From 6a5413b4924024a8687f7a8d9423663676f52182 Mon Sep 17 00:00:00 2001 From: Liam Brydon <62733830+MyCreativityOutlet@users.noreply.github.com> Date: Fri, 7 Nov 2025 08:09:06 +1300 Subject: [PATCH] pyproject.toml update and merge from develop --- epdb/management/commands/dump_enviformer.py | 59 +++++++++++++ epdb/management/commands/load_enviformer.py | 81 +++++++++++++++++ epdb/models.py | 13 +-- epdb/views.py | 11 ++- pyproject.toml | 2 +- templates/objects/compound.html | 20 ++++- uv.lock | 97 ++++++++++++++------- 7 files changed, 242 insertions(+), 41 deletions(-) create mode 100644 epdb/management/commands/dump_enviformer.py create mode 100644 epdb/management/commands/load_enviformer.py diff --git a/epdb/management/commands/dump_enviformer.py b/epdb/management/commands/dump_enviformer.py new file mode 100644 index 00000000..e333248a --- /dev/null +++ b/epdb/management/commands/dump_enviformer.py @@ -0,0 +1,59 @@ +import json +import os +import tarfile +from tempfile import TemporaryDirectory + +from django.conf import settings as s +from django.core.management.base import BaseCommand +from django.db import transaction + +from epdb.models import EnviFormer + + +class Command(BaseCommand): + def add_arguments(self, parser): + parser.add_argument( + "model", + type=str, + help="Model UUID of the Model to Dump", + ) + parser.add_argument("--output", type=str) + + def package_dict_and_folder(self, dict_data, folder_path, output_path): + with TemporaryDirectory() as tmpdir: + dict_filename = os.path.join(tmpdir, "data.json") + + with open(dict_filename, "w", encoding="utf-8") as f: + json.dump(dict_data, f, indent=2) + + with tarfile.open(output_path, "w:gz") as tar: + tar.add(dict_filename, arcname="data.json") + tar.add(folder_path, arcname=os.path.basename(folder_path)) + + os.remove(dict_filename) + + @transaction.atomic + def handle(self, *args, **options): + output = options["output"] + + if os.path.exists(output): + raise ValueError(f"Output file {output} already exists") + + model = EnviFormer.objects.get(uuid=options["model"]) + + data = { + "uuid": str(model.uuid), + "name": model.name, + "description": model.description, + "kv": model.kv, + "data_packages_uuids": [str(p.uuid) for p in model.data_packages.all()], + "eval_packages_uuids": [str(p.uuid) for p in model.data_packages.all()], + "threshold": model.threshold, + "eval_results": model.eval_results, + "multigen_eval": model.multigen_eval, + "model_status": model.model_status, + } + + model_folder = os.path.join(s.MODEL_DIR, "enviformer", str(model.uuid)) + + self.package_dict_and_folder(data, model_folder, output) diff --git a/epdb/management/commands/load_enviformer.py b/epdb/management/commands/load_enviformer.py new file mode 100644 index 00000000..b2f9c3e3 --- /dev/null +++ b/epdb/management/commands/load_enviformer.py @@ -0,0 +1,81 @@ +import json +import os +import shutil +import tarfile +from tempfile import TemporaryDirectory + +from django.conf import settings as s +from django.core.management.base import BaseCommand +from django.db import transaction + +from epdb.models import EnviFormer, Package + + +class Command(BaseCommand): + def add_arguments(self, parser): + parser.add_argument( + "input", + type=str, + help=".tar.gz file containing the Model dump.", + ) + parser.add_argument( + "package", + type=str, + help="Package UUID where the Model should be loaded to.", + ) + + def read_dict_and_folder_from_archive(self, archive_path, extract_to="extracted_folder"): + with tarfile.open(archive_path, "r:gz") as tar: + tar.extractall(extract_to) + + dict_path = os.path.join(extract_to, "data.json") + + if not os.path.exists(dict_path): + raise FileNotFoundError("data.json not found in the archive.") + + with open(dict_path, "r", encoding="utf-8") as f: + data_dict = json.load(f) + + extracted_items = os.listdir(extract_to) + folders = [item for item in extracted_items if item != "data.json"] + folder_path = os.path.join(extract_to, folders[0]) if folders else None + + return data_dict, folder_path + + @transaction.atomic + def handle(self, *args, **options): + if not os.path.exists(options["input"]): + raise ValueError(f"Input file {options['input']} does not exist.") + + target_package = Package.objects.get(uuid=options["package"]) + + with TemporaryDirectory() as tmpdir: + data, folder = self.read_dict_and_folder_from_archive(options["input"], tmpdir) + + model = EnviFormer() + model.package = target_package + # model.uuid = data["uuid"] + model.name = data["name"] + model.description = data["description"] + model.kv = data["kv"] + model.threshold = float(data["threshold"]) + model.eval_results = data["eval_results"] + model.multigen_eval = data["multigen_eval"] + model.model_status = data["model_status"] + model.save() + + for p_uuid in data["data_packages_uuids"]: + p = Package.objects.get(uuid=p_uuid) + model.data_packages.add(p) + + for p_uuid in data["eval_packages_uuids"]: + p = Package.objects.get(uuid=p_uuid) + model.eval_packages.add(p) + + target_folder = os.path.join(s.MODEL_DIR, "enviformer", str(model.uuid)) + + shutil.copytree(folder, target_folder) + os.rename( + os.path.join(s.MODEL_DIR, "enviformer", str(model.uuid), f"{data['uuid']}.ckpt"), + os.path.join(s.MODEL_DIR, "enviformer", str(model.uuid), f"{model.uuid}.ckpt"), + ) diff --git a/epdb/models.py b/epdb/models.py index 61cd3f1a..b7f9e82a 100644 --- a/epdb/models.py +++ b/epdb/models.py @@ -311,7 +311,7 @@ class ExternalDatabase(TimeStampedModel): }, { "database": ExternalDatabase.objects.get(name="ChEBI"), - "placeholder": "ChEBI ID without prefix e.g. 12345", + "placeholder": "ChEBI ID without prefix e.g. 10576", }, ], "structure": [ @@ -329,7 +329,7 @@ class ExternalDatabase(TimeStampedModel): }, { "database": ExternalDatabase.objects.get(name="ChEBI"), - "placeholder": "ChEBI ID without prefix e.g. 12345", + "placeholder": "ChEBI ID without prefix e.g. 10576", }, ], "reaction": [ @@ -343,7 +343,7 @@ class ExternalDatabase(TimeStampedModel): }, { "database": ExternalDatabase.objects.get(name="UniProt"), - "placeholder": "Query ID for UniPro e.g. rhea:12345", + "placeholder": "Query ID for UniProt e.g. rhea:12345", }, ], } @@ -478,7 +478,7 @@ class ChemicalIdentifierMixin(ExternalIdentifierMixin): return self.add_external_identifier("CAS", cas_number) def get_pubchem_identifiers(self): - return self.get_external_identifier("PubChem Compound") or self.get_external_identifier( + return self.get_external_identifier("PubChem Compound") | self.get_external_identifier( "PubChem Substance" ) @@ -3001,6 +3001,7 @@ class EnviFormer(PackageBasedModel): @cached_property def model(self): from enviformer import load + ckpt = os.path.join(s.MODEL_DIR, "enviformer", str(self.uuid), f"{self.uuid}.ckpt") mod = load(device=s.ENVIFORMER_DEVICE, ckpt_path=ckpt) return mod @@ -3020,7 +3021,9 @@ class EnviFormer(PackageBasedModel): start = datetime.now() products_list = self.model.predict_batch(canon_smiles) end = datetime.now() - logger.info(f"Prediction took {(end - start).total_seconds():.2f} seconds. Got results {products_list}") + logger.info( + f"Prediction took {(end - start).total_seconds():.2f} seconds. Got results {products_list}" + ) results = [] for products in products_list: diff --git a/epdb/views.py b/epdb/views.py index bf545bf3..7f8d2c41 100644 --- a/epdb/views.py +++ b/epdb/views.py @@ -1251,7 +1251,16 @@ def package_compound_structures(request, package_uuid, compound_uuid): structure_smiles = request.POST.get("structure-smiles") structure_description = request.POST.get("structure-description") - cs = current_compound.add_structure(structure_smiles, structure_name, structure_description) + try: + cs = current_compound.add_structure( + structure_smiles, structure_name, structure_description + ) + except ValueError: + return error( + request, + "Adding structure failed!", + "The structure could not be added as normalized structures don't match!", + ) return redirect(cs.url) diff --git a/pyproject.toml b/pyproject.toml index 295f8b55..26371296 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,7 @@ dependencies = [ ] [tool.uv.sources] -enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", branch = "enhancement/dataset_support" } +enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.4" } envipy-plugins = { git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git", rev = "v0.1.0" } envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git", rev = "v0.1.7"} envipy-ambit = { git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git" } diff --git a/templates/objects/compound.html b/templates/objects/compound.html index 98083ca6..90e3e1db 100644 --- a/templates/objects/compound.html +++ b/templates/objects/compound.html @@ -183,7 +183,7 @@
- {% if compound.get_pubchem_identifiers %} + {% if compound.get_pubchem_compound_identifiers %}

@@ -193,12 +193,28 @@

- {% for eid in compound.get_pubchem_identifiers %} + {% for eid in compound.get_pubchem_compound_identifiers %} CID{{ eid.identifier_value }} {% endfor %}
{% endif %} + {% if compound.get_pubchem_substance_identifiers %} +
+

+ PubChem Substance Identifier +

+
+
+ {% for eid in compound.get_pubchem_substance_identifiers %} + SID{{ eid.identifier_value }} + {% endfor %} +
+ {% endif %} {% if compound.get_chebi_identifiers %}
diff --git a/uv.lock b/uv.lock index ffa473be..0cd84139 100644 --- a/uv.lock +++ b/uv.lock @@ -1,6 +1,10 @@ version = 1 revision = 2 requires-python = ">=3.12" +resolution-markers = [ + "sys_platform == 'linux' or sys_platform == 'win32'", + "sys_platform != 'linux' and sys_platform != 'win32'", +] [[package]] name = "aiohappyeyeballs" @@ -538,13 +542,14 @@ wheels = [ [[package]] name = "enviformer" version = "0.1.0" -source = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git?branch=enhancement%2Fdataset_support#8edc3f30c46749af30c033a4faf9abe062b47970" } +source = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git?rev=v0.1.4#7094be5767748fd63d4a84a5d71f06cf02ba07f3" } dependencies = [ { name = "joblib" }, { name = "lightning" }, { name = "pytorch-lightning" }, { name = "scikit-learn" }, - { name = "torch" }, + { name = "torch", version = "2.8.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, + { name = "torch", version = "2.8.0+cu128", source = { registry = "https://download.pytorch.org/whl/cu128" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, ] [[package]] @@ -600,7 +605,7 @@ requires-dist = [ { name = "django-oauth-toolkit", specifier = ">=3.0.1" }, { name = "django-polymorphic", specifier = ">=4.1.0" }, { name = "django-stubs", marker = "extra == 'dev'", specifier = ">=5.2.4" }, - { name = "enviformer", git = "ssh://git@git.envipath.com/enviPath/enviformer.git?branch=enhancement%2Fdataset_support" }, + { name = "enviformer", git = "ssh://git@git.envipath.com/enviPath/enviformer.git?rev=v0.1.4" }, { name = "envipy-additional-information", git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?rev=v0.1.7" }, { name = "envipy-ambit", git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git" }, { name = "envipy-plugins", git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git?rev=v0.1.0" }, @@ -609,7 +614,7 @@ requires-dist = [ { name = "msal", marker = "extra == 'ms-login'", specifier = ">=1.33.0" }, { name = "networkx", specifier = ">=3.4.2" }, { name = "poethepoet", marker = "extra == 'dev'", specifier = ">=0.37.0" }, - { name = "polars", specifier = "==1.34.0" }, + { name = "polars", specifier = "==1.35.1" }, { name = "pre-commit", marker = "extra == 'dev'", specifier = ">=4.3.0" }, { name = "psycopg2-binary", specifier = ">=2.9.10" }, { name = "python-dotenv", specifier = ">=1.1.0" }, @@ -882,7 +887,8 @@ dependencies = [ { name = "packaging" }, { name = "pytorch-lightning" }, { name = "pyyaml" }, - 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