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New "finders" structure ToolFinder page structure update Thanks @uwwint
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| from .common import Dataprovider | ||
| from .toolfinder import Tool, ToolDB, ToolMatrixDataProvider, ZeusDataProvider, MagnusDataProvider, QriscloudDataProvider, GadiDataProvider, if89DataProvider, GalaxyDataProvider, BiotoolsDataProvider, SetonixDataProvider | ||
| from .workflowfinder import Workflow, WorkflowDB, WorkflowHubSpaceDataProvider |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,163 @@ | ||
| import datetime | ||
| from enum import Enum | ||
| from abc import abstractmethod | ||
| import pandas as pd | ||
| from typing import List | ||
| import numpy as np | ||
|
|
||
| class Dataprovider: | ||
| """ | ||
| Class representing a data source, which enriches information about a tool. | ||
| """ | ||
| class FIELD_NAMES(Enum): | ||
| # toolfinder | ||
| REPOSITORY_URL = "FIELD_NAMES.REPOSITORY_URL" | ||
| NAME = "FIELD_NAMES.NAME" | ||
| TOOL_IDENTIFIER = "FIELD_NAMES.TOOL_IDENTIFIER" | ||
| BIOTOOLS_ID = "FIELD_NAMES.BIOTOOLS_ID" | ||
| INCLUSION = "FIELD_NAMES.INCLUSION" | ||
| BIOCOMMONS_DOCUMENTATION_DESCRIPTION = "FIELD_NAMES.BIOCOMMONS_DOCUMENTATION_DESCRIPTION" | ||
| BIOCOMMONS_DOCUMENTATION_LINK = "FIELD_NAMES.BIOCOMMONS_DOCUMENTATION_LINK" | ||
| DESCRIPTION = "FIELD_NAMES.DESCRIPTION" | ||
| LICENSE = "FIELD_NAMES.LICENSE" | ||
| EDAM_TOPICS = "FIELD_NAMES.EDAM_TOPICS" | ||
| PUBLICATIONS = "FIELD_NAMES.PUBLICATIONS" | ||
| GALAXY_AUSTRALIA_LAUNCH_LINK = "FIELD_NAMES.GALAXY_AUSTRALIA_LAUNCH_LINK" | ||
| NCI_GADI_VERSION = "FIELD_NAMES.NCI_GADI_VERSION" | ||
| NCI_IF89_VERSION = "FIELD_NAMES.NCI_IF89_VERSION" | ||
| PAWSEY_ZEUS_VERSION = "FIELD_NAMES.PAWSEY_ZEUS_VERSION" | ||
| PAWSEY_MAGNUS_VERSION = "FIELD_NAMES.PAWSEY_MAGNUS_VERSION" | ||
| QRISCLOUD_VERSION = "FIELD_NAMES.QRISCLOUD_VERSION" | ||
| PAWSEY_SETONIX_VERSION = "FIELD_NAMES.PAWSEY_SETONIX_VERSION" | ||
| # workflowfinder | ||
| UPDATED_AT = "FIELD_NAMES.UPDATED_AT" | ||
| PROJECTS = "FIELD_NAMES.PROJECTS" | ||
| TITLE = "FIELD_NAMES.TITLE" | ||
| TAGS = "FIELD_NAMES.TAGS" | ||
| DOI = "FIELD_NAMES.DOI" | ||
| EDAM_OPS = "FIELD_NAMES.EDAM_OPS" | ||
| EDAM_TOP = "FIELD_NAMES.EDAM_TOP" | ||
| URL = "FIELD_NAMES.URL" | ||
| LAUNCH_LINK = "FIELD_NAMES.LAUNCH_LINK" | ||
| GUIDE_LINK = "FIELD_NAMES.GUIDE_LINK" | ||
|
|
||
| def __init__(self): | ||
| self.identifier = "" | ||
| """available_data is keyed by the toolid and should contain all information received by this data provider""" | ||
| self.available_data = {} | ||
| self.unmatched_data = {} | ||
| self.last_queried = datetime.datetime.min | ||
|
|
||
| def _save_unmatched_(self, key, data): | ||
| self.unmatched_data[key] = data | ||
|
|
||
| def query_remote(self): | ||
| if self._needs_querying(): | ||
| self._query_remote() | ||
| self.last_queried = datetime.datetime.now() | ||
|
|
||
| """ | ||
| _query_remote queries a remote data source, transforms the information received into internal identifiers to be later joined onto all available tools. | ||
| """ | ||
|
|
||
| @abstractmethod | ||
| def _query_remote(self): | ||
| pass | ||
|
|
||
| """needs re-querying if data is more than 7 days old""" | ||
|
|
||
| def _needs_querying(self): | ||
| return (datetime.datetime.now() - self.last_queried) > datetime.timedelta(days=7) | ||
|
|
||
| """get information """ | ||
|
|
||
| def get_information(self, uid): | ||
| if uid in self.available_data: | ||
| return self.available_data[uid] | ||
| else: | ||
| return None | ||
|
|
||
| """Data provider are keyed by id""" | ||
|
|
||
| def __eq__(self, other): | ||
| if isinstance(other, Dataprovider): | ||
| return self.identifier == other.identifier | ||
| else: | ||
| return False | ||
|
|
||
| """public wrapper for _render""" | ||
|
|
||
| def render(self, tool): | ||
| data = tool.get_data(self) | ||
| if data is not None: | ||
| return self._render(data) | ||
| return {} | ||
|
|
||
| """render information""" | ||
|
|
||
| @abstractmethod | ||
| def _render(self, data): | ||
| pass | ||
|
|
||
| def get_alt_ids(self): | ||
| return{} | ||
|
|
||
|
|
||
| class DB: | ||
| """represents the database for all known tools""" | ||
|
|
||
| def __init__(self): | ||
| self.db = {} | ||
| self.dataprovider: List[Dataprovider] | ||
| self.dataprovider = [] | ||
| self.alternateids = {} | ||
|
|
||
| """enrich the DB with what the dataprovider has queried from its datasource""" | ||
|
|
||
| def _enrich(self, dataprovider: Dataprovider): | ||
|
|
||
| alt_ids = dataprovider.get_alt_ids() | ||
| # https://stackoverflow.com/a/26853961 & https://www.python.org/dev/peps/pep-0584/ | ||
| self.alternateids = {**self.alternateids, **alt_ids} | ||
|
|
||
| dataprovider.query_remote() | ||
|
|
||
| for i in self.db: | ||
| tool = self.db[i] | ||
| tool.add_data(dataprovider) | ||
|
|
||
| def get_id_from_alt(self, provider:str, unique_id:str): | ||
| #unique_id = unique_id.lower() | ||
| if provider in self.alternateids: | ||
| if unique_id in self.alternateids[provider]: | ||
| return self.alternateids[provider][unique_id] | ||
| return [] | ||
|
|
||
| def get_unmatched_ids(self, dp:Dataprovider): | ||
| a = dp.unmatched_data | ||
| unmatched_ids = set(dp.available_data.keys()).difference(self.db.keys()) | ||
| return(a, unmatched_ids) | ||
|
|
||
|
|
||
| """add a dataprovider to the list of providers""" | ||
|
|
||
| def add_provider(self, provider: Dataprovider): | ||
| self.dataprovider.append(provider) | ||
| self._enrich(provider) | ||
|
|
||
| def get_data(self): | ||
| data = [] | ||
| for i in self.db: | ||
| line = [] | ||
| for dp in self.dataprovider: | ||
| line.append(dp.render(self.db[i])) | ||
| result = {} | ||
| for element in line: | ||
| result.update(element) | ||
| data.append(result) | ||
|
|
||
| return pd.DataFrame(data) | ||
|
|
||
| @abstractmethod | ||
| def get_formatted_table(self) -> pd.DataFrame: | ||
| pass |
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