.get_child_annotations()) == 0818        if batch_size is None:819            ctx.write_to_ode()820        else:821            ctx.write_to_ode(batch_size=batch_size)822        oas = fixture.get_child_annotations()823        assert len(oas) == fixture.annCount824        fixture.assert_child_annotations(oas)825    def _test_delete_map_annotation_context(self, fixture, batch_size):826        # self._test_bulk_to_map_annotation_context()827        assert len(fixture.get_child_annotations()) == fixture.annCount828        cfg = fixture.get_cfg()829        target = fixture.get_target()830        ctx = DeleteMapAnnotationContext(self.client, target, cfg=cfg)831        ctx.parse()832        assert len(fixture.get_child_annotations()) == fixture.annCount833        if batch_size is None:834            ctx.write_to_ode()835        else:836            ctx.write_to_ode(batch_size=batch_size)837        assert len(fixture.get_child_annotations()) == 0838        assert len(fixture.get_all_map_annotations()) == 0839@pythonminver840class TestPopulateMetadataHelperPerMethod(TestPopulateMetadataHelper):841    # Some tests in this file check the counts of annotations in a fixed842    # namespace, and therefore require a new client for each test method843    def setup_class(cls):844        pass845    def teardown_class(cls):846        pass847    def setup_method(self, method):848        super(TestPopulateMetadataHelperPerMethod, self).setup_class()849    def teardown_method(self, method):850        super(TestPopulateMetadataHelperPerMethod, self).teardown_class()851@pythonminver852class TestPopulateMetadata(TestPopulateMetadataHelper):853    METADATA_FIXTURES = (854        Screen2Plates(),855        Plate2Wells(),856        Dataset2Images(),857        Dataset2Images1Missing(),858        Dataset101Images(),859        Project2Datasets(),860        GZIP(),861    )862    METADATA_IDS = [x.__class__.__name__ for x in METADATA_FIXTURES]863    METADATA_NS_FIXTURES = (864        Plate2WellsNs(),865        Plate2WellsNs2(),866    )867    METADATA_NS_IDS = [x.__class__.__name__ for x in METADATA_NS_FIXTURES]868    @mark.parametrize("fixture", METADATA_FIXTURES, ids=METADATA_IDS)869    @mark.parametrize("batch_size", (None, 1, 10))870    def testPopulateMetadata(self, fixture, batch_size):871        """872        We should really test each of the parsing contexts in separate tests873        but in practice each one uses data created by the others, so for874        now just run them all together875        """876        fixture.init(self)877        t = self._test_parsing_context(fixture, batch_size)878        self._assert_parsing_context_values(t, fixture)879        self._test_bulk_to_map_annotation_context(fixture, batch_size)880        self._test_delete_map_annotation_context(fixture, batch_size)881    @mark.parametrize("fixture", METADATA_NS_FIXTURES, ids=METADATA_NS_IDS)882    def testPopulateMetadataNsAnns(self, fixture):883        """884        Test complicated annotations (multiple ns/groups) on a single Bhojpur ODE885        data type, as opposed to testPopulateMetadata which tests simple886        annotations on multiple Bhojpur ODE data types887        """888        fixture.init(self)889        t = self._test_parsing_context(fixture, 2)890        cols = t.getHeaders()891        rows = t.getNumberOfRows()892        fixture.assert_rows(rows)893        data = [c.values for c in t.read(range(len(cols)), 0, rows).columns]894        rowValues = zip(*data)895        assert len(rowValues) == fixture.count896        fixture.assert_row_values(rowValues)897        self._test_bulk_to_map_annotation_context(fixture, 2)898        self._test_delete_map_annotation_context(fixture, 2)899    def testPopulateMetadataNsAnnsUnavailableHeader(self):900        """901        Similar to testPopulateMetadataNsAnns but use two plates and check902        MapAnnotations aren't duplicated903        """904        fixture_empty = Plate2WellsNs2UnavailableHeader()905        fixture_empty.init(self)906        self._test_parsing_context(fixture_empty, 2)907        self._test_bulk_to_map_annotation_context(fixture_empty, 2)908    def testPopulateMetadataNsAnnsFail(self):909        """910        Similar to testPopulateMetadataNsAnns but use two plates and check911        MapAnnotations aren't duplicated912        """913        fixture_fail = Plate2WellsNs2Fail()914        fixture_fail.init(self)915        self._test_parsing_context(fixture_fail, 2)916        with raises(MapAnnotationPrimaryKeyException):917            self._test_bulk_to_map_annotation_context(fixture_fail, 2)918@pythonminver919class TestPopulateMetadataDedup(TestPopulateMetadataHelperPerMethod):920    # Hard-code the number of expected map-annotations in these tests921    # since the code in this file is complicated enough without trying922    # to parameterise this923    def _test_bulk_to_map_annotation_dedup(self, fixture1, fixture2, ns):924        options = {}925        if ns:926            options['ns'] = ns927        ann_count = fixture1.annCount928        assert fixture2.annCount == ann_count929        assert len(fixture1.get_child_annotations()) == ann_count930        assert len(fixture2.get_child_annotations()) == 0931        cfg = fixture2.get_cfg()932        target = fixture2.get_target()933        anns = fixture2.get_annotations()934        fileid = anns[0].file.id.val935        ctx = BulkToMapAnnotationContext(936            self.client, target, fileid=fileid, cfg=cfg, options=options)937        ctx.parse()938        assert len(fixture1.get_child_annotations()) == ann_count939        assert len(fixture2.get_child_annotations()) == 0940        ctx.write_to_ode()941        oas1 = fixture1.get_child_annotations()942        oas2 = fixture2.get_child_annotations()943        assert len(oas1) == ann_count944        if ns == NSBULKANNOTATIONS:945            assert len(oas2) == 8946            fixture1.assert_child_annotations(oas1)947            fixture2.assert_child_annotations(oas2, ns)948        if ns == MAPR_NS_GENE:949            assert len(oas2) == 8950            fixture1.assert_child_annotations(oas1)951            fixture2.assert_child_annotations(oas2, ns)952        if ns is None:953            assert len(oas2) == ann_count954            fixture1.assert_child_annotations(oas1)955            fixture2.assert_child_annotations(oas2)956        # The gene mapannotations should be common957        ids1 = set(unwrap(o[0].getId()) for o in oas1)958        ids2 = set(unwrap(o[0].getId()) for o in oas2)959        common = ids1.intersection(ids2)960        if ns == NSBULKANNOTATIONS:961            assert len(common) == 0962        else:963            assert len(common) == 4964    def _test_delete_map_annotation_context_dedup(965            self, fixture1, fixture2, ns):966        # Sanity checks in case the test code or fixtures are modified967        assert fixture1.annCount == 16968        assert fixture2.annCount == 16969        options = {}970        if ns:971            options['ns'] = ns972        assert len(fixture1.get_child_annotations()) == 16973        assert len(fixture1.get_child_annotations(NSBULKANNOTATIONS)) == 8974        assert len(fixture1.get_child_annotations(MAPR_NS_GENE)) == 8975        assert len(fixture2.get_child_annotations()) == 16976        assert len(fixture2.get_child_annotations(NSBULKANNOTATIONS)) == 8977        assert len(fixture2.get_child_annotations(MAPR_NS_GENE)) == 8978        assert len(fixture2.get_all_map_annotations()) == 20979        ctx = DeleteMapAnnotationContext(980            self.client, fixture1.get_target(), cfg=fixture1.get_cfg(),981            options=options)982        ctx.parse()983        ctx.write_to_ode(loops=10, ms=250)984        if ns == NSBULKANNOTATIONS:985            assert len(fixture1.get_child_annotations()) == 8986            assert len(fixture2.get_child_annotations()) == 16987            assert len(fixture2.get_all_map_annotations()) == 12988        if ns == MAPR_NS_GENE:989            assert len(fixture1.get_child_annotations()) == 8990            assert len(fixture2.get_child_annotations()) == 16991            assert len(fixture2.get_all_map_annotations()) == 20992        if ns is None:993            assert len(fixture1.get_child_annotations()) == 0994            assert len(fixture2.get_child_annotations()) == 16995            assert len(fixture2.get_all_map_annotations()) == 12996        ctx = DeleteMapAnnotationContext(997            self.client, fixture2.get_target(), cfg=fixture2.get_cfg(),998            options=options)999        ctx.parse()1000        ctx.write_to_ode(loops=10, ms=250)1001        if ns == NSBULKANNOTATIONS:1002            assert len(fixture1.get_child_annotations()) == 81003            assert len(fixture1.get_child_annotations(MAPR_NS_GENE)) == 81004            assert len(fixture2.get_child_annotations()) == 81005            assert len(fixture2.get_child_annotations(MAPR_NS_GENE)) == 81006            assert len(fixture2.get_all_map_annotations()) == 41007        if ns == MAPR_NS_GENE:1008            assert len(fixture1.get_child_annotations()) == 81009            assert len(fixture1.get_child_annotations(NSBULKANNOTATIONS)) == 81010            assert len(fixture2.get_child_annotations()) == 81011            assert len(fixture2.get_child_annotations(NSBULKANNOTATIONS)) == 81012            assert len(fixture2.get_all_map_annotations()) == 161013        if ns is None:1014            assert len(fixture1.get_child_annotations()) == 01015            assert len(fixture2.get_child_annotations()) == 01016            assert len(fixture2.get_all_map_annotations()) == 01017    @mark.parametrize("ns", [None, NSBULKANNOTATIONS, MAPR_NS_GENE])1018    def testPopulateMetadataNsAnnsDedup(self, ns):1019        """1020        Similar to testPopulateMetadataNsAnns but use two plates, check1021        MapAnnotations aren't duplicated, and filter by namespace1022        """1023        fixture1 = Plate2WellsNs2()1024        fixture1.init(self)1025        self._test_parsing_context(fixture1, 2)1026        self._test_bulk_to_map_annotation_context(fixture1, 2)1027        fixture2 = Plate2WellsNs2()1028        fixture2.init(self)1029        self._test_parsing_context(fixture2, 2)1030        self._test_bulk_to_map_annotation_dedup(fixture1, fixture2, ns)1031    @mark.parametrize("ns", [None, NSBULKANNOTATIONS, MAPR_NS_GENE])1032    def testPopulateMetadataNsAnnsDedupDelete(self, ns):1033        """1034        Similar to testPopulateMetadataNsAnns but use two plates, check1035        MapAnnotations aren't duplicated, and delete by namespace1036        """1037        fixture1 = Plate2WellsNs2()1038        fixture1.init(self)1039        self._test_parsing_context(fixture1, 2)1040        self._test_bulk_to_map_annotation_context(fixture1, 2)1041        fixture2 = Plate2WellsNs2()1042        fixture2.init(self)1043        self._test_parsing_context(fixture2, 2)1044        self._test_bulk_to_map_annotation_dedup(fixture1, fixture2, None)1045        self._test_delete_map_annotation_context_dedup(1046            fixture1, fixture2, ns)1047@pythonminver1048class TestPopulateMetadataConfigFiles(TestPopulateMetadataHelperPerMethod):1049    def _init_fixture_attach_cfg(self):1050        fixture = Plate2Wells()1051        fixture.init(self)1052        target = fixture.get_target()1053        ofile = self.client.upload(fixture.get_cfg()).proxy()1054        link = PlateAnnotationLinkI()1055        link.parent = target.proxy()1056        link.child = FileAnnotationI()1057        link.child.ns = rstring(NSBULKANNOTATIONSCONFIG)1058        link.child.file = ofile1059        link = self.client.sf.getUpdateService().saveAndReturnObject(link)1060        return fixture1061    def _get_annotations_config(self, fixture):1062        anns = []1063        for ann in fixture.get_annotations():1064            if not isinstance(ann, FileAnnotationI):1065                pass1066            if unwrap(ann.getNs()) == NSBULKANNOTATIONS:1067                continue1068            assert unwrap(ann.ns) == NSBULKANNOTATIONSCONFIG1069            anns.append(ann)1070        return anns1071    @mark.parametrize("ns", [None, NSBULKANNOTATIONS, NSBULKANNOTATIONSCONFIG])1072    @mark.parametrize("attach", [True, False])1073    def test_delete_attach(self, ns, attach):1074        fixture = self._init_fixture_attach_cfg()1075        target = fixture.get_target()1076        before = self._get_annotations_config(fixture)1077        assert len(before) == 11078        options = {}1079        if ns:1080            options['ns'] = ns1081        ctx = DeleteMapAnnotationContext(1082            self.client, target, attach=attach, options=options)1083        ctx.parse()1084        ctx.write_to_ode()1085        after = self._get_annotations_config(fixture)1086        if attach and ns != NSBULKANNOTATIONS:1087            assert len(after) == 01088        else:1089            assert before[0].id == after[0].id1090            assert before[0].file.id == after[0].file.id1091class MockMeasurementCtx(AbstractMeasurementCtx):1092    def well_name_to_number(self, well):1093        m = re.match("(?P<COL>[a-z]+)(?P<ROW>\d+)",1094                     well, re.IGNORECASE)1095        if not m:1096            raise Exception("Bad well: %s" % well)1097        col = m.group("COL").upper()1098        row = m.group("ROW")1099        row_num = int(row) - 11100        col_num = 01101        for c in col:1102            i = string.ascii_uppercase.find(c)1103            col_num += i + 11104        # wellnumber_from_colrow1105        numcols = self.analysis_ctx.numcols1106        return (col_num * numcols) + row_num1107    def parse(self):1108        provider = self.original_file_provider1109        data = provider.get_original_file_data(self.original_file)1110        try:1111            rows = list(csv.reader(data, delimiter=","))1112        finally:1113            data.close()1114        columns = [1115            ImageColumn("Image", "", list()),1116            RoiColumn("ROI", "", list()),1117            StringColumn("Type", "", 12, list()),1118        ]1119        for row in rows[1:]:1120            wellnumber = self.well_name_to_number(row[0])1121            image = self.analysis_ctx.\1122                image_from_wellnumber(wellnumber)1123            #  TODO: what to do with the field?!1124            #  field = int(row[1])1125            #  image = images[field]1126            roi = RoiI()1127            shape = PointI()1128            shape.x = rdouble(float(row[2]))1129            shape.y = rdouble(float(row[3]))1130            shape.textValue = rstring(row[4])1131            roi.addShape(shape)1132            roi.image = image.proxy()1133            rid = self.update_service\1134                .saveAndReturnIds([roi])[0]1135            columns[0].values.append(image.id.val)1136            columns[1].values.append(rid)1137            columns[2].values.append(row[4])1138        return MeasurementParsingResult([columns])1139    def get_name(self, *args, **kwargs):1140        # Strip .csv1141        return self.original_file.name.val[:-4]1142    def parse_and_populate_roi(self, columns):1143        # Remove from interface1144        # Using this as a place to set file annotation1145        self.file_annotation =\1146            self.update_service.saveAndReturnObject(1147                self.file_annotation)1148        rois = columns[1].values1149        for roi in rois:1150            link = RoiAnnotationLinkI()1151            link.parent = RoiI(roi, False)1152            link.child = self.file_annotation.proxy()1153            self.update_service\1154                .saveObject(link)1155    def populate(self, columns):1156        self.update_table(columns)1157class MockPlateAnalysisCtx(AbstractPlateAnalysisCtx):1158    def __init__(self, images, original_files,1159                 original_file_image_map,1160                 plate_id, service_factory):1161        super(MockPlateAnalysisCtx, self).__init__(1162            images, original_files, original_file_image_map,1163            plate_id, service_factory1164        )1165        for original_file in original_files:1166            name = original_file.name.val1167            if name.endswith("csv"):1168                self.measurements[len(self.measurements)] = \1169                    original_file1170    def is_this_type(klass, original_files):1171        for original_file in original_files:1172            name = unwrap(original_file.name)1173            if name.endswith(".csv"):1174                return True1175    is_this_type = classmethod(is_this_type)1176    def get_measurement_count(self):1177        return len(self.measurements)1178    def get_measurement_ctx(self, index):1179        sf = self.service_factory1180        provider = self.DEFAULT_ORIGINAL_FILE_PROVIDER(sf)1181        return MockMeasurementCtx(1182            self, sf, provider,1183            self.measurements[index], None)1184    def get_result_file_count(self, index):1185        return 11186class ROICSV(Fixture):1187    def __init__(self):1188        self.count = 11189        self.annCount = 21190        self.csvName = self.createCsv(1191            colNames="Well,Field,X,Y,Type",1192            rowData=("A1,0,15,15,Test",))1193        self.rowCount = 11194        self.colCount = 11195        self.plate = None1196    def get_target(self):1197        if not self.plate:1198            self.plate = self.createPlate(1199                self.rowCount, self.colCount)1200        return self.plate1201@pythonminver1202class TestPopulateRois(ITest):1203    def testPopulateRoisPlate(self):1204        """1205            Create a small csv file, use populate_roi.py to parse and1206            attach to Plate. Then query to check table has expected content.1207        """1208        fixture = ROICSV()1209        fixture.init(self)1210        plate = fixture.get_target()1211        # As opposed to the ParsingContext, here we are expected1212        # to link the file ourselves1213        ofile = self.client.upload(fixture.csvName).proxy()1214        ann = FileAnnotationI()1215        ann.file = ofile1216        link = PlateAnnotationLinkI()1217        link.parent = plate.proxy()1218        link.child = ann1219        link = self.client.sf.getUpdateService()\1220            .saveAndReturnObject(link)1221        # End linking1222        factory = PlateAnalysisCtxFactory(self.client.sf)1223        factory.implementations = (MockPlateAnalysisCtx,)1224        ctx = factory.get_analysis_ctx(plate.id.val)1225        assert 1 == ctx.get_measurement_count()1226        meas = ctx.get_measurement_ctx(0)1227        meas.parse_and_populate()1228        # Get file annotations1229        query = """select p from Plate p1230            left outer join fetch p.annotationLinks links1231            left outer join fetch links.child as ann1232            left outer join fetch ann.file as file1233            where p.id=%s""" % plate.id.val1234        qs = self.client.sf.getQueryService()1235        plate = qs.findByQuery(query, None)1236        anns = plate.linkedAnnotationList()1237        # Only expect a single annotation which is a 'bulk annotation'1238        # the other is the original CSV1239        assert len(anns) == 21240        files = dict(1241            [(a.ns.val, a.file.id.val) for a in anns if a.ns])1242        fileid = files[NSMEASUREMENT]1243        # Open table to check contents1244        r = self.client.sf.sharedResources()1245        t = r.openTable(OriginalFileI(fileid), None)1246        cols = t.getHeaders()1247        rows = t.getNumberOfRows()1248        assert rows == 11249        data = t.read(range(len(cols)), 0, 1)1250        imag = data.columns[0].values[0]1251        rois = self.client.sf.getRoiService()1252        anns = rois.getRoiMeasurements(imag, RoiOptions())...

test_environment_resource.py

Source:test_environment_resource.py

1"""2Tests for EnvironmentResource api.3"""4from tests.case.api.crud import ApiCrudCases5import logging6logger = logging.getLogger("moztrap.test")7class EnvironmentResourceTest(ApiCrudCases):8    @property9    def factory(self):10        """The model factory for this object."""11        return self.F.EnvironmentFactory()12    @property13    def resource_name(self):14        return "environment"15    @property16    def permission(self):17        """The permissions needed to modify this object type."""18        return "environments.manage_environments"19    @property20    def new_object_data(self):21        """Generates a dictionary containing the field names and auto-generated22        values needed to create a unique object.23        The output of this method can be sent in the payload parameter of a24        POST message.25        """26        self.profile_fixture = self.F.ProfileFactory()27        self.category_fixture1 = self.F.CategoryFactory(name="A")28        self.category_fixture2 = self.F.CategoryFactory(name="B")29        self.category_fixture3 = self.F.CategoryFactory(name="C")30        self.element_fixture1 = self.F.ElementFactory(category=self.category_fixture1, name="A 2")31        self.element_fixture2 = self.F.ElementFactory(category=self.category_fixture2, name="B 2")32        self.element_fixture3 = self.F.ElementFactory(category=self.category_fixture3, name="C 2")33        self.element_fixture_list = [34            self.element_fixture1, self.element_fixture2, self.element_fixture3]35        return {36            u"profile": unicode(37                self.get_detail_url("profile", str(self.profile_fixture.id))),38            u"elements": [unicode(39                self.get_detail_url(40                    "element", str(elem.id))41                ) for elem in self.element_fixture_list],42            }43    def backend_object(self, id):44        """Returns the object from the backend, so you can query it's values in45        the database for validation.46        """47        return self.model.Environment.everything.get(id=id)48    def backend_data(self, backend_obj):49        """Query's the database for the object's current values. Output is a50        dictionary that should match the result of getting the object's detail51        via the API, and can be used to verify API output.52        Note: both keys and data should be in unicode53        """54        return {55            u"id": backend_obj.id,56            u"profile": unicode(self.get_detail_url("profile", str(backend_obj.profile.id))),57            u"elements": [unicode(58                self.get_detail_url("element", str(elem.id))59            ) for elem in backend_obj.elements.all()],60            u"resource_uri": unicode(61                self.get_detail_url(self.resource_name, str(backend_obj.id))),62        }63    def test_elements_must_be_from_different_categories(self):64        """A post with two elements from the same category should error."""65        logger.info("test_elements_must_be_from_different_categories")66        # get data for creation & munge it67        fields = self.new_object_data68        self.element_fixture2.category = self.element_fixture1.category69        self.element_fixture2.save()70        # do the create71        res = self.post(72            self.get_list_url(self.resource_name),73            params=self.credentials,74            payload=fields,75            status=400,76            )77        error_msg = "Elements must each belong to a different Category."78        self.assertEqual(res.text, error_msg)79    def test_basic_combinatorics_patch(self):80        """A Patch request with profile and categories should do combinatorics81        on the categories and create environments."""82        logger.info("test_basic_combinatorics_patch")83        fields = self.new_object_data84        # create more elements for each category85        for x in range(2):86            self.F.ElementFactory(category=self.category_fixture1, name="A %s" % x)87            self.F.ElementFactory(category=self.category_fixture2, name="B %s" % x)88            self.F.ElementFactory(category=self.category_fixture3, name="C %s" % x)89        # modify fields to send categories rather than elements90        fields.pop('elements')91        fields['categories'] = [92            unicode(self.get_detail_url(93                "category", str(self.category_fixture1.id))),94            unicode(self.get_detail_url(95                "category", str(self.category_fixture2.id))),96            unicode(self.get_detail_url(97                "category", str(self.category_fixture3.id))),98        ]99        # do the create100        res = self.patch(101            self.get_list_url(self.resource_name),102            params=self.credentials,103            payload=fields,104            )105        # check that it made the right number of environments106        self._test_filter_list_by(u'profile', self.profile_fixture.id, 27)107    def test_patch_without_categories_error(self):108        """'categories' must be provided in PATCH."""109        logger.info("test_patch_without_categories_error")110        fields = self.new_object_data111        # do the create112        res = self.patch(113            self.get_list_url(self.resource_name),114            params=self.credentials,115            payload=fields,116            status=400,117            )118        error_msg = "PATCH request must contain categories list."119        self.assertEqual(res.text, error_msg)120    def test_patch_categories_not_list_error(self):121        """'categories' must be a list in PATCH."""122        logger.info("test_patch_categories_not_list_error")123        fields = self.new_object_data124        fields.pop("elements")125        fields[u'categories'] = unicode(126            self.get_detail_url("category", str(self.category_fixture1.id)))127        # do the create128        res = self.patch(129            self.get_list_url(self.resource_name),130            params=self.credentials,131            payload=fields,132            status=400,133            )134        error_msg = "PATCH request must contain categories list."135        self.assertEqual(res.text, error_msg)136    def test_patch_categories_list_not_string_or_hash_error(self):137        """'categories' must be a list in PATCH."""138        logger.info("test_patch_categories_list_not_string_or_hash_error")139        fields = self.new_object_data140        fields.pop("elements")141        fields[u'categories'] = [1, 2, 3]142        # do the create143        res = self.patch(144            self.get_list_url(self.resource_name),145            params=self.credentials,146            payload=fields,147            status=400,148            )149        error_msg = "categories list must contain resource uris or hashes."150        self.assertEqual(res.text, error_msg)151    def test_patch_with_exclude(self):152        """Combinatorics excluding some elements."""153        logger.info("test_patch_with_exclude")154        fields = self.new_object_data155        # create more elements for each category156        for x in range(2):157            self.F.ElementFactory(category=self.category_fixture1, name="A %s" % x)158            self.F.ElementFactory(category=self.category_fixture2, name="B %s" % x)159            self.F.ElementFactory(category=self.category_fixture3, name="C %s" % x)160        # modify fields to send categories rather than elements161        fields.pop('elements')162        fields['categories'] = [163            {164                u'category': unicode(self.get_detail_url(165                    "category", str(self.category_fixture1.id))),166                u'exclude': [unicode(self.get_detail_url(167                    "element", str(self.element_fixture1.id))), ],168            },169            {170                u'category': unicode(self.get_detail_url(171                    "category", str(self.category_fixture2.id))),172                u'exclude': [unicode(self.get_detail_url(173                    "element", str(self.element_fixture2.id))), ],174            },175            {176                u'category': unicode(self.get_detail_url(177                    "category", str(self.category_fixture3.id))),178                u'exclude': [unicode(self.get_detail_url(179                    "element", str(self.element_fixture3.id))), ],180            }, ]181        # do the create182        res = self.patch(183            self.get_list_url(self.resource_name),184            params=self.credentials,185            payload=fields,186            )187        # check that it made the right number of environments188        self._test_filter_list_by(u'profile', self.profile_fixture.id, 8)189    def test_patch_with_include(self):190        """Combinatorics including some elements."""191        logger.info("test_patch_with_include")192        fields = self.new_object_data193        # create more elements for each category194        for x in range(2):195            self.F.ElementFactory(category=self.category_fixture1, name="A %s" % x)196            self.F.ElementFactory(category=self.category_fixture2, name="B %s" % x)197            self.F.ElementFactory(category=self.category_fixture3, name="C %s" % x)198        # modify fields to send categories rather than elements199        fields.pop('elements')200        fields['categories'] = [201            {202                u'category': unicode(self.get_detail_url(203                    "category", str(self.category_fixture1.id))),204                u'include': [unicode(self.get_detail_url(205                    "element", str(self.element_fixture1.id))), ],206                },207            {208                u'category': unicode(self.get_detail_url(209                    "category", str(self.category_fixture2.id))),210                u'include': [unicode(self.get_detail_url(211                    "element", str(self.element_fixture2.id))), ],212                },213            {214                u'category': unicode(self.get_detail_url(215                    "category", str(self.category_fixture3.id))),216                u'include': [unicode(self.get_detail_url(217                    "element", str(self.element_fixture3.id))), ],218                }, ]219        # do the create220        res = self.patch(221            self.get_list_url(self.resource_name),222            params=self.credentials,223            payload=fields,224            )225        # check that it made the right number of environments226        self._test_filter_list_by(u'profile', self.profile_fixture.id, 1)227    def test_patch_no_include_no_exclude(self):228        """Sending hashes without include or exclude should do the same as229        sending regular uri strings."""230        logger.info("test_patch_no_include_no_exclude")231        fields = self.new_object_data232        # create more elements for each category233        for x in range(2):234            self.F.ElementFactory(category=self.category_fixture1, name="A %s" % x)235            self.F.ElementFactory(category=self.category_fixture2, name="B %s" % x)236            self.F.ElementFactory(category=self.category_fixture3, name="C %s" % x)237        # modify fields to send categories rather than elements238        fields.pop('elements')239        fields['categories'] = [240            {241                u'category': unicode(self.get_detail_url(242                    "category", str(self.category_fixture1.id))),243                },244            {245                u'category': unicode(self.get_detail_url(246                    "category", str(self.category_fixture2.id))),247                },248            {249                u'category': unicode(self.get_detail_url(250                    "category", str(self.category_fixture3.id))),251                }, ]252        # do the create253        res = self.patch(254            self.get_list_url(self.resource_name),255            params=self.credentials,256            payload=fields,257            )258        # check that it made the right number of environments...

Cinematic.spec.js

Source:Cinematic.spec.js

1/* eslint-env jasmine */2import {3  getLeftCharacterThangTypeSlug,4  getRightCharacterThangTypeSlug,5  getLeftHero,6  getRightHero,7  getClearBackgroundObject,8  getBackgroundObject,9  getBackgroundObjectDelay,10  getBackground,11  getClearText,12  getSpeaker,13  getBackgroundSlug,14  getExitCharacter,15  getTextPosition,16  getText,17  getCamera,18  getTextAnimationLength,19  getSpeakingAnimationAction,20  getSetupMusic,21  getSoundEffects,22  getWaitUserInput,23  getLanguageFilter,24  getHeroPet25} from '../../../app/schemas/models/selectors/cinematic'26/**27 * This data can be used to check that none of the selectors that match28 * the left or right character work.29 * Intentionally invalid data.30 */31const invalidThangTypesSetupData = [32  { shotSetup: {} },33  { dialogNodes: [] },34  { shotSetup: { camera: 'dual' } },35  { shotSetup: { rightThangType: {} } },36  { shotSetup: { backgroundArt: {} } },37  { shotSetup: { leftThangType: undefined } },38  { shotSetup: { leftThangType: { slug: 'abc', rand: 123 } } },39  { shotSetup: { rightThangType: undefined } },40  { shotSetup: { rightThangType: { slug: 'abc', rand: 123 } } }41]42describe('Cinematic', () => {43  describe('Selectors', () => {44    getCharacterThangTypeSlugTest(getLeftCharacterThangTypeSlug, 'getLeftCharacterThangTypeSlug', invalidThangTypesSetupData, 'leftThangType')45    getCharacterThangTypeSlugTest(getRightCharacterThangTypeSlug, 'getRightCharacterThangTypeSlug', invalidThangTypesSetupData, 'rightThangType')46    it('getLeftCharacterThangTypeSlug', () => {47      const result = getLeftCharacterThangTypeSlug(shotFixture1)48      expect(result).toBeUndefined()49      const result2 = getLeftCharacterThangTypeSlug(shotFixture2)50      expect(result2).toEqual({ slug: 'fake-slug-thangtype', enterOnStart: false, thang: { scaleX: 1.2, scaleY: 1.2, pos: { x: -30, y: -72 } } })51    })52    it('getRightCharacterThangTypeSlug', () => {53      const result = getRightCharacterThangTypeSlug(shotFixture2)54      expect(result).toBeUndefined()55      const result2 = getRightCharacterThangTypeSlug(shotFixture1)56      expect(result2).toEqual({ slug: 'fake-slug-thangtype', enterOnStart: false, thang: { scaleX: 1.2, scaleY: 1.2, pos: { x: 30, y: -72 } } })57    })58    it('getLeftHero', () => {59      const result = getLeftHero(shotFixture1)60      expect(result).toEqual({ enterOnStart: true, thang: { scaleX: 1, scaleY: 13, pos: { x: 3, y: 10 } } })61      const result2 = getLeftHero(shotFixture2)62      expect(result2).toBeUndefined()63    })64    it('getRightHero', () => {65      const result = getRightHero(shotFixture2)66      expect(result).toEqual({ enterOnStart: true, thang: { scaleX: 1, scaleY: 13, pos: { x: 3, y: 10 } } })67      const result2 = getRightHero(shotFixture1)68      expect(result2).toBeUndefined()69    })70    it('getClearBackgroundObject', () => {71      const result = getClearBackgroundObject(shotFixture1.dialogNodes[0])72      expect(result).toEqual(7331)73      const result2 = getClearBackgroundObject(shotFixture2.dialogNodes[0])74      expect(result2).toBeUndefined()75    })76    it('getBackgroundObject', () => {77      const result = getBackgroundObject(shotFixture1.dialogNodes[0])78      expect(result).toEqual({ scaleX: 1, scaleY: 1, pos: { x: 0, y: 0 }, type: { slug: 'background-obj-fixture' } })79      const result2 = getBackgroundObject(shotFixture2.dialogNodes[0])80      expect(result2).toBeUndefined()81    })82    it('getBackgroundObjectDelay', () => {83      const result = getBackgroundObjectDelay(shotFixture1.dialogNodes[0])84      expect(result).toEqual(1337)85      const result2 = getBackgroundObjectDelay(shotFixture2.dialogNodes[0])86      expect(result2).toBeUndefined()87    })88    it('getBackground', () => {89      const result = getBackground(shotFixture1)90      expect(result).toEqual({ slug: 'background-fixture-slug', thang: { scaleX: 0.3, scaleY: 0.2, pos: { x: 17, y: 18 } } })91      const result2 = getBackground(shotFixture2)92      expect(result2).toBeUndefined()93    })94    it('getClearText', () => {95      const result = getClearText(shotFixture1.dialogNodes[0])96      expect(result).toEqual(false)97      const result2 = getClearText(shotFixture2.dialogNodes[0])98      expect(result2).toEqual(true)99    })100    it('getSpeaker', () => {101      const result = getSpeaker(shotFixture1.dialogNodes[0])102      expect(result).toEqual('left')103      const result2 = getSpeaker(shotFixture2.dialogNodes[0])104      expect(result2).toEqual('right')105    })106    it('getBackgroundSlug', () => {107      const result = getBackgroundSlug(shotFixture1)108      expect(result).toEqual('background-fixture-slug')109      const result2 = getBackgroundSlug(shotFixture2)110      expect(result2).toBeUndefined()111    })112    it('getExitCharacter', () => {113      const result = getExitCharacter(shotFixture1.dialogNodes[0])114      expect(result).toEqual('both')115      const result2 = getExitCharacter(shotFixture2.dialogNodes[0])116      expect(result2).toBeUndefined()117    })118    it('getTextPosition', () => {119      const result = getTextPosition(shotFixture1.dialogNodes[0])120      expect(result).toBeUndefined()121      const result2 = getTextPosition(shotFixture2.dialogNodes[0])122      expect(result2).toEqual({123        x: 40,124        y: 10125      })126    })127    it('getText', () => {128      const result = getText(shotFixture1.dialogNodes[0])129      expect(result).toEqual('hello, world')130      const result2 = getText(shotFixture2.dialogNodes[0])131      expect(result2).toBeUndefined()132    })133    it('getCamera', () => {134      const result = getCamera(shotFixture1)135      expect(result).toEqual({ pos: { x: 2, y: 0 }, zoom: 2 })136      const result2 = getCamera(shotFixture2)137      expect(result2).toBeUndefined()138      expect(getCamera(undefined)).toBeUndefined()139    })140    it('getTextAnimationLength', () => {141      const result = getTextAnimationLength(shotFixture1.dialogNodes[1])142      expect(result).toEqual(42)143      const result2 = getTextAnimationLength(shotFixture2.dialogNodes[0])144      expect(result2).toBeUndefined()145    })146    it('getSpeakingAnimationAction', () => {147      const result = getSpeakingAnimationAction(shotFixture1.dialogNodes[1])148      expect(result).toEqual('talkyAnimation')149      const result2 = getSpeakingAnimationAction(shotFixture2.dialogNodes[0])150      expect(result2).toBeUndefined()151    })152    it('getSoundEffects', () => {153      const result = getSoundEffects(shotFixture1.dialogNodes[0])154      expect(result).toEqual([ { sound: { mp3: 'path/music' }, triggerStart: 0 } ])155      const result2 = getSoundEffects(shotFixture2.dialogNodes[0])156      expect(result2).toEqual([ { sound: { mp3: 'path/music' }, triggerStart: 30 } ])157    })158    it('getSetupMusic', () => {159      const result = getSetupMusic(shotFixture1)160      expect(result).toEqual({ ogg: 'path/music', mp3: 'path/music/mp3' })161      const result2 = getSetupMusic(shotFixture2)162      expect(result2).toBeUndefined()163    })164    it('getWaitUserInput', () => {165      expect(getWaitUserInput({ waitUserInput: false })).toEqual(false)166      expect(getWaitUserInput({})).toEqual(true)167      expect(getWaitUserInput()).toEqual(true)168      expect(getWaitUserInput({ waitUserInput: true })).toEqual(true)169    })170    it('getLanguageFilter', () => {171      expect(getLanguageFilter({})).toBeUndefined()172      expect(getLanguageFilter()).toBeUndefined()173      expect(getLanguageFilter({ programmingLanguageFilter: 'python' })).toEqual('python')174      expect(getLanguageFilter({ programmingLanguageFilter: 'javascript' })).toEqual('javascript')175    })176    it('getHeroPet', () => {177      const result = getHeroPet(shotFixture1)178      expect(result).toEqual({ slug: 'hero-dog-slug', thang: { scaleX: 1, scaleY: 2, pos: { x: 2, y: 0 } } })179      const result2 = getHeroPet(shotFixture2)180      expect(result2).toBeUndefined()181    })182  })183})184// Test for left and right character selectors.185function getCharacterThangTypeSlugTest (selector, side, data, characterProperty) {186  describe(`${side}`, () => {187    it('returns undefined when passed nothing', () => {188      expect(selector(undefined)).toBeUndefined()189    })190    it('returns undefined if the left thangType doesn\'t have type', () => {191      for (const testData of data) {192        expect(selector(testData)).toBeUndefined()193      }194    })195  })196}197// Fixture testing selectors for cinematics.198var shotFixture1 = {199  shotSetup: {200    leftThangType: {201      thangType: {202        type: 'hero',203        pos: {204          x: 3,205          y: 10206        },207        scaleX: 1,208        scaleY: 13209      },210      enterOnStart: true211    },212    rightThangType: {213      thangType: {214        type: {215          slug: 'fake-slug-thangtype'216        }217      }218    },219    heroPetThangType: {220      type: {221        slug: 'hero-dog-slug'222      },223      pos: {224        x: 2225      },226      scaleY: 2227    },228    backgroundArt: {229      type: {230        slug: 'background-fixture-slug'231      },232      pos: {233        x: 17,234        y: 18235      },236      scaleX: 0.3,237      scaleY: 0.2238    },239    camera: {240      pos: {241        x: 2242      },243      zoom: 2244    },245    music: {246      ogg: 'path/music',247      mp3: 'path/music/mp3'248    }249  },250  dialogNodes: [251    {252      dialogClear: false,253      exitCharacter: 'both',254      text: 'hello, world',255      triggers: {256        backgroundObject: {257          thangType: {258            type: {259              slug: 'background-obj-fixture'260            }261          },262          triggerStart: 1337263        },264        clearBackgroundObject: {265          triggerStart: 7331266        },267        soundFxTriggers: [268          {269            sound: {270              mp3: 'path/music'271            }272          }273        ]274      }275    },276    {277      dialogClear: false,278      textAnimationLength: 42,279      speakingAnimationAction: 'talkyAnimation'280    }281  ]282}283var shotFixture2 = {284  shotSetup: {285    rightThangType: {286      thangType: {287        type: 'hero',288        pos: {289          x: 3,290          y: 10291        },292        scaleX: 1,293        scaleY: 13294      },295      enterOnStart: true296    },297    leftThangType: {298      thangType: {299        type: {300          slug: 'fake-slug-thangtype'301        }302      }303    }304  },305  dialogNodes: [306    {307      speaker: 'right',308      triggers: {309        soundFxTriggers: [310          {311            sound: {312              mp3: 'path/music'313            },314            triggerStart: 30315          }316        ]317      },318      textLocation: {319        x: 40,320        y: 10321      }322    }323  ]...

extract_google_test_list_test.py

Source:extract_google_test_list_test.py

1# Copyright 2014 The Chromium Authors. All rights reserved.2# Use of this source code is governed by a BSD-style license that can be3# found in the LICENSE file.4import StringIO5import unittest6from src.build.util.test import extract_google_test_list7class TestExtractGoogleTestList(unittest.TestCase):8  def _parse_cpp_test_list(self, content):9    """Simple wrapper of _parse_test_list for C++ testing."""10    return extract_google_test_list._parse_test_list(11        StringIO.StringIO(content),12        extract_google_test_list._CPP_TEST_METHOD_PATTERN)13  def test_parser_cpp_test_list(self):14    # Simple cases for TEST_F.15    self.assertEquals(16        ['Fixture1#test_method1',17         'Fixture1#test_method2',18         'Fixture2#test_method1',19         'Fixture2#test_method2'],20        self._parse_cpp_test_list('\n'.join([21            'TEST_F(Fixture1, test_method1) {',22            '  // test body',23            '}',24            '',25            'TEST_F(Fixture1, test_method2) {',26            '  // test body',27            '}',28            '',29            'TEST_F(Fixture2, test_method1) {',30            '  // test body',31            '}',32            '',33            'TEST_F(Fixture2, test_method2) {',34            '  // test body',35            '}'])))36    # Simple cases for TEST.37    self.assertEquals(38        ['Fixture1#test_method1',39         'Fixture1#test_method2',40         'Fixture2#test_method1',41         'Fixture2#test_method2'],42        self._parse_cpp_test_list('\n'.join([43            'TEST(Fixture1, test_method1) {',44            '  // test body',45            '}',46            '',47            'TEST(Fixture1, test_method2) {',48            '  // test body',49            '}',50            '',51            'TEST(Fixture2, test_method1) {',52            '  // test body',53            '}',54            '',55            'TEST(Fixture2, test_method2) {',56            '  // test body',57            '}'])))58    # Line breaks around fixture and test name.59    self.assertEquals(60        ['Fixture1#test_method1',61         'Fixture1#test_method2',62         'Fixture1#test_method3'],63        self._parse_cpp_test_list('\n'.join([64            'TEST_F(Fixture1,'65            '       test_method1) {',66            '  // test body',67            '}',68            '',69            'TEST_F('70            '    Fixture1, test_method2) {',71            '  // test body',72            '}',73            '',74            'TEST_F('75            '    Fixture1,'76            '    test_method3) {',77            '  // test body',78            '}'])))79  def _parse_javascript_test_list(self, content):80    """Simple wrapper of _parse_test_list for JavaScript testing."""81    return extract_google_test_list._parse_test_list(82        StringIO.StringIO(content),83        extract_google_test_list._JAVASCRIPT_TEST_METHOD_PATTERN)84  def test_parse_javascript_test_list(self):85    # Simple cases.86    self.assertEquals(87        ['Fixture1#test_method1',88         'Fixture1#test_method2',89         'Fixture2#test_method1',90         'Fixture2#test_method2'],91        self._parse_javascript_test_list('\n'.join([92            'TEST_F(Fixture1, "test_method1", function() {',93            '  // Some test body code;',94            '});',95            '',96            'TEST_F(Fixture1, "test_method2", function() {',97            '  // Some test body code;',98            '});',99            '',100            'TEST_F(Fixture2, "test_method1", function() {',101            '  // Some test body code;',102            '});',103            '',104            'TEST_F(Fixture2, "test_method2", function() {',105            '  // Some test body code;',106            '});',107            ''])))108    # Some line breaks around the parameters.109    self.assertEquals(110        ['Fixture1#test_method1',111         'Fixture1#test_method2',112         'Fixture1#test_method3',113         'Fixture1#test_method4'],114        self._parse_javascript_test_list('\n'.join([115            'TEST_F(Fixture1, "test_method1",',116            '       function() {',117            '  // Some test body code;',118            '});',119            '',120            'TEST_F(Fixture1,',121            '       "test_method2", function() {',122            '  // Some test body code;',123            '});',124            '',125            'TEST_F(',126            '    Fixture1, "test_method3", function() {',127            '  // Some test body code;',128            '});',129            '',130            'TEST_F(',131            '    Fixture1,',132            '    "test_method4",',133            '    function() {',134            '  // Some test body code;',135            '});',136            ''])))137    # The definition of TEST_F should not be included.138    self.assertEquals(139        [],140        self._parse_javascript_test_list('\n'.join([141            'function TEST_F(fixtureClass, testName, '142            'testFunc, opt_caseName) {',143            '  // The definition code line 1.',144            '  // The definition code line 2.',145            '  // The definition code line 3.',146            '}'])))147if __name__ == '__main__':...

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