Remove export nexus

bluepyemodel/export_emodel/export_emodel.py

@@ -20,11 +20,9 @@
 import os
 import pathlib
 import shutil
-import time
 
 import h5py
 
-from bluepyemodel.access_point.forge_access_point import DEFAULT_NEXUS_ENDPOINT
 from bluepyemodel.evaluation.evaluation import compute_responses
 from bluepyemodel.evaluation.evaluation import get_evaluator_from_access_point
 from bluepyemodel.export_emodel.utils import get_hoc_file_path
@@ -246,141 +244,3 @@ def export_emodels_hoc(
         if not cell_model.morphology.morph_modifiers:  # Turn [] into None
             cell_model.morphology.morph_modifiers = None
         _export_emodel_hoc(cell_model, mo, output_dir=None, new_emodel_name=new_emodel_name)
-
-
-def export_emodels_nexus(
-    local_access_point,
-    nexus_organisation,
-    nexus_project,
-    nexus_endpoint=DEFAULT_NEXUS_ENDPOINT,
-    forge_path=None,
-    forge_ontology_path=None,
-    access_token=None,
-    only_validated=False,
-    only_best=True,
-    seeds=None,
-    description=None,
-    sleep_time=10,
-    sonata=True,
-):
-    """Transfer e-models from the LocalAccessPoint to a Nexus project
-
-    Args:
-        local_access_point (LocalAccessPoint): The local access point containing the e-models.
-        nexus_organisation (str): The Nexus organisation to which the e-models will be transferred.
-        nexus_project (str): The Nexus project to which the e-models will be transferred.
-        nexus_endpoint (str, optional): The Nexus endpoint.
-            Defaults to DEFAULT_NEXUS_ENDPOINT.
-        forge_path (str, optional): The path to the forge.
-        forge_ontology_path (str, optional): The path to the forge ontology.
-        access_token (str, optional): The access token for Nexus.
-        only_validated (bool, optional): If True, only validated e-models will be transferred.
-        only_best (bool, optional): If True, only the best e-models will be transferred.
-        seeds (list, optional): The chosen seeds to export.
-        description (str, optional): Optional description to add to the resources in Nexus.
-        sleep_time (int, optional):  time to wait between two Nexus requests
-            (in case of slow indexing).
-        sonata (bool, optional): Determines the format for registering e-models.
-            If True (default), uses Sonata hoc format. Otherwise, uses NEURON hoc format.
-
-    Returns:
-        None
-    """
-
-    from bluepyemodel.access_point.nexus import NexusAccessPoint
-
-    emodels = local_access_point.get_emodels()
-    emodels = select_emodels(
-        local_access_point.emodel_metadata.emodel,
-        emodels,
-        only_validated=only_validated,
-        only_best=only_best,
-        seeds=seeds,
-    )
-    if not emodels:
-        return
-
-    metadata = vars(local_access_point.emodel_metadata)
-    iteration = metadata.pop("iteration")
-    metadata.pop("allen_notation")
-    nexus_access_point = NexusAccessPoint(
-        **metadata,
-        iteration_tag=iteration,
-        project=nexus_project,
-        organisation=nexus_organisation,
-        endpoint=nexus_endpoint,
-        access_token=access_token,
-        forge_path=forge_path,
-        forge_ontology_path=forge_ontology_path,
-        sleep_time=sleep_time,
-    )
-
-    pipeline_settings = local_access_point.pipeline_settings
-    fitness_configuration = local_access_point.get_fitness_calculator_configuration()
-    model_configuration = local_access_point.get_model_configuration()
-    targets_configuration = local_access_point.get_targets_configuration()
-
-    # Register the resources
-    logger.info("Exporting the emodel %s to Nexus...", local_access_point.emodel_metadata.emodel)
-    logger.info("Registering EModelPipelineSettings...")
-    nexus_access_point.store_pipeline_settings(pipeline_settings)
-
-    logger.info("Registering ExtractionTargetsConfiguration...")
-    # Set local filepath to None to avoid discrepancies between local and Nexus paths
-    for file in targets_configuration.files:
-        file.filepath = None
-    nexus_access_point.store_targets_configuration(targets_configuration)
-
-    logger.info("Registering EModelConfiguration...")
-    # Remove unused local data from the model configuration before uploading to Nexus
-    model_configuration.morphology.path = None
-    nexus_access_point.store_model_configuration(model_configuration)
-
-    logger.info("Registering EModelWorkflow...")
-    filters = {"type": "EModelWorkflow", "eModel": metadata["emodel"], "iteration": iteration}
-    filters_legacy = {
-        "type": "EModelWorkflow",
-        "emodel": metadata["emodel"],
-        "iteration": iteration,
-    }
-    nexus_access_point.access_point.deprecate(filters, filters_legacy)
-    time.sleep(sleep_time)
-    emw = nexus_access_point.create_emodel_workflow(state="done")
-    nexus_access_point.store_or_update_emodel_workflow(emw)
-
-    logger.info("Registering FitnessCalculatorConfiguration...")
-    time.sleep(sleep_time)
-    nexus_access_point.store_fitness_calculator_configuration(fitness_configuration)
-
-    for mo in emodels:
-        time.sleep(sleep_time)
-        mo.emodel_metadata.allen_notation = nexus_access_point.emodel_metadata.allen_notation
-        mo.copy_pdf_dependencies_to_new_path(seed=mo.seed)
-        logger.info("Registering EModel %s...", mo.emodel_metadata.emodel)
-        nexus_access_point.store_emodel(mo, description=description)
-
-    time.sleep(sleep_time)
-    if sonata:
-        logger.info(
-            "Registering EModelScript (in sonata hoc format with threshold_current and "
-            "holding_current in node.h5 file) for circuit building using neurodamus..."
-        )
-        nexus_access_point.store_emodels_sonata(
-            only_best=only_best,
-            only_validated=only_validated,
-            seeds=seeds,
-            description=description,
-        )
-    else:
-        logger.info("Registering EModelScript (in hoc format to run e-model using NEURON)...")
-        nexus_access_point.store_emodels_hoc(
-            only_best=only_best,
-            only_validated=only_validated,
-            seeds=seeds,
-            description=description,
-        )
-
-    logger.info(
-        "Exporting the emodel %s to Nexus done.",
-        local_access_point.emodel_metadata.emodel,
-    )