def execute(self, exp, *args, **kwargs):
self.set_out_var("result", None)
self.collect_options()
mRNA_train_es = self.get_input_var("mRNA_train_es")
mRNA_test_es = self.get_input_var("mRNA_test_es")
miRNA_train_es = self.get_input_var("miRNA_train_es")
miRNA_test_es = self.get_input_var("miRNA_test_es")
self.celery_task = wrapper_task.s(
apply_ncf_classifier,
exp=exp, block=self,
mRNA_train_es=mRNA_train_es, mRNA_test_es=mRNA_test_es,
miRNA_train_es=miRNA_train_es, miRNA_test_es=miRNA_test_es,
classifier_name=self.classifier_name,
classifier_options=self.classifier_options,
fit_options=self.fit_options,
base_folder=exp.get_data_folder(),
base_filename="%s_%s" % (self.uuid, self.classifier_name),
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
cs = self.get_input_var("cs")
""":type :ComoduleSet"""
es = self.get_input_var("es")
""":type :ExpressionSet"""
# gene_platform = self.upload_gene2gene_platform
gene2gene = self.get_input_var("gene2gene")
""":type :BinaryInteraction"""
# gene_platform = gene_platform.get_file()
# with open(gene_platform.path) as f:
# for line in f:
# gene_platform = line.split(',')
# self.clean_errors()
self.celery_task = wrapper_task.s(
compute_edges,
exp,
self,
m_rna_es=es,
comodule_set=cs,
gene2gene=gene2gene,
# gene_platform = gene_platform,
base_filename="%s_pattern_edges" % self.uuid)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
cs = self.get_input_var("cs")
""":type :ComoduleSet"""
es = self.get_input_var("es")
""":type :ExpressionSet"""
# gene_platform = self.upload_gene2gene_platform
gene2gene = self.get_input_var("gene2gene")
""":type :BinaryInteraction"""
# gene_platform = gene_platform.get_file()
# with open(gene_platform.path) as f:
# for line in f:
# gene_platform = line.split(',')
# self.clean_errors()
self.celery_task = wrapper_task.s(
compute_edges,
exp, self,
m_rna_es = es,
comodule_set = cs,
gene2gene = gene2gene,
# gene_platform = gene_platform,
base_filename="%s_pattern_edges" % self.uuid
)
exp.store_block(self)
self.celery_task.apply_async()
def process_upload(self, exp, *args, **kwargs):
"""
@param exp: Experiment
"""
self.clean_errors()
# sep = getattr(self, "csv_sep", " ")
# platform = getattr(self, "platform", " ")
try:
if len(self.pheno_matrices) != len(self.es_matrices):
raise RuntimeError("Different number of phenotypes and expression sets")
self.labels = es_matrix_names = sorted(self.es_matrices)
pheno_matrix_names = sorted(self.pheno_matrices)
self.pheno_by_es_names = {
es_name: pheno_name for
es_name, pheno_name
in zip(es_matrix_names, pheno_matrix_names)
}
self.clean_errors()
self.celery_task = wrapper_task.s(
bunch_upload_task,
exp,
self,
success_action="processing_done",
error_action="error_on_processing"
)
exp.store_block(self)
self.celery_task.apply_async()
except Exception as e:
exp.log(self.uuid, e, severity="CRITICAL")
log.exception(e)
self.errors.append(e)
self.do_action("error_on_processing", exp, e)
def execute(self, exp, *args, **kwargs):
self.set_out_var("result", None)
self.collect_options()
mRNA_train_es = self.get_input_var("mRNA_train_es")
mRNA_test_es = self.get_input_var("mRNA_test_es")
miRNA_train_es = self.get_input_var("miRNA_train_es")
miRNA_test_es = self.get_input_var("miRNA_test_es")
self.celery_task = wrapper_task.s(
apply_ncf_classifier,
exp=exp,
block=self,
mRNA_train_es=mRNA_train_es,
mRNA_test_es=mRNA_test_es,
miRNA_train_es=miRNA_train_es,
miRNA_test_es=miRNA_test_es,
classifier_name=self.classifier_name,
classifier_options=self.classifier_options,
fit_options=self.fit_options,
base_folder=exp.get_data_folder(),
base_filename="%s_%s" % (self.uuid, self.classifier_name),
)
exp.store_block(self)
self.celery_task.apply_async()
def process_upload(self, exp, *args, **kwargs):
self.clean_errors()
self.celery_task = wrapper_task.s(
user_upload_complex_task,
exp,
self
)
exp.store_block(self)
self.celery_task.apply_async()
def start_preprocess(self, exp, *args, **kwargs):
self.celery_task_preprocess = wrapper_task.s(
preprocess_soft,
exp,
self,
source_file=self.source_file,
success_action="successful_preprocess",
error_action="error_during_preprocess")
exp.store_block(self)
self.celery_task_preprocess.apply_async()
def start_preprocess(self, exp, *args, **kwargs):
self.celery_task_preprocess = wrapper_task.s(
preprocess_soft,
exp, self,
source_file=self.source_file,
success_action="successful_preprocess",
error_action="error_during_preprocess"
)
exp.store_block(self)
self.celery_task_preprocess.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
self.celery_task = wrapper_task.s(global_test_task,
exp,
self,
es=self.get_input_var("es"),
gene_sets=self.get_input_var("gs"),
table_result=self.result)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
self.celery_task = wrapper_task.s(
global_test_task,
exp, self,
es=self.get_input_var("es"),
gene_sets=self.get_input_var("gs"),
table_result=self.result
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
es = self.get_input_var("es")
self.celery_task = wrapper_task.s(
quant_norm_task,
exp, self,
es=es,
base_filename="%s_%s_flt" % (self.uuid, 'quantile_norm')
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
# import ipdb; ipdb.set_trace()
self.celery_task = wrapper_task.s(
merge_two_es,
exp, self,
es_1 = self.get_input_var("es_1"),
es_2 = self.get_input_var("es_2"),
base_filename="%s_merged" % self.uuid,
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
es = self.get_input_var("es")
gs = self.get_input_var("gs")
base_filename = "%s_gs_agg" % (self.uuid, )
self.celery_task = wrapper_task.s(do_gs_agg, exp, self, es, gs,
self.agg_method, base_filename)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
es = self.get_input_var("es")
self.celery_task = wrapper_task.s(zscore_task,
exp,
self,
es=es,
base_filename="%s_%s_flt" %
(self.uuid, 'zscore'))
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
# import ipdb; ipdb.set_trace()
self.celery_task = wrapper_task.s(
merge_two_es,
exp,
self,
es_1=self.get_input_var("es_1"),
es_2=self.get_input_var("es_2"),
base_filename="%s_merged" % self.uuid,
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
es = self.get_input_var("es")
# T = self.get_input_var("T")
self.celery_task = wrapper_task.s(
threshold_task,
exp, self,
es=es,
T=self.T,
base_filename="%s_%s_thr" % (self.uuid, 'threshold')
)
exp.store_block(self)
self.celery_task.apply_async()
def start_fetch(self, exp, *args, **kwargs):
"""
@param exp: Experiment
"""
self.clean_errors()
self.celery_task_fetch = wrapper_task.s(
fetch_geo_gse, exp, self,
geo_uid=self.geo_uid,
success_action="successful_fetch", error_action="error_during_fetch",
ignore_cache=False
)
exp.store_block(self)
self.celery_task_fetch.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
es = self.get_input_var("es")
# T = self.get_input_var("T")
self.celery_task = wrapper_task.s(threshold_task,
exp,
self,
es=es,
T=self.T,
base_filename="%s_%s_thr" %
(self.uuid, 'threshold'))
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
self.celery_task = wrapper_task.s(
feature_selection_by_cut,
exp=exp, block=self,
src_es=self.get_input_var("es"),
rank_table=self.get_input_var("rank_table"),
cut_property=self.cut_property,
threshold=self.threshold,
cut_direction=self.cut_direction,
base_filename="%s_feature_selection" % self.uuid,
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
gs, ann = self.get_input_var("gs"), self.get_input_var("ann")
# import ipdb; ipdb.set_trace()
self.celery_task = wrapper_task.s(map_gene_sets_to_probes,
exp,
self,
base_dir=exp.get_data_folder(),
base_filename="%s_merged" %
self.uuid,
ann_gene_sets=ann.gene_sets,
src_gene_sets=gs)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
es = self.get_input_var("es")
self.celery_task = wrapper_task.s(
filter_task,
exp, self,
filter_type=self.filter_method,
q=self.q,
es=es,
base_filename="%s_%s_flt" % (self.uuid, self.filter_method)
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
self.collect_options()
self.celery_task = wrapper_task.s(apply_ranking,
exp=exp,
block=self,
es=self.get_input_var("es"),
ranking_name=self.ranking_name,
result_table=self.result,
options=self.ranking_options)
exp.store_block(self)
self.celery_task.apply_async()
log.debug("Sent ranking computation to queue")
def execute(self, exp, *args, **kwargs):
self.clean_errors()
gs = self.get_input_var("gs")
h2 = self.get_input_var("H2_genes")
self.celery_task = wrapper_task.s(
enrichment_task,
exp, self,
gs = gs,
H2 = h2,
T=self.T,
base_filename="%s_%s_enrich" % (self.uuid, 'enrichment')
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
gs = self.get_input_var("gs")
cs = self.get_input_var("cs")
self.celery_task = wrapper_task.s(
enrichment_no_t_task,
exp, self,
T = self.T,
gs = gs,
cs = cs,
base_filename="%s_%s_enrich" % (self.uuid, 'enrichment_cont')
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
gs = self.get_input_var("gs")
cs = self.get_input_var("patterns")
self.celery_task = wrapper_task.s(enrichment_no_t_task,
exp,
self,
T=self.T,
gs=gs,
patterns=cs,
base_filename="%s_%s_enrich" %
(self.uuid, 'enrichment_cont'))
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
gs, ann = self.get_input_var("gs"), self.get_input_var("ann")
# import ipdb; ipdb.set_trace()
self.celery_task = wrapper_task.s(
map_gene_sets_to_probes,
exp, self,
base_dir=exp.get_data_folder(),
base_filename="%s_merged" % self.uuid,
ann_gene_sets=ann.gene_sets,
src_gene_sets=gs
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
self.collect_options()
self.celery_task = wrapper_task.s(
apply_ranking,
exp=exp, block=self,
es=self.get_input_var("es"),
ranking_name=self.ranking_name,
result_table=self.result,
options=self.ranking_options
)
exp.store_block(self)
self.celery_task.apply_async()
log.debug("Sent ranking computation to queue")
def execute(self, exp, *args, **kwargs):
self.clean_errors()
self.celery_task = wrapper_task.s(
feature_selection_by_cut,
exp=exp,
block=self,
src_es=self.get_input_var("es"),
rank_table=self.get_input_var("rank_table"),
cut_property=self.cut_property,
threshold=self.threshold,
cut_direction=self.cut_direction,
base_filename="%s_feature_selection" % self.uuid,
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
self.celery_task = wrapper_task.s(
pattern_filter_task,
exp,
self,
m_rna_es=self.get_input_var("mRNA"),
mi_rna_es=self.get_input_var("miRNA"),
gene_sets=self.get_input_var("gs"),
metric=self.metric,
n_best=self.n_best,
base_filename="%s_comodule_sets" % self.uuid)
exp.store_block(self)
self.celery_task.apply_async()
def start_fetch(self, exp, *args, **kwargs):
"""
@param exp: Experiment
"""
self.clean_errors()
self.celery_task_fetch = wrapper_task.s(
fetch_geo_gse,
exp,
self,
geo_uid=self.geo_uid,
success_action="successful_fetch",
error_action="error_during_fetch",
ignore_cache=False)
exp.store_block(self)
self.celery_task_fetch.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
self.celery_task = wrapper_task.s(
pattern_filter_task,
exp, self,
m_rna_es = self.get_input_var("mRNA"),
mi_rna_es = self.get_input_var("miRNA"),
gene_sets = self.get_input_var("gs"),
metric = self.metric,
n_best = self.n_best,
base_filename="%s_comodule_sets" % self.uuid
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
cs_1 = self.get_input_var("cs_1")
cs_2 = self.get_input_var("cs_2")
self.celery_task = wrapper_task.s(merge_comodules_task,
exp,
self,
cs_1=cs_1,
cs_2=cs_2,
cs_1_name=self.cs_1_name,
cs_2_name=self.cs_2_name,
base_filename="%s_%s_thr" %
(self.uuid, 'merge_cs'))
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
es = self.get_input_var("es")
gs = self.get_input_var("gs")
base_filename = "%s_gs_agg" % (self.uuid, )
self.celery_task = wrapper_task.s(
do_gs_agg,
exp, self,
es, gs, self.agg_method,
base_filename
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
cs_1 = self.get_input_var("cs_1")
cs_2 = self.get_input_var("cs_2")
self.celery_task = wrapper_task.s(
merge_comodules_task,
exp, self,
cs_1=cs_1,
cs_2=cs_2,
cs_1_name=self.cs_1_name,
cs_2_name=self.cs_2_name,
base_filename="%s_%s_thr" % (self.uuid, 'merge_cs')
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
mRNA_es = self.get_input_var("mRNA_es")
miRNA_es = self.get_input_var("miRNA_es")
interaction_matrix = self.get_input_var("interaction")
self.celery_task = wrapper_task.s(
filter_by_bi,
exp, self,
m_rna_es=mRNA_es,
mi_rna_es=miRNA_es,
interaction_matrix=interaction_matrix,
base_filename="%s_filtered_by_BI" % self.uuid,
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
mRNA_es = self.get_input_var("mRNA_es")
miRNA_es = self.get_input_var("miRNA_es")
interaction_matrix = self.get_input_var("interaction")
self.celery_task = wrapper_task.s(
filter_by_bi,
exp,
self,
m_rna_es=mRNA_es,
mi_rna_es=miRNA_es,
interaction_matrix=interaction_matrix,
base_filename="%s_filtered_by_BI" % self.uuid,
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
self.inner_output_manager.reset()
es_dict = {inp_name: self.get_input_var(inp_name) for inp_name in self.es_inputs}
self.celery_task = wrapper_task.s(
generate_cv_folds,
exp,
self,
folds_num=self.folds_num,
repeats_num=self.repeats_num,
es_dict=es_dict,
inner_output_es_names_map=self.inner_output_es_names_map,
success_action="on_folds_generation_success",
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
train_es = self.get_input_var("train_es")
test_es = self.get_input_var("test_es")
gene_sets = self.get_input_var("gs")
self.celery_task = wrapper_task.s(
agg_task_cv,
exp, self,
train_es=train_es,
test_es=test_es,
gene_sets=gene_sets,
method=self.agg_method,
base_filename="%s_%s_agg" % (self.uuid, "pca_cv")
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
train_es = self.get_input_var("train_es")
test_es = self.get_input_var("test_es")
gene_sets = self.get_input_var("gs")
self.celery_task = wrapper_task.s(
agg_task_cv,
exp, self,
train_es=train_es,
test_es=test_es,
gene_sets=gene_sets,
method=self.agg_method,
base_filename="%s_%s_agg" % (self.uuid, "pca_cv")
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
exp.log(self.uuid, "Execute called")
self.celery_task = wrapper_task.s(
pattern_search,
exp, self,
m_rna_es = self.get_input_var("mRNA"),
mi_rna_es = self.get_input_var("miRNA"),
gene2gene=self.get_input_var("gene2gene"),
miRNA2gene=self.get_input_var("miRNA2gene"),
radius=self.d,
min_imp=self.min_imp,
metric=self.get_input_var("metric"),
base_filename="%s_comodule_sets" % self.uuid,
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
mRNA_es = self.get_input_var("mRNA_es")
miRNA_es = self.get_input_var("miRNA_es")
interaction_matrix = self.get_input_var("interaction")
self.celery_task = wrapper_task.s(
aggregation_task,
exp, self,
mode=self.mode,
c=self.c,
m_rna_es=mRNA_es,
mi_rna_es=miRNA_es,
interaction_matrix=interaction_matrix,
base_filename="%s_%s_agg" % (self.uuid, self.mode)
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
# self.celery_task = wrapper_task.s(
#
# )
self.inner_output_manager.reset()
es_dict = {
inp_name: self.get_input_var(inp_name)
for inp_name in self.es_inputs
}
self.celery_task = wrapper_task.s(
prepare_folds,
exp,
self,
features=self.features,
es_dict=es_dict,
inner_output_es_names_map=self.inner_output_es_names_map,
success_action="on_folds_generation_success")
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
# self.celery_task = wrapper_task.s(
#
# )
self.inner_output_manager.reset()
es_dict = {
inp_name: self.get_input_var(inp_name)
for inp_name in self.es_inputs
}
self.celery_task = wrapper_task.s(
prepare_folds,
exp, self,
features=self.features,
es_dict=es_dict,
inner_output_es_names_map=self.inner_output_es_names_map,
success_action="on_folds_generation_success"
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
exp.log(self.uuid, "Execute called")
self.celery_task = wrapper_task.s(
pattern_search,
exp,
self,
m_rna_es=self.get_input_var("mRNA"),
mi_rna_es=self.get_input_var("miRNA"),
gene2gene=self.get_input_var("gene2gene"),
miRNA2gene=self.get_input_var("miRNA2gene"),
radius=self.d,
min_imp=self.min_imp,
number_of_genes=self.genes_num,
metric=self.get_input_var("metric"),
base_filename="%s_comodule_sets" % self.uuid,
)
exp.store_block(self)
self.celery_task.apply_async()
def execute(self, exp, *args, **kwargs):
self.clean_errors()
self.inner_output_manager.reset()
es_dict = {
inp_name: self.get_input_var(inp_name)
for inp_name in self.es_inputs
}
self.celery_task = wrapper_task.s(
generate_cv_folds,
exp,
self,
folds_num=self.folds_num,
repeats_num=self.repeats_num,
es_dict=es_dict,
inner_output_es_names_map=self.inner_output_es_names_map,
success_action="on_folds_generation_success",
)
exp.store_block(self)
self.celery_task.apply_async()
def process_upload(self, exp, *args, **kwargs):
"""
@param exp: Experiment
"""
self.clean_errors()
try:
if len(self.pheno_matrices) != len(self.es_mRNA_matrices):
raise RuntimeError("Different number of phenotypes and mRNA expression sets")
if self.es_miRNA_matrices:
if len(self.pheno_matrices) != len(self.es_miRNA_matrices):
raise RuntimeError("Different number of phenotypes and miRNA expression sets")
self.labels = es_mRNA_matrix_names = sorted(self.es_mRNA_matrices)
es_miRNA_matrix_names = sorted(self.es_miRNA_matrices)
pheno_matrix_names = sorted(self.pheno_matrices)
if len(es_miRNA_matrix_names) == 0:
es_miRNA_matrix_names = len(es_mRNA_matrix_names) * [None]
self.pheno_by_es_names = {
pheno_name: es_name for
es_name, pheno_name
in zip(zip(es_mRNA_matrix_names, es_miRNA_matrix_names), pheno_matrix_names)
}
self.clean_errors()
self.celery_task = wrapper_task.s(
bunch_upload_task,
exp,
self,
success_action="processing_done",
error_action="error_on_processing"
)
exp.store_block(self)
self.celery_task.apply_async()
except Exception as e:
exp.log(self.uuid, e, severity="CRITICAL")
log.exception(e)
self.errors.append(e)
self.do_action("error_on_processing", exp, e)
def execute(self, exp, *args, **kwargs):
self.clean_errors()
mRNA = self.get_input_var("mRNA")
miRNA = self.get_input_var("miRNA")
#DNAmethyl = self.get_input_var("DNAmethyl")
Gene2Gene = self.get_input_var("Gene2Gene")
miRNA2gene = self.get_input_var("miRNA2gene")
#Gene2DNAmethyl = self.get_input_var("Gene2DNAmethyl")
self.celery_task = wrapper_task.s(
nimfa_snmnmf_task,
exp,
self,
mRNA=mRNA,
miRNA=miRNA,
#DNAmethyl = DNAmethyl,
gene2gene=Gene2Gene,
miRNA2gene=miRNA2gene,
#gene2DNAmethylation = Gene2DNAmethyl,
params={'l1': self.l1, 'l2': self.l2, 'g1': self.g1, 'g2': self.g2, 'rank': self.rank},
base_filename="%s_nimfa_snmnmf" % self.uuid
)
exp.store_block(self)
self.celery_task.apply_async()
def process_upload(self, exp, *args, **kwargs):
self.clean_errors()
self.celery_task = wrapper_task.s(user_upload_complex_task, exp, self)
exp.store_block(self)
self.celery_task.apply_async()
