class FindMergesBase(luigi.Task):
task_name = 'find_merges'
src_file = os.path.abspath(__file__)
allow_retry = False
path = luigi.Parameter()
key = luigi.Parameter()
out_path = luigi.Parameter()
clear_ids = luigi.ListParameter()
min_overlap = luigi.IntParameter()
dependency = luigi.TaskParameter()
def requires(self):
return self.dependency
def run_impl(self):
# get the global config and init configs
shebang = self.global_config_values()[0]
self.init(shebang)
# load the task config
config = self.get_task_config()
config.update({'path': self.path, 'key': self.key,
'clear_ids': self.clear_ids,
'out_path': self.out_path, 'min_overlap': self.min_overlap})
# prime and run the jobs
n_jobs = 1
self.prepare_jobs(n_jobs, None, config)
self.submit_jobs(n_jobs)
# wait till jobs finish and check for job success
self.wait_for_jobs()
self.check_jobs(n_jobs)
class NeuroproofLearnTaskMixin:
prob_loading_plan_path = luigi.Parameter(
description="Location of the probability prediction volume")
additional_locations = luigi.ListParameter(
default=[],
description="Additional probability map locations for Neuroproof")
seg_loading_plan_path = luigi.Parameter(
description="Location of the pipeline's watershed segmentation")
gt_loading_plan_path = luigi.Parameter(
description="Location of the ground truth segmentation")
output_location = luigi.Parameter(
description="Location for the classifier file. Use an .xml extension "
"to use the OpenCV random forest classifier. Use an .h5 extension "
"to use the Vigra random forest classifier")
def input(self):
loading_plans = [self.prob_loading_plan_path,
self.seg_loading_plan_path,
self.gt_loading_plan_path] + \
list(self.additional_locations)
for loading_plan in loading_plans:
for tgt in DestVolumeReader(loading_plan).get_source_targets():
yield tgt
def output(self):
return luigi.LocalTarget(self.output_location)
class ScheduledExternalProgramTask(ExternalProgramTask):
"""
Variant of :class:`luigi.contrib.external_program.ExternalProgramTask` that
executes the task with a :class:`Scheduler`.
"""
scheduler = luigi.ChoiceParameter(default=cfg.scheduler, choices=['local'] + [blurb for blurb in _schedulers], positional=False, significant=False, description='Scheduler to use for running the task')
scheduler_partition = luigi.OptionalParameter(default=cfg.scheduler_partition, positional=False, significant=False, description='Scheduler partition (or queue) to use if supported')
scheduler_extra_args = luigi.ListParameter(default=cfg.scheduler_extra_args, positional=False, significant=False, description='Extra arguments to pass to the scheduler')
walltime = luigi.TimeDeltaParameter(default=datetime.timedelta(), positional=False, significant=False, description='Amout of time to allocate for the task, default value of zero implies unlimited time')
cpus = luigi.IntParameter(default=1, positional=False, significant=False, description='Number of CPUs to allocate for the task')
memory = luigi.FloatParameter(default=1, positional=False, significant=False, description='Amount of memory (in gigabyte) to allocate for the task')
def __init__(self, *kwargs, **kwds):
super(ScheduledExternalProgramTask, self).__init__(*kwargs, **kwds)
try:
if self.scheduler != 'local':
self._scheduler = _schedulers[self.scheduler]
except KeyError:
raise ValueError('Unsupported scheduler {}'.format(self.scheduler))
@property
def resources(self):
if self.scheduler == 'local':
# local_jobs is actually constrained by the number of workers
return {'cpus': self.cpus, 'memory': self.memory}
else:
return {'{}_jobs'.format(self.scheduler): 1}
def run(self):
if self.scheduler == 'local':
return super(ScheduledExternalProgramTask, self).run()
else:
return self._scheduler.run_task(self)
class BootstrapSpokeAsTask(tasks.PuppetTask):
puppet_account_id = luigi.Parameter()
account_id = luigi.Parameter()
iam_role_arns = luigi.ListParameter()
role_name = luigi.Parameter()
permission_boundary = luigi.Parameter()
puppet_role_name = luigi.Parameter()
puppet_role_path = luigi.Parameter()
def params_for_results_display(self):
return {
"puppet_account_id": self.puppet_account_id,
"account_id": self.account_id,
}
def run(self):
partition = config.get_partition()
iam_role_arns_to_use = [
iam_role_arn for iam_role_arn in self.iam_role_arns
]
iam_role_arns_to_use.append(
f"arn:{partition}:iam::{self.account_id}:role/{self.role_name}")
sdk.bootstrap_spoke_as(
self.puppet_account_id,
iam_role_arns_to_use,
self.permission_boundary,
self.puppet_role_name,
self.puppet_role_path,
)
self.write_output(self.params_for_results_display())
class DeleteStoragePlan(RunMixin, RequiresMixin, luigi.Task):
'''a task to delete a storage plan's .tif files'''
task_namespace = "ariadne_microns_pipeline"
dependency_outputs = luigi.ListParameter(
default=[],
description="The outputs of this task's dependencies. The task "
"requests these as inputs so that all of them must be present "
"before the storage plan is deleted.")
storage_plan_path = luigi.Parameter(description="Storage plan to delete")
def input(self):
yield SrcVolumeTarget(self.storage_plan_path)
for dependency_output in self.dependency_outputs:
yield luigi.LocalTarget(dependency_output)
def output(self):
return luigi.LocalTarget(
SrcVolumeTarget.storage_plan_path_to_deleted_file(
self.storage_plan_path))
def ariadne_run(self):
self.input().next().remove()
with self.output().open("w") as fd:
fd.write("So sorry.\n")
class StringTieMerge(SlurmExecutableTask, CheckTargetNonEmpty):
lib_list = luigi.ListParameter()
output_prefix = luigi.Parameter()
library = None
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
# Set the SLURM request params for this task
self.mem = 2000
self.n_cpu = 4
self.partition = "nbi-medium"
def requires(self):
return [self.clone(StringTie, library=lib) for lib in self.lib_list]
def output(self):
return LocalTarget(os.path.join(self.base_dir, VERSION, PIPELINE, self.output_prefix, 'stringtie.gtf'))
def work_script(self):
self.temp = TemporaryFile()
return '''#!/bin/bash
source stringtie-1.3.0;
set -euo pipefail
echo '{input}' > {temp}
stringtie -p {n_cpu} --merge {temp} > {output}.temp
mv {output}.temp {output}
'''.format(input="\n".join([x.path for x in self.input()]),
output=self.output().path,
temp=self.temp.path,
n_cpu=self.n_cpu,
)
class CreateBwaIndices(FtarcTask):
fa_path = luigi.Parameter()
bwa = luigi.Parameter(default='bwa')
use_bwa_mem2 = luigi.BoolParameter(default=False)
add_index_args = luigi.ListParameter(default=list())
sh_config = luigi.DictParameter(default=dict())
priority = 100
def output(self):
return [
luigi.LocalTarget(f'{self.fa_path}.{s}')
for s in (['0123', 'amb', 'ann', 'pac', 'bwt.2bit.64'] if self.
use_bwa_mem2 else ['pac', 'bwt', 'ann', 'amb', 'sa'])
]
def run(self):
fa = Path(self.fa_path)
run_id = fa.stem
self.print_log(f'Create BWA indices:\t{run_id}')
self.setup_shell(run_id=run_id,
commands=self.bwa,
cwd=fa.parent,
**self.sh_config)
self.run_shell(args=(f'set -e && {self.bwa} index' +
''.join(f' {a}'
for a in self.add_index_args) + f' {fa}'),
input_files_or_dirs=fa,
output_files_or_dirs=[o.path for o in self.output()])
class CybersourceDataValidationTask(WarehouseMixin, luigi.WrapperTask):
import_date = luigi.DateParameter()
cybersource_merchant_ids = luigi.ListParameter(
config_path={'section': 'payment', 'name': 'cybersource_merchant_ids'},
)
def requires(self):
config = get_config()
for merchant_id in self.cybersource_merchant_ids:
section_name = 'cybersource:' + merchant_id
interval_start = luigi.DateParameter().parse(config.get(section_name, 'interval_start'))
interval_end = self.import_date
merchant_close_date = config.get(section_name, 'merchant_close_date', '')
if merchant_close_date:
parsed_date = luigi.DateParameter().parse(merchant_close_date)
interval_end = min(self.import_date, parsed_date)
cybersource_interval = date_interval.Custom(interval_start, interval_end)
for date in cybersource_interval:
filename = "cybersource_{}.tsv".format(merchant_id)
url = url_path_join(self.warehouse_path, 'payments', 'dt=' + date.isoformat(), filename)
yield ExternalURL(url=url)
class SmaliList(luigi.Task):
pkg = luigi.Parameter()
apks = luigi.ListParameter(significant=False)
def requires(self):
return [ApiExtractorRun(file_name=fn, pkg=self.pkg) for fn in self.apks]
def output(self):
output_file = os.path.join(cfg.soot_smalilist_folder,
self.pkg,
self.pkg + ".json")
return ExternalFileTarget(output_file)
def run(self):
app_smalilist = {}
for i in self.input():
with i['loc'].open() as data_file:
_, ver, _ = commons().get_apk_data(i['loc'].path)
smali = json.load(data_file)
# cast to set to remove duplicates
app_smalilist[ver] = list(set(smali))
with self.output().open('w') as data_file:
json.dump(app_smalilist, data_file, indent=2)
class TestDockerBuildBase(DockerBuildBase):
goals = luigi.ListParameter([])
def get_goal_class_map(self) -> Dict[str, DockerAnalyzeImageTask]:
goal_class_map = {
"test-analyze-image-1":
self.create_child_task(
task_class=TestDockerBuildBaseTestAnalyzeImage,
task_name="test-analyze-image-1"),
"test-analyze-image-2":
self.create_child_task(TestDockerBuildBaseTestAnalyzeImage,
task_name="test-analyze-image-2")
}
return goal_class_map
def get_default_goals(self) -> Set[str]:
goals = {"test-analyze-image-1"}
return goals
def get_goals(self):
return self.goals
def run_task(self):
build_tasks = self.create_build_tasks(False)
image_infos_futures = yield from self.run_dependencies(build_tasks)
image_infos = self.get_values_from_futures(image_infos_futures)
self.return_object(image_infos)
class PostImportDatabaseTask(SchemaManagementTask):
"""
Task needed to run after importing database into warehouse.
"""
# Override the standard roles here since these tables will be rather raw. We may want to restrict access to a
# subset of users.
roles = luigi.ListParameter(config_path={
'section': 'vertica-export',
'name': 'business_intelligence_team_roles'
}, )
@property
def queries(self):
return [
"DROP SCHEMA IF EXISTS {schema} CASCADE;".format(
schema=self.schema),
"ALTER SCHEMA {schema_loading} RENAME TO {schema};".format(
schema_loading=self.schema_loading, schema=self.schema),
"GRANT USAGE ON SCHEMA {schema} TO {roles};".format(
schema=self.schema, roles=self.vertica_roles),
"GRANT SELECT ON ALL TABLES IN SCHEMA {schema} TO {roles};".format(
schema=self.schema, roles=self.vertica_roles),
]
@property
def marker_name(self):
return 'post_database_import_{schema}_{date}'.format(
schema=self.schema, date=self.date.strftime('%Y-%m-%d'))
class lvl1(luigi.Task):
files = luigi.ListParameter()
outputpath = ""
def __init__(self,*args, **kwargs):
super(lvl1, self).__init__(*args, **kwargs)
self.conf = initConf()
self.preparePaths()
@basicLoggerDecorator(pipelineLogger)
def preparePaths(self):
self.outputpath = self.conf['lvl1_outputpath']
@basicLoggerDecorator(pipelineLogger)
def requires(self):
return []
@basicLoggerDecorator(pipelineLogger)
def output(self):
return luigi.LocalTarget(self.outputpath)
@basicLoggerDecorator(pipelineLogger)
def run(self):
with self.output().open('w') as f:
dakd.extract.prepareFiles(self.files,f)
class RGBAnnotationMapImage(luigi.Task):
input_path = luigi.Parameter()
rgb_components = luigi.ListParameter(default=[0, 1, 2])
src_data_path = luigi.Parameter()
render_tiles = luigi.BoolParameter(default=False)
def make_plot(self, da_emb):
return make_rgb_annotation_map_image(
da=da_emb,
rgb_components=self.rgb_components,
dataset_path=self.dataset_path,
)
def run(self):
da_emb = xr.open_dataarray(self.input_path)
fig, axes = self.make_plot(da_emb=da_emb)
Path(self.output().fn).parent.mkdir(exist_ok=True, parents=True)
plt.savefig(self.output().fn, fig=fig, bbox_inches="tight")
def output(self):
image_fullpath = Path(self.input_path)
src_path, src_fn = image_fullpath.parent, image_fullpath.name
fn_out = src_fn.replace(
".nc",
".rgb_map.{}__comp.png".format("_".join(
[str(v) for v in self.rgb_components])),
)
p = Path(src_path) / fn_out
return luigi.LocalTarget(str(p))
class PreprocessingPipeline(luigi.Task):
datasets = luigi.ListParameter(description="Names of the datasets to use")
export_csv = luigi.BoolParameter(
description="If specified, exports spectra as csv files",
significant=False,
visibility=luigi.parameter.ParameterVisibility.HIDDEN)
pool_size = luigi.IntParameter(
default=os.cpu_count() or 1,
description=
'Size of parallel pool to use for computations. Choose carefully '
'to not exceed the memory.',
significant=False,
visibility=luigi.parameter.ParameterVisibility.HIDDEN)
def requires(self):
for dataset in self.datasets:
yield AssembleMetadata(dataset=dataset, pool_size=self.pool_size)
for dataset in self.datasets:
yield MergeDataset(dataset=dataset,
datasets=self.datasets,
pool_size=self.pool_size)
if self.export_csv:
for dataset in self.datasets:
yield ExportCsv(dataset=dataset,
datasets=self.datasets,
pool_size=self.pool_size)
class NeuralNetworkClassificatorTask(ClassificatorTask):
_name = 'neural_network'
solver = luigi.Parameter(default='lbfgs')
activation = luigi.Parameter(default='relu')
hidden_layer_sizes = luigi.ListParameter()
batch_size = luigi.Parameter(default='auto')
def build_and_train(self, x, y):
from sklearn.neural_network import MLPClassifier
from sklearn.multiclass import OneVsRestClassifier
lx,ly,lz = x.shape
self.meta.update({
"word_vec_size": lz,
"len_words": ly,
})
x_train = x.reshape(lx, ly*lz)
model = MLPClassifier(
hidden_layer_sizes=list(self.hidden_layer_sizes),
solver=self.solver,
activation=self.activation,
batch_size='auto' if self.batch_size == 'auto' else int(self.batch_size)
)
if self.ovr_strategy:
model = OneVsRestClassifier(model)
model.fit(x_train, y)
score = model.score(x_train, y)
self.meta['score'] = score
self.set_status_message(f'Model fit complete. Score {score}')
return model
class UploadFilesToAzureAndRecord(luigi.Task):
"""
Just copies the result of the parent task into the task DB
"""
part_id = luigi.Parameter()
path_list = luigi.ListParameter()
task_namespace = 'azure'
def requires(self):
return UploadFilesToAzure(self.part_id, self.path_list)
def run(self):
# Record output in DB too:
for item in self.path_list:
tr = UploadToAzure(item).output()
if not tr.exists():
tr.touch()
# All done, so log this task as complete:
self.output().touch()
def output(self):
"""If this all works, record success in the DB"""
return taskdb_target( 'azure_upload_set', '%s UPLOADED' % self.part_id)
class MergeBam(SlurmExecutableTask, CheckTargetNonEmpty):
base_dir = luigi.Parameter(significant=False)
scratch_dir = luigi.Parameter(default="/tgac/scratch/buntingd/", significant=False)
lib_list = luigi.ListParameter()
output_prefix = luigi.Parameter()
library = None
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
# Set the SLURM request params for this task
self.mem = 16000
self.n_cpu = 3
self.partition = "nbi-medium"
def requires(self):
return [self.clone(Library.MarkDuplicates, library=lib) for lib in self.lib_list]
def output(self):
return LocalTarget(os.path.join(self.scratch_dir, VERSION, PIPELINE, self.output_prefix, 'merged.bam'))
def work_script(self):
self.temp = TemporaryFile()
return '''#!/bin/bash
source samtools-1.3;
set -euo pipefail
echo '{input}' > {temp}
samtools merge -f {output}.temp.bam -b {temp} --threads 2
mv {output}.temp.bam {output}
'''.format(input="\n".join([x.path for x in self.input()]),
output=self.output().path,
temp=self.temp.path)
class DownloadArticle(luigi.Task):
lexology_urls = luigi.ListParameter() # luigi parameter
def run(self):
for lexology_url in self.lexology_urls:
r = requests.get(lexology_url)
html = r.text
soup = BeautifulSoup(html, 'html.parser')
article_header = soup.select('h4')
article_link_list = []
for links in article_header:
article_links = links.find_all('a', href=True)
for link in article_links:
article_link = link.get('href')
article_link_list.append(article_link)
#print(article_link_list)
all_text = []
for article_link in article_link_list:
try:
text = get_article(article_link)
all_text.append(text)
except Exception as e:
print(f'error in {article_link}, {e}')
df = pd.DataFrame(all_text,
columns=['article_title', 'article_date', 'text'])
df.to_pickle(self.output().open('w').path)
def output(self):
return luigi.LocalTarget(f'data/raw/raw_articles.pkl')
class PairwiseDistanceWorkflow(WorkflowBase):
input_path = luigi.Parameter()
input_key = luigi.Parameter()
morphology_path = luigi.Parameter()
morphology_key = luigi.Parameter()
output_path = luigi.Parameter()
max_distance = luigi.FloatParameter()
resolution = luigi.ListParameter()
max_size = luigi.IntParameter(default=None)
def requires(self):
distance_task = getattr(distance_tasks,
self._get_task_name('ObjectDistances'))
dep = distance_task(tmp_folder=self.tmp_folder, max_jobs=self.max_jobs,
config_dir=self.config_dir,
input_path=self.input_path, input_key=self.input_key,
morphology_path=self.morphology_path,
morphology_key=self.morphology_key,
max_distance=self.max_distance, resolution=self.resolution,
max_size=self.max_size)
dep = MergePairwiseDistances(tmp_folder=self.tmp_folder, max_jobs=self.max_jobs,
output_path=self.output_path, dependency=dep)
return dep
@staticmethod
def get_config():
configs = super(PairwiseDistanceWorkflow, PairwiseDistanceWorkflow).get_config()
configs.update({'object_distances': distance_tasks.ObjectDistancesLocal.default_task_config()})
return configs
class MergeSampleBams(luigi.Task):
"""Merge Multiple Bam Files for One Sample and Coverage Statistics
Attributes:
inbams (list): a list of bam files
outbam (str): output bam filename
Output:
- {outdir}/mapping/{sample}.merged.bam
"""
resources = {"cpu": 2, "memory": 1}
outbam = luigi.Parameter()
inbams = luigi.ListParameter()
def requires(self):
return []
def output(self):
return luigi.LocalTarget(self.outbam)
def run(self):
cmd = """samtools merge - {bams} | tee {outfile} \
| samtools index - {outfile}.bai """.format(
bams = " ".join(self.inbams), outfile = self.outbam,
)
logging.info(cmd)
subprocess.run(cmd, shell=True)
class CreateSequenceDictionary(FtarcTask):
fa_path = luigi.Parameter()
gatk = luigi.Parameter(default='gatk')
add_createsequencedictionary_args = luigi.ListParameter(default=list())
n_cpu = luigi.IntParameter(default=1)
memory_mb = luigi.FloatParameter(default=4096)
sh_config = luigi.DictParameter(default=dict())
priority = 70
def output(self):
fa = Path(self.fa_path).resolve()
return luigi.LocalTarget(fa.parent.joinpath(f'{fa.stem}.dict'))
def run(self):
run_id = Path(self.fa_path).stem
self.print_log(f'Create a sequence dictionary:\t{run_id}')
fa = Path(self.fa_path).resolve()
seq_dict_path = self.output().path
self.setup_shell(run_id=run_id,
commands=self.gatk,
cwd=fa.parent,
**self.sh_config,
env={
'JAVA_TOOL_OPTIONS':
self.generate_gatk_java_options(
n_cpu=self.n_cpu, memory_mb=self.memory_mb)
})
self.run_shell(
args=(f'set -e && {self.gatk} CreateSequenceDictionary' +
f' --REFERENCE {fa}' +
''.join(f' {a}'
for a in self.add_createsequencedictionary_args) +
f' --OUTPUT {seq_dict_path}'),
input_files_or_dirs=fa,
output_files_or_dirs=seq_dict_path)
class Freebayes(luigi.Task):
"""Freebayes Calling Variants
Attributes:
inbam (file): input dedup bam file
outvcf (str): output vcf file
"""
resources = {"cpu": 1, "memory": 1}
inbam = luigi.ListParameter()
outvcf = luigi.Parameter()
def requires(self):
return []
def output(self):
return luigi.LocalTarget(self.outvcf)
def run(self):
cmd = "freebayes -f {genome} {bam} > {outfile}".format(
genome=Reference().genome, bam=self.inbam, outfile=self.outvcf
)
# bcftools filter -e 'QUAL < 20' -s LOWQUAL {rawvcf} {outvcf}
logging.info(cmd)
subprocess.run(cmd, shell=True)
class WideRecommender(ClassifierWithTransferLearningKerasModelTraining):
input_shape: Tuple[int, int] = luigi.TupleParameter(default=(100, ))
batch_size: int = luigi.IntParameter(default=10)
learning_rate = luigi.FloatParameter(default=1e-5)
dense_layers: List[int] = luigi.ListParameter(default=[512, 512])
dropout: float = luigi.FloatParameter(default=None)
activation_function: str = luigi.ChoiceParameter(
choices=KERAS_ACTIVATION_FUNCTIONS.keys(), default="relu")
kernel_initializer: str = luigi.ChoiceParameter(
choices=KERAS_WEIGHT_INIT.keys(), default="glorot_uniform")
def create_base_model(self) -> Model:
x_input = Input(shape=self.input_shape, name='wide_inp')
wide = Dense(self.input_shape[0],
activation=self.activation_function,
kernel_initializer=self.kernel_initializer,
name='wide_mlp')(x_input)
output = Dense(1,
activation='sigmoid',
kernel_initializer=self.kernel_initializer)(wide)
model = Model(x_input, output, name='Wide')
return model
def create_model_with(self, base_model: Model) -> Model:
return base_model
class Mpileup(luigi.Task):
"""Bcftools Mpileup calling variants
Attributes:
inbam (file): input dedup bam file
outvcf (str): output vcf file
"""
resources = {"cpu": 1, "memory": 1}
inbam = luigi.ListParameter()
outvcf = luigi.Parameter()
def requires(self):
return []
def output(self):
return luigi.LocalTarget(self.outvcf)
def run(self):
cmd = """bcftools mpileup -f {genome} {bam} \
| bcftools call -mv --ploidy {ploidy} -o {outvcf}""".format(
bam=self.inbam, vcf=self.outvcf,
genome=Reference().genome, ploidy=Reference().genome_version
)
logging.info(cmd)
subprocess.run(cmd, shell=True)
class AbyssSealerReduced(CheckTargetNonEmpty, SlurmExecutableTask):
sealer_klist = luigi.ListParameter()
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
# Set the SLURM request params for this task
self.mem = 6000
self.n_cpu = 2
self.partition = "nbi-medium"
def output(self):
return LocalTarget(os.path.join(self.base_dir, PIPELINE, VERSION, "sealer", "SOAP", 'K' + str(self.K), 'K' + str(self.K) + "_scaffold.fa"))
def requires(self):
return {'bloomfilters': [self.clone(Assemble.AbyssBloomBuild, bloom_k=k) for k in self.sealer_klist],
'scaffolds': self.clone(SOAPNremap)}
def work_script(self):
return '''#!/bin/bash
source abyss-2.0.2;
mkdir -p {output}/temp
set -euo pipefail
abyss-sealer {k_args} -P25 --flank-length=150 -j {n_cpu} -o {output}/temp/{prefix} -S {scaffolds} {bloomfilters}
mv {output}/temp/{prefix}* {output}/
'''.format(k_args=' '.join(['-k' + str(k) for k in self.sealer_klist]),
bloomfilters=' '.join(['-i ' + x.path for x in self.input()['bloomfilters']]),
scaffolds=self.input()['scaffolds'].path,
n_cpu=self.n_cpu,
output=os.path.dirname(self.output().path),
prefix='K' + str(self.K))
class _Tracking2DExtraction(luigi.Task):
"""
Base task for extracting fields from object tracking in 2D. This should
never be called directly. Instead use either TrackingVariable2D or TrackingLabels2D
"""
base_name = luigi.Parameter()
track_without_gal_transform = luigi.BoolParameter(default=False)
tracking_type = luigi.EnumParameter(enum=TrackingType)
tracking_timestep_interval = luigi.ListParameter(default=[])
def requires(self):
U_tracking_offset = None
if self.track_without_gal_transform:
meta = _get_dataset_meta_info(self.base_name)
U_tracking_offset = meta.get("U_gal", None)
if U_tracking_offset is None:
raise Exception(
"To remove the Galilean transformation before tracking"
" please define the transform velocity"
" as `U_gal` in datasources.yaml for"
" dataset `{}`".format(self.base_name))
return PerformObjectTracking2D(
base_name=self.base_name,
tracking_type=self.tracking_type,
timestep_interval=self.tracking_timestep_interval,
U_offset=U_tracking_offset,
)
class RunFeatureUnion(PickleTask):
dataset = luigi.Parameter()
levels = luigi.ListParameter()
sig_type = luigi.Parameter(default='logsig')
def output(self):
levels_name = '_'.join(map(str, self.levels))
filename = f"{self.sig_type}_concat_{levels_name}.pkl"
return luigi.LocalTarget(PIPELINE_DIR / self.dataset / filename)
def run(self):
X_train, y_train, X_test, y_test = load_data(self.dataset)
logit = LogisticRegression(random_state=42)
r = []
for level in self.levels:
m = classifiers.create_concatenator(logit,
sig_type=self.sig_type,
level=level)
# start timing
start = timeit.default_timer()
m.fit(X_train, y_train)
elapsed = timeit.default_timer() - start
# end timing
r.append([m.score(X_test, y_test), elapsed])
self.dump(
pd.DataFrame(r, columns=["Score", "Elapsed"], index=self.levels))
class MultiSampleWorkflow(sl.WorkflowTask):
"""
This workflow is meant to take an entire dataset description and run the the SingleSampleWorkflow on each sample
"""
midas_db = sl.Parameter()
dataset_description = sl.Parameter()
workdir = sl.Parameter()
contaminant_removal_method = sl.Parameter(default="bbsplit")
filter_genomes = luigi.ListParameter()
ref_info_dir = sl.Parameter()
ref_combo_hash = sl.Parameter()
def workflow(self):
dataset_spec = json.load(self.dataset_description)
tasks = []
if len(self.filter_genomes) > 0:
index_task = self.new_task("ref_index",
CreateIndexForContamRemoval)
tasks.append(index_task)
# Samples are in an array in the json. Each sample has a prefix and two read files
for sample in dataset_spec["samples"]:
wf = self.new_task('SampleWorkflow_' + sample["prefix"],
SingleSampleWorkflow,
workdir=self.workdir,
prefix=sample["prefix"],
in_fastq1=sample["in_fastq1"],
in_fastq2=sample["in_fastq2"],
midas_db=self.midas_db,
filter_genomes=self.filter_genomes,
ref_info_dir=self.ref_info_dir,
ref_combo_hash=self.ref_combo_hash)
tasks.append(wf)
return tasks
class AggregateArtists(luigi.Task):
months = luigi.ListParameter()
user_id = luigi.Parameter()
def output(self):
return luigi.LocalTarget(
"output/artist_streams_{}_{}.csv".format(
self.user_id, "-".join(self.months)
),
format=luigi.format.Nop,
)
def requires(self):
return [Streams(month, self.user_id) for month in self.months]
def run(self):
main_df = None
for t in self.input():
with t.open("r") as in_file:
df = pd.read_csv(in_file)
if main_df is None:
main_df = df
else:
main_df = main_df.append(df)
counts = (
main_df.groupby("Artist Name")
.count()["Apple Id Number"]
.sort_values(ascending=False)
.rename("Count")
)
with self.output().open("w") as out_file:
counts.to_csv(out_file)
class B(PipeTask):
""" B required by A """
int_array = luigi.ListParameter(default=None)
def pipe_run(self):
print("B saving type [{}]".format(type(self.int_array)))
return self.int_array