Merge pull request #101 from databio/dev

release 0.4.0

.gitignore

@@ -25,4 +25,6 @@ bedhost/static/bedhost-ui/
 # For building
 geniml
 
-local_cache
+local_cache
+
+environment/

.vscode/launch.json

@@ -0,0 +1,17 @@
+{
+  // Use IntelliSense to learn about possible attributes.
+  // Hover to view descriptions of existing attributes.
+  // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "name": "Python Debugger: FastAPI",
+      "type": "debugpy",
+      "request": "launch",
+      "module": "uvicorn",
+      "args": ["bedhost.main:app", "--reload"],
+      "jinja": true,
+      "justMyCode": false
+    }
+  ]
+}

Dockerfile

@@ -21,6 +21,11 @@ COPY . /app
 
 RUN python -m pip install --upgrade pip
 
+# Need this command due to geniml dependency on hnswlib
+ENV HNSWLIB_NO_NATIVE=1
+RUN apt-get install -y python3-dev
+RUN apt-get install -y build-essential
+
 # Install CPU-only pytorch, eliminating huge nvidia dependencies
 RUN pip install torch==2.1.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
 RUN pip install https://github.com/pepkit/pipestat/archive/refs/heads/dev.zip

bedhost/_version.py

@@ -1 +1 @@
-__version__ = "0.3.0"
+__version__ = "0.4.0"

bedhost/cli.py

@@ -1,8 +1,6 @@
 from . import PKG_NAME
 from ._version import __version__
 from ubiquerg import VersionInHelpParser
-from yacman import select_config
-from bbconf.const import CFG_ENV_VARS
 
 
 def build_parser():
@@ -12,7 +10,7 @@ def build_parser():
     :return argparse.ArgumentParser
     """
 
-    env_var_val = select_config(config_env_vars=CFG_ENV_VARS)
+    # env_var_val = select_config(config_env_vars=CFG_ENV_VARS)
 
     banner = "%(prog)s - REST API for the bedstat pipeline produced statistics"
     additional_description = (
@@ -45,7 +43,6 @@ def add_subparser(cmd, description):
             required=False,
             dest="config",
             help="A path to the bedhost config file (YAML). If not provided, "
-            f"the first available environment variable among: {', '.join(CFG_ENV_VARS)} will be used if set."
-            f" Currently: {env_var_val}",
+            f"the first available environment variable among: {', '.join(CFG_ENV_VARS)} will be used if set.",
         )
     return parser

bedhost/const.py

@@ -1,13 +1,10 @@
 import os
-from enum import Enum
 from platform import python_version
-
 from bbconf import __version__ as bbconf_v
 
 from ._version import __version__ as SERVER_VERSION
 
 PKG_NAME = "bedhost"
-LOG_FORMAT = "%(levelname)s in %(funcName)s: %(message)s"
 
 # for now bedstat version is hard coded
 ALL_VERSIONS = {
@@ -16,30 +13,8 @@
     "python_version": python_version(),
 }
 TEMPLATES_DIRNAME = "templates"
-TEMPLATES_PATH = os.path.join(
-    os.path.dirname(os.path.abspath(__file__)), TEMPLATES_DIRNAME
-)
 STATIC_DIRNAME = "../docs"
 STATIC_PATH = os.path.join(os.path.dirname(os.path.abspath(__file__)), STATIC_DIRNAME)
 
-UI_PATH = os.path.join(os.path.dirname(__file__), "static", "bedhost-ui")
-
-BEDFILE_API_ENDPOINT = "bedfile"
-BEDSET_API_ENDPOINT = "bedset"
-TYPES_MAPPING = {"integer": "integer", "number": "double", "string": "string"}
-VALIDATIONS_MAPPING = {
-    "integer": {"min": 0, "step": 1},
-    "number": {"min": 0, "step": 0.01},
-    "string": None,
-}
-
-
-class FIG_FORMAT(str, Enum):
-    png = "png"
-    pdf = "pdf"
-
-
-class TABLE_NAME(str, Enum):
-    bedfiles = "bedfiles"
-    bedsets = "bedsets"
-    bedset_bedfiles = "bedset_bedfiles"
+EXAMPLE_BED = "bbad85f21962bb8d972444f7f9a3a932"
+EXAMPLE_BEDSET = "gse218680"

bedhost/data_models.py

@@ -1,9 +1,6 @@
-from typing import Dict, List, Union, Any
 from fastapi import Path
 from pydantic import BaseModel
 from enum import Enum
-from .model_parser import yaml_to_pydantic
-from .main import bbc
 
 RemoteClassEnum = Enum(
     "RemoteClassEnum",
@@ -27,42 +24,41 @@ class BedList(BaseModel):
     # example=ex_bed_digest,
 )
 
-chromosome_number = Path(
+CROM_NUMBERS = Path(
     ...,
     description="Chromosome number",
     regex=r"^\S+$",
     example=ex_chr,
 )
 
 
-class BedsetResponse(BaseModel):
-    bedset_record_id: str
-    number_of_bedfiles: int
-    bedfile_metadata: List[Dict]
+class Type(BaseModel):
+    group: str
+    artifact: str
+    version: str
 
 
-BedFile = yaml_to_pydantic("BedFile", bbc.bed._schema_path)
+class Organization(BaseModel):
+    name: str
+    url: str
 
 
-class BedMetadataResponse(BaseModel):
-    record_identifier: str
-    metadata: BedFile
-    raw: Union[Dict[str, Any], None] = None
+class ComponentVersions(BaseModel):
+    bedhost_version: str
+    bbconf_version: str
+    python_version: str
+    openapi_version: str
 
 
-class RecordsIdReturn(BaseModel):
-    record_identifier: str = None
-    name: Union[str, None] = (None,)
-
-
-class ListBedFilesResponse(BaseModel):
-    total_size: int
-    page_size: int
-    next_page_token: int
-    records: List[RecordsIdReturn]
-
-
-class BedSetMetadataResponse(BaseModel):
-    record_identifier: str
-    metadata: yaml_to_pydantic("BedSet", bbc.bedset._schema_path)
-    raw: Union[Dict[str, Any], None] = None
+class ServiceInfoResponse(BaseModel):
+    id: str
+    name: str
+    type: Type
+    description: str
+    organization: Organization
+    contactUrl: str
+    documentationUrl: str
+    updatedAt: str
+    environment: str
+    version: str
+    component_versions: ComponentVersions