How to use include_partition method in autotest

Best Python code snippet using autotest_python

storage_layers_test.py

Source:storage_layers_test.py

1#!/usr/bin/env python2# This software was developed at the National Institute of Standards3# and Technology in whole or in part by employees of the Federal4# Government in the course of their official duties. Pursuant to5# title 17 Section 105 of the United States Code portions of this6# software authored by NIST employees are not subject to copyright7# protection and are in the public domain. For portions not authored8# by NIST employees, NIST has been granted unlimited rights. NIST9# assumes no responsibility whatsoever for its use by other parties,10# and makes no guarantees, expressed or implied, about its quality,11# reliability, or any other characteristic.12#13# We would appreciate acknowledgement if the software is used.14__version__ = "0.3.1"15import os16import sys17import hashlib18import logging19import typing20import dfxml.objects as Objects21import libtest22_logger = logging.getLogger(os.path.basename(__file__))23TEST_BYTE_STRING_1 = b"Test string 1"24TEST_BYTE_STRING_2 = b"Test string 2"25TEST_BYTE_STRING_3 = b"Test string 3"26TEST_BYTE_STRING_4 = b"Test string 4"27TEST_BYTE_STRING_5 = b"Test string 5"28tmphash = hashlib.sha512()29tmphash.update(TEST_BYTE_STRING_1)30TEST_HASH_1 = tmphash.hexdigest()31tmphash = hashlib.sha512()32tmphash.update(TEST_BYTE_STRING_2)33TEST_HASH_2 = tmphash.hexdigest()34tmphash = hashlib.sha512()35tmphash.update(TEST_BYTE_STRING_3)36TEST_HASH_3 = tmphash.hexdigest()37tmphash = hashlib.sha512()38tmphash.update(TEST_BYTE_STRING_4)39TEST_HASH_4 = tmphash.hexdigest()40tmphash = hashlib.sha512()41tmphash.update(TEST_BYTE_STRING_5)42TEST_HASH_5 = tmphash.hexdigest()43def _test_file_in_non_fs_levels_deep(44  include_disk_image : bool,45  include_partition_system : bool,46  include_partition : bool,47  include_file_system : bool48) -> None:49    """50    This test follows a simple, vertical storage layer stack, but adds a file at each layer.51    """52    dobj = Objects.DFXMLObject(version="1.2.0")53    # Add file to top-level document.54    fobj_dobj = Objects.FileObject()55    fobj_dobj.alloc_inode = False56    fobj_dobj.alloc_name = False57    fobj_dobj.sha512 = TEST_HASH_158    dobj.append(fobj_dobj)59    appender_stack : typing.List[Objects.AbstractParentObject] = [dobj]60    if include_disk_image:61        # Add disk image to top-level document.62        diobj = Objects.DiskImageObject()63        appender_stack[-1].append(diobj)64        appender_stack.append(diobj)65        # Add file to disk image.66        fobj_diobj = Objects.FileObject()67        fobj_diobj.alloc_inode = False68        fobj_diobj.alloc_name = False69        fobj_diobj.sha512 = TEST_HASH_270        diobj.append(fobj_diobj)71    if include_partition_system:72        # Add partition system to disk image.73        psobj = Objects.PartitionSystemObject()74        appender_stack[-1].append(psobj)75        appender_stack.append(psobj)76        # Add file to partition system.77        fobj_psobj = Objects.FileObject()78        fobj_psobj.alloc_inode = False79        fobj_psobj.alloc_name = False80        fobj_psobj.sha512 = TEST_HASH_381        psobj.append(fobj_psobj)82    if include_partition:83        # Add partition to partition system, but not disk image.84        if not (include_disk_image and not include_partition_system):85            pobj = Objects.PartitionObject()86            appender_stack[-1].append(pobj)87            appender_stack.append(pobj)88            # Add file to partition.89            fobj_pobj = Objects.FileObject()90            fobj_pobj.alloc_inode = False91            fobj_pobj.alloc_name = False92            fobj_pobj.sha512 = TEST_HASH_493            pobj.append(fobj_pobj)94    if include_file_system:95        # Add file system to anything but a partition system.96        if not (include_partition_system and not include_partition):97            vobj = Objects.VolumeObject()98            appender_stack[-1].append(vobj)99            appender_stack.append(vobj)100            # Add file to file system.101            fobj_vobj = Objects.FileObject()102            fobj_vobj.sha512 = TEST_HASH_5103            vobj.append(fobj_vobj)104    # Do file I/O round trip.105    (tmp_filename, dobj_reconst) = libtest.file_round_trip_dfxmlobject(dobj)106    try:107        container_stack = [dobj_reconst]108        assert dobj_reconst.files[0].sha512 == TEST_HASH_1109        if include_disk_image:110            diobj_reconst = container_stack[-1].disk_images[0]111            container_stack.append(diobj_reconst)112            assert diobj_reconst.files[0].sha512 == TEST_HASH_2113        if include_partition_system:114            psobj_reconst = container_stack[-1].partition_systems[0]115            container_stack.append(psobj_reconst)116            assert psobj_reconst.files[0].sha512 == TEST_HASH_3117        if include_partition:118            if not (include_disk_image and not include_partition_system):119                pobj_reconst = container_stack[-1].partitions[0]120                container_stack.append(pobj_reconst)121                assert pobj_reconst.files[0].sha512 == TEST_HASH_4122        if include_file_system:123            if not (include_partition_system and not include_partition):124                vobj_reconst = container_stack[-1].volumes[0]125                assert vobj_reconst.files[0].sha512 == TEST_HASH_5126    except:127        _logger.debug("tmp_filename = %r." % tmp_filename)128        raise129    os.remove(tmp_filename)130def test_file_in_non_fs_levels_deep() -> None:131    for include_disk_image in [True, False]:132        for include_partition_system in [True, False]:133            for include_partition in [True, False]:134                for include_file_system in [True, False]:135                    try:136                        _test_file_in_non_fs_levels_deep(137                          include_disk_image,138                          include_partition_system,139                          include_partition,140                          include_file_system141                        )142                    except:143                        _logger.debug("include_disk_image = %r." % include_disk_image)144                        _logger.debug("include_partition_system = %r." % include_partition_system)145                        _logger.debug("include_partition = %r." % include_partition)146                        _logger.debug("include_file_system = %r." % include_file_system)147                        raise148def _test_file_in_non_fs_levels_flat(149  include_disk_image : bool,150  include_partition_system : bool,151  include_partition : bool,152  include_file_system : bool153) -> None:154    """155    This test follows a simple, horizontal storage layer stack (every container attached to top document object), and adds a file for each container.156    """157    dobj = Objects.DFXMLObject(version="1.2.0")158    # Add file to top-level document.159    fobj_dobj = Objects.FileObject()160    fobj_dobj.alloc_inode = False161    fobj_dobj.alloc_name = False162    fobj_dobj.sha512 = TEST_HASH_1163    dobj.append(fobj_dobj)164    if include_disk_image:165        # Add disk image.166        diobj = Objects.DiskImageObject()167        dobj.append(diobj)168        # Add file to disk image.169        fobj_diobj = Objects.FileObject()170        fobj_diobj.alloc_inode = False171        fobj_diobj.alloc_name = False172        fobj_diobj.sha512 = TEST_HASH_2173        diobj.append(fobj_diobj)174    if include_partition_system:175        # Add partition system.176        psobj = Objects.PartitionSystemObject()177        dobj.append(psobj)178        # Add file to partition system.179        fobj_psobj = Objects.FileObject()180        fobj_psobj.alloc_inode = False181        fobj_psobj.alloc_name = False182        fobj_psobj.sha512 = TEST_HASH_3183        psobj.append(fobj_psobj)184    if include_partition:185        # Add partition.186        pobj = Objects.PartitionObject()187        dobj.append(pobj)188        # Add file to partition.189        fobj_pobj = Objects.FileObject()190        fobj_pobj.alloc_inode = False191        fobj_pobj.alloc_name = False192        fobj_pobj.sha512 = TEST_HASH_4193        pobj.append(fobj_pobj)194    if include_file_system:195        # Add file system.196        vobj = Objects.VolumeObject()197        dobj.append(vobj)198        # Add file to file system.199        fobj_vobj = Objects.FileObject()200        fobj_vobj.sha512 = TEST_HASH_5201        vobj.append(fobj_vobj)202    # Do file I/O round trip.203    (tmp_filename, dobj_reconst) = libtest.file_round_trip_dfxmlobject(dobj)204    try:205        assert dobj_reconst.files[0].sha512 == TEST_HASH_1206        if include_disk_image:207            diobj_reconst = dobj_reconst.disk_images[0]208            assert diobj_reconst.files[0].sha512 == TEST_HASH_2209        if include_partition_system:210            psobj_reconst = dobj_reconst.partition_systems[0]211            assert psobj_reconst.files[0].sha512 == TEST_HASH_3212        if include_partition:213            pobj_reconst = dobj_reconst.partitions[0]214            assert pobj_reconst.files[0].sha512 == TEST_HASH_4215        if include_file_system:216            vobj_reconst = dobj_reconst.volumes[0]217            assert vobj_reconst.files[0].sha512 == TEST_HASH_5218    except:219        _logger.debug("tmp_filename = %r." % tmp_filename)220        raise221    os.remove(tmp_filename)222def test_file_in_non_fs_levels_flat() -> None:223    for include_disk_image in [True, False]:224        for include_partition_system in [True, False]:225            for include_partition in [True, False]:226                for include_file_system in [True, False]:227                    try:228                        _test_file_in_non_fs_levels_flat(229                          include_disk_image,230                          include_partition_system,231                          include_partition,232                          include_file_system233                        )234                    except:235                        _logger.debug("include_disk_image = %r." % include_disk_image)236                        _logger.debug("include_partition_system = %r." % include_partition_system)237                        _logger.debug("include_partition = %r." % include_partition)238                        _logger.debug("include_file_system = %r." % include_file_system)239                        raise240def test_solaris_ps_in_partition() -> None:241    dobj = Objects.DFXMLObject(version="1.2.0")242    psobj_outer = Objects.PartitionSystemObject()243    dobj.append(psobj_outer)244    # Add file to outer partition system.245    fobj_psobj_outer = Objects.FileObject()246    fobj_psobj_outer.alloc_inode = False247    fobj_psobj_outer.alloc_name = False248    fobj_psobj_outer.sha512 = TEST_HASH_1249    psobj_outer.append(fobj_psobj_outer)250    pobj = Objects.PartitionObject()251    psobj_outer.append(pobj)252    # Add file to partition.253    fobj_pobj = Objects.FileObject()254    fobj_pobj.alloc_inode = False255    fobj_pobj.alloc_name = False256    fobj_pobj.sha512 = TEST_HASH_2257    pobj.append(fobj_pobj)258    psobj_inner = Objects.PartitionSystemObject()259    pobj.append(psobj_inner)260    # Add file to inner partition system.261    fobj_psobj_inner = Objects.FileObject()262    fobj_psobj_inner.alloc_inode = False263    fobj_psobj_inner.alloc_name = False264    fobj_psobj_inner.sha512 = TEST_HASH_3265    psobj_inner.append(fobj_psobj_inner)266    # Do file I/O round trip.267    (tmp_filename, dobj_reconst) = libtest.file_round_trip_dfxmlobject(dobj)268    try:269        psobj_outer_reconst = dobj_reconst.partition_systems[0]270        pobj_reconst = psobj_outer_reconst.partitions[0]271        psobj_inner_reconst = pobj_reconst.partition_systems[0]272        assert psobj_outer_reconst.files[0].sha512 == TEST_HASH_1273        assert pobj_reconst.files[0].sha512 == TEST_HASH_2274        assert psobj_inner_reconst.files[0].sha512 == TEST_HASH_3275    except:276        _logger.debug("tmp_filename = %r." % tmp_filename)277        raise278    os.remove(tmp_filename)279def test_partition_in_partition() -> None:280    #TODO Remove "+" on DFXML Schema 1.3.0 tracking.281    dobj = Objects.DFXMLObject(version="1.2.0+")282    psobj = Objects.PartitionSystemObject()283    psobj.pstype_str = "mbr"284    dobj.append(psobj)285    pobj_outer = Objects.PartitionObject()286    psobj.append(pobj_outer)287    pobj_inner = Objects.PartitionObject()288    pobj_outer.append(pobj_inner)289    # Do file I/O round trip.290    (tmp_filename, dobj_reconst) = libtest.file_round_trip_dfxmlobject(dobj)291    try:292        psobj_reconst = dobj_reconst.partition_systems[0]293        pobj_outer_reconst = psobj_reconst.partitions[0]294        pobj_inner_reconst = pobj_outer_reconst.partitions[0]295        assert isinstance(pobj_inner_reconst, Objects.PartitionObject)296    except:297        _logger.debug("tmp_filename = %r." % tmp_filename)298        raise299    os.remove(tmp_filename)300def test_hfsplus_in_hfs() -> None:301    dobj = Objects.DFXMLObject(version="1.2.0")302    vobj_outer = Objects.VolumeObject()303    vobj_outer.ftype_str = "hfs"304    dobj.append(vobj_outer)305    vobj_inner = Objects.VolumeObject()306    vobj_inner.ftype_str = "hfsplus"307    vobj_outer.append(vobj_inner)308    # Do file I/O round trip.309    (tmp_filename, dobj_reconst) = libtest.file_round_trip_dfxmlobject(dobj)310    try:311        vobj_outer_reconst = dobj_reconst.volumes[0]312        vobj_inner_reconst = vobj_outer_reconst.volumes[0]313        assert isinstance(vobj_inner_reconst, Objects.VolumeObject)314        assert vobj_outer_reconst.ftype_str == "hfs"315        assert vobj_inner_reconst.ftype_str == "hfsplus"316    except:317        _logger.debug("tmp_filename = %r." % tmp_filename)318        raise319    os.remove(tmp_filename)320def test_disk_image_in_file_system() -> None:321    dobj = Objects.DFXMLObject(version="1.2.0")322    vobj = Objects.VolumeObject()323    vobj.ftype_str = "iso9660"324    dobj.append(vobj)325    fobj_vobj = Objects.FileObject()326    fobj_vobj.sha512 = TEST_HASH_1327    vobj.append(fobj_vobj)328    diobj = Objects.DiskImageObject()329    vobj.append(diobj)330    fobj_diobj = Objects.FileObject()331    fobj_diobj.alloc_inode = False332    fobj_diobj.alloc_name = False333    fobj_diobj.sha512 = TEST_HASH_2334    diobj.append(fobj_diobj)335    # Do file I/O round trip.336    (tmp_filename, dobj_reconst) = libtest.file_round_trip_dfxmlobject(dobj)337    try:338        vobj_reconst = dobj_reconst.volumes[0]339        diobj_reconst = vobj_reconst.disk_images[0]340        assert vobj_reconst.files[0].sha512 == TEST_HASH_1341        assert diobj_reconst.files[0].sha512 == TEST_HASH_2342    except:343        _logger.debug("tmp_filename = %r." % tmp_filename)344        raise...

ps1.py

Source:ps1.py

1###########################2# 6.00.2x Problem Set 1: Space Cows 3from ps1_partition import get_partitions4import time5import datetime6#================================7# Part A: Transporting Space Cows8#================================9def load_cows(filename):10    """11    Read the contents of the given file.  Assumes the file contents contain12    data in the form of comma-separated cow name, weight pairs, and return a13    dictionary containing cow names as keys and corresponding weights as values.14    Parameters:15    filename - the name of the data file as a string16    Returns:17    a dictionary of cow name (string), weight (int) pairs18    """19    cow_dict = dict()20    f = open(filename, 'r')21    22    for line in f:23        line_data = line.split(',')24        cow_dict[line_data[0]] = int(line_data[1])25    return cow_dict26# Problem 127def greedy_cow_transport(cows,limit=10):28    """29    Uses a greedy heuristic to determine an allocation of cows that attempts to30    minimize the number of spaceship trips needed to transport all the cows. The31    returned allocation of cows may or may not be optimal.32    The greedy heuristic should follow the following method:33    1. As long as the current trip can fit another cow, add the largest cow that will fit34        to the trip35    2. Once the trip is full, begin a new trip to transport the remaining cows36    Does not mutate the given dictionary of cows.37    Parameters:38    cows - a dictionary of name (string), weight (int) pairs39    limit - weight limit of the spaceship (an int)40    41    Returns:42    A list of lists, with each inner list containing the names of cows43    transported on a particular trip and the overall list containing all the44    trips45    """46    start = time.perf_counter_ns()47    trips = []48    # count = 049    moved_cows = []50    sorted_cows = sorted(cows.items(), key=lambda kv: kv[1], reverse=True)51    # print(sorted_cows)52    while len(moved_cows) < len(cows):53        current_weight = 054        cargo = []55        for cow_name, weight in sorted_cows:56            if cow_name not in moved_cows:57                # count += 158                if current_weight + weight <= limit:59                    # del sorted_cows[count - 1]60                    current_weight += weight61                    cargo.append(cow_name)62                    moved_cows.append(cow_name)63        trips.append(cargo)64    end = time.perf_counter_ns() - start65    print(end / 1000000)  # convert nanoseconds to milliseconds66    return trips67# Problem 268def brute_force_cow_transport(cows,limit=10):69    """70    Finds the allocation of cows that minimizes the number of spaceship trips71    via brute force.  The brute force algorithm should follow the following method:72    1. Enumerate all possible ways that the cows can be divided into separate trips73    2. Select the allocation that minimizes the number of trips without making any trip74        that does not obey the weight limitation75            76    Does not mutate the given dictionary of cows.77    Parameters:78    cows - a dictionary of name (string), weight (int) pairs79    limit - weight limit of the spaceship (an int)80    81    Returns:82    A list of lists, with each inner list containing the names of cows83    transported on a particular trip and the overall list containing all the84    trips85    """86    trips = []87    names = []88    count = 089    start = time.perf_counter_ns()90    # start = datetime.datetime.now()91    # start = time.time()92    for partition in get_partitions(sorted(cows.items(), key=lambda kv: kv[1], reverse=True)):93        # print("partition created", partition)94        count += 195        include_partition = True96        for cow_name_array in partition:97            if sum([c[1] for c in cow_name_array]) > limit:98                include_partition = False99                break100            else:101                names.append([c[0] for c in cow_name_array])102        if include_partition:103            print("Valid partition: ", partition)104            trips = names105            names = []106            # break after first valid partition is found, which contains the least about of trips107            break108    end = time.perf_counter_ns() - start109    # end = datetime.datetime.now() - start110    # end = time.time()111    # print(end - start)112    print(end)113    print(end / 1000000)  # convert nanoseconds to milliseconds114    print("brute force1", count)115    return trips116def brute_force_cow_transport_2(cows,limit=10):117    trip = []118    count = 0119    # start = datetime.datetime.now()120    # start = time.time()121    start = time.perf_counter_ns()122    # for partition in sorted(get_partitions(sorted(cows.items(), key=lambda kv: kv[1], reverse=True)), reverse=True):123    # for partition in get_partitions(sorted(cows.items(), key=lambda kv: kv[1], reverse=True)):124    for partition in sorted(get_partitions(cows.items()),  key=lambda x: len(x)):125        # print("partition created", partition)126        count += 1127        include_partition = True128        for cow_name_array in partition:129            total_weight = 0130            names = []131            for c in cow_name_array:132                name, weight = c133                total_weight += weight134                if total_weight > limit:135                    include_partition = False136                    break137                else:138                    names.append(name)139            if not include_partition:140                break141            else:142                trip.append(names)143            # if sum([c[1] for c in cow_name_array]) > limit:144            #     include_partition = False145            # else:146            #     names = [c[0] for c in cow_name_array]147        if include_partition:148            print("Valid partition: ", partition)149            # trip.append(names)150            # break after first valid partition is found, which contains the least about of trips151            break152    end = time.perf_counter_ns() - start153    # end = datetime.datetime.now() - start154    # end = time.time()155    # print(end - start)156    print(end)157    print(end / 1000000)  # convert nanoseconds to milliseconds158    print("brute force 2", count)159    return trip160def brute_force_cow_transport_clean(cows, limit=10):161    start = time.perf_counter_ns()162    trip = []163    for partition in sorted(get_partitions(cows.items()), key=lambda x: len(x)):164        include_partition = True165        trip = []166        for cow_name_array in partition:167            total_weight = 0168            names = []169            for c in cow_name_array:170                name, weight = c171                total_weight += weight172                if total_weight > limit:173                    include_partition = False174                    break175                else:176                    names.append(name)177            if not include_partition:178                break179            else:180                trip.append(names)181        if include_partition:182            # all_options.append(trip)183            # break after first valid partition is found, which contains the least about of trips184            break185    end = time.perf_counter_ns() - start186    print(end / 1000000)  # convert nanoseconds to milliseconds187    return trip188# Problem 3189def compare_cow_transport_algorithms():190    """191    Using the data from ps1_cow_data.txt and the specified weight limit, run your192    greedy_cow_transport and brute_force_cow_transport functions here. Use the193    default weight limits of 10 for both greedy_cow_transport and194    brute_force_cow_transport.195    196    Print out the number of trips returned by each method, and how long each197    method takes to run in seconds.198    Returns:199    Does not return anything.200    """201    # TODO: Your code here202    pass203"""204Here is some test data for you to see the results of your algorithms with. 205Do not submit this along with any of your answers. Uncomment the last two206lines to print the result of your problem.207"""208cows = load_cows("ps1_cow_data.txt")209limit=10210print(cows)211print(greedy_cow_transport(cows, limit))212# print(brute_force_cow_transport(cows, limit))213# print(brute_force_cow_transport_2(cows, limit))214print(brute_force_cow_transport_clean(cows, limit))215# cows = {'Lotus': 40, 'Horns': 25, 'Boo': 20, 'Milkshake': 40, 'MooMoo': 50, 'Miss Bella': 25}216# print(brute_force_cow_transport_2(cows, 100))217# print(brute_force_cow_transport_clean(cows, 100))218'''219cargo = []220part_cargo_count = 0221for cow_name_array in partition:222    # print(cow_name_array)223    current_weight = 0224    for cow_name in cow_name_array:225        current_weight += cows[cow_name]226        # current_weight = [c[1] for c in cows if c[0] == cow_name]227        # cargo_weight += current_weight228        cargo.append(cow_name)229        if current_weight > limit:230            cargo = []231            break232    if len(cargo) == 0:233        break234    part_cargo_count += 1235if part_cargo_count == len(partition):236    trips.append(partition)237    238      # print(count)  # 115975239    # print(cows)240    start = time.time()241    for partition in get_partitions(sorted(cows.items(), key=lambda kv: kv[1], reverse=True)):242        # print(partition)243        count += 1244    end = time.time()245    print(end - start)  # 0.5056478977203369246    print(count)  # 115975247    print(cows)    248   249   250   251               if sum([c[1] for c in cow_name_array]) <= limit:252                trips.append([c[0] for c in cow_name_array])253            else:254    ...

all_untampered_bulk_primary_cells_with_data.py

Source:all_untampered_bulk_primary_cells_with_data.py

1####################################################################################2#   This creates a list of experiments corresponding to untampered bulk experiments.3#   By 'untampered' I mean all experiments that have been treated in such a way that4#   a purposeful change in gene expression was induced.  This does not include5#   experiments that have been transfected with a control vector.6####################################################################################7from optparse import OptionParser8import json9import graph_lib10from graph_lib import graph11import kallisto_quantified_data_manager_hdf5_py3 as kqdm12EXCLUDE_TAGS = set([13    "experimental_treatment",14    "in_vitro_differentiated_cells",15    "stimulation",16    "infected",17    "diseased_cells",18    "alternate_assay",19    "cell_line",20    "single_cell",21    "tissue"22])23EXCEPT_EXCLUDE_TAGS = set([24    "transduced_control",25    "transfected_control",26    "sirna_treatment_control",27    "shrna_treatment_control"28])29def main():30    usage = "" # TODO 31    parser = OptionParser(usage=usage)32    parser.add_option("-o", "--out_file", help="Output file")33    (options, args) = parser.parse_args()34    annotation_f = args[0]35    out_f = options.out_file    36    with open(annotation_f, 'r') as f:37        annotation = json.load(f)38    tags_f = "/ua/mnbernstein/projects/tbcp/phenotyping/manage_data/tags/tags.json"39    tags_graph = import_tags_graph(tags_f)40    exclude_tags = set(EXCLUDE_TAGS)41    for ex_tag in EXCLUDE_TAGS:42        exclude_tags.update(tags_graph.ancestor_nodes(ex_tag))43    include_experiments = set()44    for annot_data in annotation['annotated_studies']:    45        for partition in annot_data['partitions']:46            include_partition = True47            for tag in partition['tags']:48                if tag not in EXCEPT_EXCLUDE_TAGS and tag in exclude_tags:49                    include_partition = False50                    break51            if include_partition:52                include_experiments.update(partition['experiments'])53    exps_w_data = set(kqdm.filter_for_experiments_in_db(include_experiments))54    include_experiments = set(include_experiments) & exps_w_data55    # Remove all experiments that have a NaN count value56    exps_list, data_matrix = kqdm.get_transcript_counts_for_experiments(57        include_experiments58    )59    found_nan_exps = set()60    for vec_i, vec in enumerate(data_matrix):61        if (vec_i + 1) % 100 == 0:62            print("Checked {}/{} vectors...".format(vec_i+1, len(data_matrix)))63        sum_vec = sum(vec)64        if sum_vec == 0.0:65            print("Experiment {} has a sum of zero...".format(exps_list[vec_i]))66            found_nan_exps.add(exps_list[vec_i])67    include_experiments = include_experiments - found_nan_exps   68 69    with open(out_f, 'w') as f:70        f.write(json.dumps(71            {72                "list_name": "all_untampered_bulk_primary_cells_with_data",73                "description": "These are all experiments that are not labelled with {}, but allows those labelled with {}.".format(74                    list(EXCLUDE_TAGS), 75                    list(EXCEPT_EXCLUDE_TAGS)76                ),77                "experiments": list(include_experiments)78            },79            indent=480        ))    81def import_tags_graph(tags_f):82    with open(tags_f, 'r') as f:83        tags_data = json.load(f)84    tags_nodes = tags_data['definitions']85    tags_source_to_targets = {86        x: []87        for x in tags_nodes88    }89    tags_source_to_targets.update(tags_data['implications'])90    tags_graph = graph.DirectedAcyclicGraph(tags_source_to_targets)91    return tags_graph92   93 94if __name__ == "__main__":...

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