Fixed #72

databio · Mar 1, 2024 · fc75de0 · fc75de0
1 parent f5ddc50
commit fc75de0
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diff --git a/README.md b/README.md
@@ -1,9 +1,25 @@
-# bedhost
+<h1 align="center">bedhost</h1>
+
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Github badge](https://img.shields.io/badge/source-github-354a75?logo=github)](https://github.com/databio/bedhost)
+
 
 `bedhost` is a Python FastAPI module for the API that powers BEDbase
 It needs a path to the *bedbase configuration file*, which can be provided either via `-c`/`--config` argument or read from `$BEDBASE_CONFIG` environment variable. 
 
+---
+
+**Deployed public instance**: <a href="https://bedbase.org/" target="_blank">https://bedbase.org/</a>
+
+**Documentation**: <a href="https://docs.bedbase.org/" target="_blank">https://docs.bedbase.org/bedhost</a>
+
+**API**: <a href="https://api.bedbase.org/" target="_blank">https://api.bedbase.org/</a>
+
+**Source Code**: <a href="https://github.com/databio/bedhost/" target="_blank">https://github.com/databio/bedhost/</a>
+
+---
+
+
 ## Running for development
 
 Running with `uvicorn` provides auto-reload. To configure, this assumes you have previously set up `databio/secrets`. 
@@ -29,6 +45,7 @@ Now, you can access the service at [http://127.0.0.1:8000](http://127.0.0.1:8000
 - 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/metadata
 - 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/metadata?attr_ids=md5sum&attr_ids=genome
 
+----
 ## Running the server in Docker
 
 ### Building image
@@ -43,6 +60,7 @@ Existing images can be found [at dockerhub](https://hub.docker.com/r/databio/bed
 
 Configuration settings and deployment instructions are in the `bedbase.org` repository.
 
+---
 
 ## Deploying updates automatically
 

diff --git a/bedhost/_version.py b/bedhost/_version.py
@@ -1 +1 @@
-__version__ = "0.2.0"
+__version__ = "0.3.0"
diff --git a/bedhost/const.py b/bedhost/const.py
@@ -32,41 +32,6 @@
     "number": {"min": 0, "step": 0.01},
     "string": None,
 }
-NUMERIC_OPERATORS = [
-    "equal",
-    "not_equal",
-    "greater",
-    "greater_or_equal",
-    "between",
-    "less",
-    "less_or_equal",
-    "is_null",
-    "is_not_null",
-]
-TEXT_OPERATORS = ["equal", "not_equal", "in", "not_in", "is_null", "is_not_null"]
-OPERATORS_MAPPING = {
-    "string": TEXT_OPERATORS,
-    "number": NUMERIC_OPERATORS,
-    "integer": NUMERIC_OPERATORS,
-}
-INIT_POSTGRES_CONDITION = "gc_content>0.5"
-INIT_QUERYBUILDER = {
-    "condition": "AND",
-    "rules": [
-        {
-            "id": "gc_content",
-            "field": "gc_content",
-            "type": "double",
-            "input": "number",
-            "operator": "greater",
-            "value": 0.5,
-        }
-    ],
-    "valid": True,
-}
-CUR_RESULT = "current_result"
-CUR_RULES = "current_rules"
-
 
 class FIG_FORMAT(str, Enum):
     png = "png"

diff --git a/bedhost/helpers.py b/bedhost/helpers.py
@@ -2,15 +2,8 @@
 
 from bbconf import BedBaseConf
 from starlette.responses import FileResponse, RedirectResponse, JSONResponse
-from typing import List
-from urllib import parse
 
 from . import _LOGGER
-from .const import (
-    TYPES_MAPPING,
-    VALIDATIONS_MAPPING,
-    OPERATORS_MAPPING,
-)
 from .exceptions import BedHostException
 
 
@@ -22,6 +15,7 @@ class BedHostConf(BedBaseConf):
     def __init__(self, config_path: str = None):
         super().__init__(config_path)
 
+    # TODO: should it be moved to bbconf?
     def serve_file(self, path: str, remote: bool = None):
         """
         Serve a local or remote file
@@ -73,111 +67,111 @@ def bedset_retrieve(self, digest: str, column: str) -> dict:
         except KeyError:
             return {}
 
-
-def get_search_setup(schema: dict):
-    """
-    Create a query setup for QueryBuilder to interface the DB.
-
-    :param dict schema: pipestat schema
-    :return list[dict]: a list dictionaries with search setup to use
-        in QueryBuilder
-    """
-    setup_dicts = []
-    for col_name, col_schema in schema.items():
-        try:
-            setup_dict = {
-                "id": col_name,
-                "label": col_schema["description"],
-                "type": TYPES_MAPPING[col_schema["type"]],
-                "validation": VALIDATIONS_MAPPING[col_schema["type"]],
-                "operators": OPERATORS_MAPPING[col_schema["type"]],
-            }
-        except (AttributeError, KeyError):
-            _LOGGER.warning(
-                f"Database column '{col_name}' of type "
-                f"'{col_schema['type']}' has no query builder "
-                f"settings predefined, skipping."
-            )
-        else:
-            setup_dicts.append(setup_dict)
-    return setup_dicts
-
-
-def construct_search_data(hits: list, request) -> List[List[str]]:
-    """
-    Construct a list of links to display as the search result
-
-    :param Iterable[str] hits: ids to compose the list for
-    :param starlette.requests.Request request: request for the context
-    :return Iterable[list]: results to display
-    """
-    template_data = []
-    for h in hits:
-        bed_data_url_template = (
-            request.url_for("bedfile") + f"?md5sum={h['md5sum']}&format="
-        )
-        template_data.append(
-            [h["name"]]
-            + [bed_data_url_template + ext for ext in ["html", "bed", "json"]]
-        )
-    return template_data
-
-
-def get_mounted_symlink_path(symlink: str) -> str:
-    """
-    Get path to the symlinks target on a mounted filesystem volume.
-    Accounts for both transformed and non-transformed symlink targets
-
-    :param str symlink: absolute symlink path
-    :return str: path to the symlink target on the mounted volume
-    """
-
-    def _find_mount_point(path):
-        path = os.path.abspath(path)
-        while not os.path.ismount(path):
-            path = os.path.dirname(path)
-        return path
-
-    link_tgt = os.readlink(symlink)
-    if not os.path.isabs(link_tgt):
-        _LOGGER.debug("Volume mounted with symlinks transformation")
-        return os.path.abspath(os.path.join(os.path.dirname(symlink), link_tgt))
-    mnt_point = _find_mount_point(symlink)
-    first = os.path.relpath(symlink, mnt_point).split("/")[0]
-    common_idx = link_tgt.split("/").index(first)
-    rel_tgt = os.path.join(*link_tgt.split("/")[common_idx:])
-    return os.path.join(mnt_point, rel_tgt)
-
-
-def get_all_bedset_urls_mapping(bbc: BedBaseConf, request):
-    """
-    Get a mapping of all bedset ids and corrsponding splaspages urls
-
-    :param bbconf.BedBaseConf bbc: bedbase configuration object
-    :param starlette.requests.Request request: request context for url generation
-    :return Mapping: a mapping of bedset ids and the urls to the corresponding splashpages
-    """
-    hits = bbc.bedset.backend.select(columns=["name", "md5sum"])
-    if not hits:
-        return
-    # TODO: don't hardcode url path element name, use operationID?
-    return {
-        hit.name: get_param_url(request.url_for("bedsetsplash"), {"md5sum": hit.md5sum})
-        for hit in hits
-    }
-
-
-def get_param_url(url, params):
-    """
-    Create parametrized URL
-
-    :param str url: URL base to parametrize
-    :param Mapping params: a mapping of URL parameters and values
-    :return str: parametrized URL
-    """
-    if not params:
-        return url
-    return url + "?" + parse.urlencode(params)
+# TODO: remove this function if everything works
+# def get_search_setup(schema: dict):
+#     """
+#     Create a query setup for QueryBuilder to interface the DB.
+#
+#     :param dict schema: pipestat schema
+#     :return list[dict]: a list dictionaries with search setup to use
+#         in QueryBuilder
+#     """
+#     setup_dicts = []
+#     for col_name, col_schema in schema.items():
+#         try:
+#             setup_dict = {
+#                 "id": col_name,
+#                 "label": col_schema["description"],
+#                 "type": TYPES_MAPPING[col_schema["type"]],
+#                 "validation": VALIDATIONS_MAPPING[col_schema["type"]],
+#                 "operators": OPERATORS_MAPPING[col_schema["type"]],
+#             }
+#         except (AttributeError, KeyError):
+#             _LOGGER.warning(
+#                 f"Database column '{col_name}' of type "
+#                 f"'{col_schema['type']}' has no query builder "
+#                 f"settings predefined, skipping."
+#             )
+#         else:
+#             setup_dicts.append(setup_dict)
+#     return setup_dicts
+#
+#
+# def construct_search_data(hits: list, request) -> List[List[str]]:
+#     """
+#     Construct a list of links to display as the search result
+#
+#     :param Iterable[str] hits: ids to compose the list for
+#     :param starlette.requests.Request request: request for the context
+#     :return Iterable[list]: results to display
+#     """
+#     template_data = []
+#     for h in hits:
+#         bed_data_url_template = (
+#             request.url_for("bedfile") + f"?md5sum={h['md5sum']}&format="
+#         )
+#         template_data.append(
+#             [h["name"]]
+#             + [bed_data_url_template + ext for ext in ["html", "bed", "json"]]
+#         )
+#     return template_data
+#
+#
+# def get_mounted_symlink_path(symlink: str) -> str:
+#     """
+#     Get path to the symlinks target on a mounted filesystem volume.
+#     Accounts for both transformed and non-transformed symlink targets
+#
+#     :param str symlink: absolute symlink path
+#     :return str: path to the symlink target on the mounted volume
+#     """
+#
+#     def _find_mount_point(path):
+#         path = os.path.abspath(path)
+#         while not os.path.ismount(path):
+#             path = os.path.dirname(path)
+#         return path
+#
+#     link_tgt = os.readlink(symlink)
+#     if not os.path.isabs(link_tgt):
+#         _LOGGER.debug("Volume mounted with symlinks transformation")
+#         return os.path.abspath(os.path.join(os.path.dirname(symlink), link_tgt))
+#     mnt_point = _find_mount_point(symlink)
+#     first = os.path.relpath(symlink, mnt_point).split("/")[0]
+#     common_idx = link_tgt.split("/").index(first)
+#     rel_tgt = os.path.join(*link_tgt.split("/")[common_idx:])
+#     return os.path.join(mnt_point, rel_tgt)
+#
+#
+# def get_all_bedset_urls_mapping(bbc: BedBaseConf, request):
+#     """
+#     Get a mapping of all bedset ids and corrsponding splaspages urls
+#
+#     :param bbconf.BedBaseConf bbc: bedbase configuration object
+#     :param starlette.requests.Request request: request context for url generation
+#     :return Mapping: a mapping of bedset ids and the urls to the corresponding splashpages
+#     """
+#     hits = bbc.bedset.backend.select(columns=["name", "md5sum"])
+#     if not hits:
+#         return
+#     # TODO: don't hardcode url path element name, use operationID?
+#     return {
+#         hit.name: get_param_url(request.url_for("bedsetsplash"), {"md5sum": hit.md5sum})
+#         for hit in hits
+#     }
+
+
+# def get_param_url(url, params):
+#     """
+#     Create parametrized URL
+#
+#     :param str url: URL base to parametrize
+#     :param Mapping params: a mapping of URL parameters and values
+#     :return str: parametrized URL
+#     """
+#     if not params:
+#         return url
+#     return url + "?" + parse.urlencode(params)
 
 
 def get_openapi_version(app):

diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
@@ -1,10 +1,9 @@
-bbconf>=0.4.0
+bbconf>=0.4.1
 fastapi>=0.103.0
 geniml>=0.1.0
 logmuse>=0.2.7
 markdown
 requests
 setuptools
 uvicorn
-yacman>=0.9.2
-markdown
+yacman>=0.9.2