From 43c0bfb7a5c5e05079e61924b11c3d493e887fca Mon Sep 17 00:00:00 2001
From: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com>
Date: Thu, 18 Jan 2024 16:06:52 +0100
Subject: [PATCH] Split code into functions for easy import (#102)

---
 datasimulator/main.py | 129 +++---
 poetry.lock           | 966 ++++++++++++++++--------------------------
 pyproject.toml        |   7 +-
 3 files changed, 451 insertions(+), 651 deletions(-)

diff --git a/datasimulator/main.py b/datasimulator/main.py
index 0227b1a..f979011 100755
--- a/datasimulator/main.py
+++ b/datasimulator/main.py
@@ -87,6 +87,68 @@ def parse_arguments():
     return parser.parse_args()
 
 
+def initialize_graph(dictionary_url, program, project, consent_codes):
+    if dictionary_url:
+        logger.info("Loading dictionary from url {}".format(dictionary_url))
+        dictionary.init(DataDictionary(url=dictionary_url))
+    else:
+        logger.info("Loading dictionary from installed dictionary")
+
+    logger.info("Initializing graph...")
+    if program and project:
+        graph = Graph(dictionary, program=program, project=project)
+    else:
+        logger.info("Using default program name and project code")
+        graph = Graph(dictionary)
+
+    if consent_codes:
+        graph.generate_nodes_from_dictionary(consent_codes)
+    else:
+        graph.generate_nodes_from_dictionary()
+
+    graph.construct_graph_edges()
+
+    return graph
+
+
+def run_simulation(
+    graph, data_path, max_samples, node_num_instances_file, random, required_only, skip
+):
+    max_samples = int(max_samples)
+
+    # just print error messages
+    graph.graph_validation(required_only=required_only)
+
+    # simulate data whether the graph passes validation or not
+    logger.info("Generating data...")
+    graph.simulate_graph_data(
+        path=data_path,
+        n_samples=max_samples,
+        node_num_instances_file=node_num_instances_file,
+        random=random,
+        required_only=required_only,
+        skip=skip,
+    )
+
+
+def run_submission_order_generation(graph, data_path, node_name=None):
+    logger.info("Generating data submission order...")
+    if node_name:
+        node = graph.get_node_with_name(node_name)
+        cmc_node = graph.get_node_with_name("core_metadata_collection")
+        if not node:
+            raise Exception(
+                f"Argument 'node_name' is '{node_name}' but this node does not exist"
+            )
+        submission_order = graph.generate_submission_order_path_to_node(node, cmc_node)
+    else:
+        submission_order = graph.generate_submission_order()
+
+    with open(os.path.join(data_path, "DataImportOrderPath.txt"), "w") as outfile:
+        for node in submission_order:
+            outfile.write(node.name + "\t" + node.category + "\n")
+
+
 # python main.py simulate --url https://s3.amazonaws.com/dictionary-artifacts/bhcdictionary/0.4.3/schema.json --path ./data-simulator/sample_test_data --program DEV --project test
 def main():
     args = parse_arguments()
@@ -104,67 +166,30 @@ def main():
         return
 
     logger.info("Data simulator initialization...")
-    if args.url:
-        logger.info("Loading dictionary from url {}".format(args.url))
-        dictionary.init(DataDictionary(url=args.url))
-    else:
-        logger.info("Loading dictionary from installed dictionary")
+    graph = initialize_graph(
+        dictionary_url=args.url if hasattr(args, "url") else None,
+        program=args.program if hasattr(args, "program") else None,
+        project=args.project if hasattr(args, "project") else None,
+        consent_codes=args.consent_codes if hasattr(args, "consent_codes") else None,
+    )
 
     if args.action == "simulate":
-        # Initialize graph
-        logger.info("Initializing graph...")
-        graph = Graph(dictionary, program=args.program, project=args.project)
-        graph.generate_nodes_from_dictionary(args.consent_codes)
-        graph.construct_graph_edges()
-        max_samples = int(args.max_samples)
-
-        # just print error messages
-        graph.graph_validation(required_only=args.required_only)
-
-        # simulate data no matter what the graph passes validation or not
-        logger.info("Generating data...")
-        graph.simulate_graph_data(
-            path=args.path,
-            n_samples=max_samples,
-            node_num_instances_file=args.node_num_instances_file,
-            random=args.random,
-            required_only=args.required_only,
-            skip=args.skip,
+        run_simulation(
+            graph,
+            args.path,
+            args.max_samples,
+            args.node_num_instances_file,
+            args.random,
+            args.required_only,
+            args.skip,
         )
 
     elif args.action == "validate":
-        # Initialize graph
-        logger.info("Initializing graph...")
-        graph = Graph(dictionary)
-        graph.generate_nodes_from_dictionary()
-        graph.construct_graph_edges()
         logger.info("Validating...")
         graph.graph_validation()
 
     elif args.action == "submission_order":
-        # Initialize graph
-        logger.info("Initializing graph...")
-        graph = Graph(dictionary)
-        graph.generate_nodes_from_dictionary()
-        graph.construct_graph_edges()
-
-        logger.info("Generating data submission order...")
-        if args.node_name:
-            node = graph.get_node_with_name(args.node_name)
-            cmc_node = graph.get_node_with_name("core_metadata_collection")
-            if not node:
-                raise Exception(
-                    f"Argument 'node_name' is '{args.node_name}' but this node does not exist"
-                )
-            submission_order = graph.generate_submission_order_path_to_node(
-                node, cmc_node
-            )
-        else:
-            submission_order = graph.generate_submission_order()
-
-        with open(os.path.join(args.path, "DataImportOrderPath.txt"), "w") as outfile:
-            for node in submission_order:
-                outfile.write(node.name + "\t" + node.category + "\n")
+        run_submission_order_generation(graph, args.path, args.node_name)
 
     logger.info("Done!")
 
diff --git a/poetry.lock b/poetry.lock
index 216072d..5e28aa9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,21 +2,22 @@
 
 [[package]]
 name = "attrs"
-version = "23.1.0"
+version = "23.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
-    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
+    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
+    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
 ]
 
 [package.extras]
 cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]", "pre-commit"]
+dev = ["attrs[tests]", "pre-commit"]
 docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
 tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
+tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "avro"
@@ -32,17 +33,6 @@ files = [
 snappy = ["python-snappy"]
 zstandard = ["zstandard"]
 
-[[package]]
-name = "boto"
-version = "2.49.0"
-description = "Amazon Web Services Library"
-optional = false
-python-versions = "*"
-files = [
-    {file = "boto-2.49.0-py2.py3-none-any.whl", hash = "sha256:147758d41ae7240dc989f0039f27da8ca0d53734be0eb869ef16e3adcfa462e8"},
-    {file = "boto-2.49.0.tar.gz", hash = "sha256:ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a"},
-]
-
 [[package]]
 name = "cdislogging"
 version = "1.1.1"
@@ -53,197 +43,114 @@ files = [
     {file = "cdislogging-1.1.1.tar.gz", hash = "sha256:77e11648244cda3a8094b8ae6081435a2303f259612846c49ef8825c7be141e3"},
 ]
 
-[[package]]
-name = "cdisutils"
-version = "1.2.2"
-description = "Miscellaneous utilities useful for interaction with CDIS systems."
-optional = false
-python-versions = "*"
-files = [
-    {file = "cdisutils-1.2.2.tar.gz", hash = "sha256:297a38210eea8aee4cd8712c16da120843242ea119d7e08a4844119485f691c3"},
-]
-
-[package.dependencies]
-boto = ">=2.36.0"
-indexclient = ">=1.5.6"
-ndg-httpsclient = ">=0.4.3"
-openpyxl = ">=2.4.0"
-pyOpenSSL = ">=16.2.0"
-python-dateutil = ">=2.4.2"
-xmltodict = ">=0.9.2"
-
 [[package]]
 name = "certifi"
-version = "2023.7.22"
+version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
-    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
+    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
+    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
 ]
 
-[[package]]
-name = "cffi"
-version = "1.16.0"
-description = "Foreign Function Interface for Python calling C code."
-optional = false
-python-versions = ">=3.8"
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 [package.dependencies]
@@ -324,87 +231,31 @@ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.1
 [package.extras]
 toml = ["tomli"]
 
-[[package]]
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-version = "41.0.5"
-description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
-optional = false
-python-versions = ">=3.7"
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-
-[package.dependencies]
-cffi = ">=1.12"
-
-[package.extras]
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-nox = ["nox"]
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-sdist = ["build"]
-ssh = ["bcrypt (>=3.1.5)"]
-test = ["pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
-test-randomorder = ["pytest-randomly"]
-
 [[package]]
 name = "dictionaryutils"
-version = "3.2.0"
-description = ""
+version = "3.4.10"
+description = "Python wrapper and metaschema for datadictionary."
 optional = false
-python-versions = "*"
+python-versions = ">=3.9,<4"
 files = [
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 [package.dependencies]
-cdislogging = ">=1.0,<2.0"
-jsonschema = ">=3.2,<4.0"
-PyYAML = ">=5.1,<6.0"
+cdislogging = ">=1.0.0,<2.0.0"
+jsonschema = ">=2.5,<4"
+PyYAML = "*"
 requests = ">=2.18,<3.0"
 
-[[package]]
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-version = "1.1.0"
-description = "An implementation of lxml.xmlfile for the standard library"
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-
 [[package]]
 name = "exceptiongroup"
-version = "1.1.3"
+version = "1.2.0"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -416,12 +267,10 @@ version = "3.1.2"
 description = ""
 optional = false
 python-versions = "*"
-files = [
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-]
+files = []
+develop = false
 
 [package.dependencies]
-cdisutils = "*"
 graphviz = ">=0.4,<1.0"
 jsonschema = ">=3.2,<4.0"
 psqlgraph = ">=3.0,<4.0"
@@ -429,20 +278,26 @@ pytz = ">=2016.4"
 sqlalchemy = ">=1.3,<2.0"
 strict-rfc3339 = "0.7"
 
+[package.source]
+type = "git"
+url = "https://github.com/uc-cdis/gdcdatamodel"
+reference = "3.1.3"
+resolved_reference = "190f99885c660a2971ec64522168548e19bea512"
+
 [[package]]
 name = "gen3dictionary"
-version = "2.0.1"
-description = "Gen3 generic data dictionary"
+version = "2.0.3"
+description = ""
 optional = false
-python-versions = "*"
+python-versions = ">=3.9,<4.0"
 files = [
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 ]
 
 [package.dependencies]
 dictionaryutils = "*"
-jsonschema = ">=2.5.1"
-PyYAML = ">=5.1,<6.0"
+jsonschema = "*"
+PyYAML = "*"
 
 [[package]]
 name = "graphviz"
@@ -462,103 +317,86 @@ test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>=
 
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 name = "greenlet"
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+version = "3.0.3"
 description = "Lightweight in-process concurrent programming"
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 python-versions = ">=3.7"
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 ]
 
 [package.extras]
-docs = ["Sphinx"]
+docs = ["Sphinx", "furo"]
 test = ["objgraph", "psutil"]
 
 [[package]]
 name = "idna"
-version = "3.4"
+version = "3.6"
 description = "Internationalized Domain Names in Applications (IDNA)"
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 python-versions = ">=3.5"
 files = [
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-
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 ]
 
-[package.dependencies]
-requests = ">=2.5.2,<3.0.0"
-
 [[package]]
 name = "iniconfig"
 version = "2.0.0"
@@ -607,36 +445,6 @@ build = ["blurb", "twine", "wheel"]
 docs = ["sphinx"]
 test = ["pytest", "pytest-cov"]
 
-[[package]]
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-
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-
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-et-xmlfile = "*"
-
 [[package]]
 name = "packaging"
 version = "23.2"
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 [[package]]
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-version = "7.4.3"
+version = "7.4.4"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -886,20 +662,6 @@ pytest = ">=4.6"
 [package.extras]
 testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
 
-[[package]]
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-
-[package.dependencies]
-six = ">=1.5"
-
 [[package]]
 name = "pytz"
 version = "2023.3.post1"
@@ -913,22 +675,61 @@ files = [
 
 [[package]]
 name = "pyyaml"
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+version = "6.0.1"
 description = "YAML parser and emitter for Python"
 optional = false
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 ]
 
 [[package]]
@@ -965,17 +766,17 @@ files = [
 
 [[package]]
 name = "setuptools"
-version = "68.2.2"
+version = "69.0.3"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.extras]
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@@ -992,57 +793,44 @@ files = [
 
 [[package]]
 name = "sqlalchemy"
-version = "1.4.49"
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 description = "Database Abstraction Library"
 optional = false
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 ]
 
 [package.dependencies]
 greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\")"}
 
 [package.extras]
-aiomysql = ["aiomysql", "greenlet (!=0.4.17)"]
-aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing-extensions (!=3.10.0.1)"]
+aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
+aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
 asyncmy = ["asyncmy (>=0.2.3,!=0.2.4)", "greenlet (!=0.4.17)"]
 mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2)"]
@@ -1052,14 +840,14 @@ mssql-pyodbc = ["pyodbc"]
 mypy = ["mypy (>=0.910)", "sqlalchemy2-stubs"]
 mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"]
 mysql-connector = ["mysql-connector-python"]
-oracle = ["cx-oracle (>=7)", "cx-oracle (>=7,<8)"]
+oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"]
 postgresql = ["psycopg2 (>=2.7)"]
 postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
 postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"]
 postgresql-psycopg2binary = ["psycopg2-binary"]
 postgresql-psycopg2cffi = ["psycopg2cffi"]
 pymysql = ["pymysql", "pymysql (<1)"]
-sqlcipher = ["sqlcipher3-binary"]
+sqlcipher = ["sqlcipher3_binary"]
 
 [[package]]
 name = "strict-rfc3339"
@@ -1084,18 +872,17 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "2.0.7"
+version = "2.1.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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-    {file = "urllib3-2.0.7.tar.gz", hash = "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84"},
+    {file = "urllib3-2.1.0-py3-none-any.whl", hash = "sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3"},
+    {file = "urllib3-2.1.0.tar.gz", hash = "sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54"},
 ]
 
 [package.extras]
 brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
-secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 
@@ -1109,18 +896,7 @@ files = [
     {file = "xlocal-0.5.zip", hash = "sha256:8ee1c1551294e366a3c307985ea2129e72717556a5736063c0e089c5fb868405"},
 ]
 
-[[package]]
-name = "xmltodict"
-version = "0.13.0"
-description = "Makes working with XML feel like you are working with JSON"
-optional = false
-python-versions = ">=3.4"
-files = [
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-]
-
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<4"
-content-hash = "455734e0df4dae8b4607acb4e2a756eb98024d1aba9253cba18f1fabf7e7e45a"
+content-hash = "8fcf07e60dbb1c84bc9a8ff7a1bde0b385725fb2c0371984674ef1e43ef36bb7"
diff --git a/pyproject.toml b/pyproject.toml
index a670a9c..e500579 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "data-simulator"
-version = "1.6.0"
+version = "1.6.1"
 description = "Gen3 Data Simulator"
 authors = ["CTDS UChicago <cdis@uchicago.edu>"]
 license = "Apache-2.0"
@@ -16,15 +16,14 @@ data-simulator = 'datasimulator.main:main'
 [tool.poetry.dependencies]
 python = ">=3.9,<4"
 cdislogging = "*"
-gen3datamodel = "*"
+gen3datamodel = {git = "https://github.com/uc-cdis/gdcdatamodel", rev = "3.1.3"}
 gen3dictionary = "*"
+pyyaml = "<7"
 rstr = ">=3,<4"
 requests = "*"
 dictionaryutils = "*"
 psqlgraph = "*"
 
-pyyaml = "<=5.1" # force version that doesn't cause "not supporting PEP 517 builds" error
-
 [tool.poetry.dev-dependencies]
 pytest = ">=7,<8"
 mock = "*"