nmdc-runtime 2.9.0__py3-none-any.whl → 2.11.0__py3-none-any.whl

nmdc_runtime/lib/load_nmdc_data.py

@@ -1,121 +0,0 @@
-## author: Bill Duncan
-## summary: Contains methods for saving or loading NMDC data into a resource.
-
-import json
-import jq
-
-
-def save_json(json_data, file_path: str):
-    ## save json with changed data types
-    with open(file_path, "w") as out_file:
-        json.dump(json_data, out_file, indent=2)
-    return json_data
-
-
-def get_json_from_file(file_path: str, replace_single_quote=False):
-    ## load json
-    with open(file_path, "r") as in_file:
-        if replace_single_quote:  # json
-            text = in_file.read()
-            json_data = json.loads(text.replace("'", '"'))
-        else:
-            json_data = json.load(in_file)
-    return json_data
-
-
-def get_json(file_path="", replace_single_quote=False):
-    if len(file_path) > 0:
-        return get_json_from_file(file_path, replace_single_quote)
-
-
-def save_nmdc_dict_as_json_to_file(nmdc_dict: dict, file_path: str):
-    with open(file_path, "w") as f:
-        json.dump(nmdc_dict, f, indent=2)
-    return json.dumps(nmdc_dict, indent=2)
-
-
-def save_nmdc_dict(nmdc_dict: dict, file_path="", data_format="json"):
-    if len(file_path) > 0:
-        if "json" == data_format:
-            return save_nmdc_dict_as_json_to_file(nmdc_dict, file_path)
-
-
-def make_nmdc_example_database(
-    gold_study_file="output/nmdc_etl/gold_study.json",
-    gold_omics_processing_file="output/nmdc_etl/gold_omics_processing.json",
-    gold_biosample_file="output/nmdc_etl/gold_biosample.json",
-    jgi_fastq_data_object_file="output/nmdc_etl/jgi_fastq_data_objects.json",
-    output_file="output/nmdc_example-database.json",
-):
-    ## load json files
-    biosample_json = get_json(gold_biosample_file)
-    projects_json = get_json(gold_omics_processing_file)
-    study_json = get_json(gold_study_file)
-    data_objects_json = get_json(jgi_fastq_data_object_file)
-
-    ## get a list of distinct omics processing study ids, and choose the first 3 studies
-    study_ids = set(
-        jq.compile(".[] | .part_of[]").input(projects_json).all()
-    )  # all returns a list
-    study_ids = list(study_ids)[0:3]
-    # study_ids =
-
-    ## build a test set of studies from the study ids
-    study_test = (
-        jq.compile(
-            ".[] | select( .id == ("
-            + ", ".join('"{0}"'.format(id) for id in study_ids)
-            + "))"
-        )
-        .input(study_json)
-        .all()
-    )  # all() returns a list
-
-    ## build a test set of projects from the study ids
-    ## note: the jq query only selects first omics found for a given study id
-    projects_test = []
-    for id in study_ids:
-        j = (
-            jq.compile(f'[.[] | select( .part_of[]? |  . == "{id}")][0]')
-            .input(projects_json)
-            .all()
-        )
-        projects_test.append(*j)
-
-    ## get list of unique biossample ids from omics processing and build biosample test set
-    biosample_ids = (
-        jq.compile(".[] | .has_input[]?").input(projects_test).all()
-    )  # all() returns a list
-    biosample_test = (
-        jq.compile(
-            ".[] | select( .id == ("
-            + ", ".join('"{0}"'.format(id) for id in biosample_ids)
-            + "))"
-        )
-        .input(biosample_json)
-        .all()
-    )  # all() returns a list
-
-    ## get a list of data object ids and build data objects test set
-    data_objects_ids = (
-        jq.compile(".[] | .has_output[]?").input(projects_test).all()
-    )  # all() returns a list
-    data_objects_test = (
-        jq.compile(
-            ".[] | select( .id == ("
-            + ", ".join('"{0}"'.format(id) for id in data_objects_ids)
-            + "))"
-        )
-        .input(data_objects_json)
-        .all()
-    )  # all() returns a list
-
-    ## compile into database object
-    database = {
-        "study_set": [*study_test],
-        "omics_processing_set": [*projects_test],
-        "biosample_set": [*biosample_test],
-        "data_object_set": [*data_objects_test],
-    }
-
-    save_json(database, output_file)