add the cli code from findpapers and install the required dependencies …

…#40

findpapers/__init__.py

@@ -0,0 +1,17 @@
+import logging
+import os
+from typing import Optional
+
+from findpapers.tools.bibtex_generator_tool import generate_bibtex
+from findpapers.tools.downloader_tool import download
+from findpapers.tools.rayyan_tool import RayyanExport
+from findpapers.tools.refiner_tool import refine
+from findpapers.tools.refman_tool import RisExport
+from findpapers.tools.search_runner_tool import search
+
+try:
+    import importlib.metadata as importlib_metadata
+except ModuleNotFoundError:
+    import importlib_metadata
+
+__version__ = importlib_metadata.version(__name__)

findpapers/cli.py

@@ -0,0 +1,328 @@
+import logging
+from datetime import datetime
+from pathlib import Path
+from typing import List
+
+import typer
+
+import findpapers
+
+app = typer.Typer()
+
+
+@app.command("search")
+def search(
+    outputpath: str = typer.Argument(..., help="A valid file path where the search result JSON file will be placed"),
+    query: str = typer.Option(
+        None,
+        "-q",
+        "--query",
+        show_default=True,
+        help="A query string that will be used to perform the papers search (If not provided it will be loaded from the environment variable FINDPAPERS_QUERY). E.g. [term A] AND ([term B] OR [term C]) AND NOT [term D]",
+    ),
+    query_filepath: str = typer.Option(
+        None,
+        "-f",
+        "--query-file",
+        show_default=True,
+        help="A file path that contains the query string that will be used to perform the papers search",
+    ),
+    since: datetime = typer.Option(
+        None,
+        "-s",
+        "--since",
+        show_default=True,
+        help="A lower bound (inclusive) date that will be used to filter the search results. Following the pattern YYYY-MM-DD. E.g. 2020-12-31",
+        formats=["%Y-%m-%d"],
+    ),
+    until: datetime = typer.Option(
+        None,
+        "-u",
+        "--until",
+        show_default=True,
+        help="A upper bound (inclusive) date that will be used to filter the search results. Following the pattern YYYY-MM-DD. E.g. 2020-12-31",
+        formats=["%Y-%m-%d"],
+    ),
+    limit: int = typer.Option(None, "-l", "--limit", show_default=True, help="The max number of papers to collect"),
+    limit_per_database: int = typer.Option(
+        None,
+        "-ld",
+        "--limit-db",
+        show_default=True,
+        help="The max number of papers to collect per each database",
+    ),
+    databases: str = typer.Option(
+        None,
+        "-d",
+        "--databases",
+        show_default=True,
+        help="A comma-separated list of databases where the search should be performed, if not specified all databases will be used (this parameter is case insensitive)",
+    ),
+    publication_types: str = typer.Option(
+        None,
+        "-p",
+        "--publication-types",
+        show_default=True,
+        help="A comma-separated list of publication types to filter when searching, if not specified all the publication types will be collected (this parameter is case insensitive). The available publication types are: journal, conference proceedings, book, other",
+    ),
+    scopus_api_token: str = typer.Option(
+        None,
+        "-ts",
+        "--token-scopus",
+        show_default=True,
+        help="A API token used to fetch data from Scopus database. If you don't have one go to https://dev.elsevier.com and get it. (If not provided it will be loaded from the environment variable FINDPAPERS_SCOPUS_API_TOKEN)",
+    ),
+    ieee_api_token: str = typer.Option(
+        None,
+        "-ti",
+        "--token-ieee",
+        show_default=True,
+        help="A API token used to fetch data from IEEE database. If you don't have one go to https://developer.ieee.org and get it. (If not provided it will be loaded from the environment variable FINDPAPERS_IEEE_API_TOKEN)",
+    ),
+    proxy: str = typer.Option(
+        None,
+        "-x",
+        "--proxy",
+        show_default=True,
+        help="proxy URL that can be used during requests",
+    ),
+    verbose: bool = typer.Option(
+        False,
+        "-v",
+        "--verbose",
+        show_default=True,
+        help="If you wanna a verbose mode logging",
+    ),
+) -> None:
+    try:
+        since = since.date() if since else None
+        until = until.date() if until else None
+        databases = [x.strip() for x in databases.split(",")] if databases else None
+        publication_types = [x.strip() for x in publication_types.split(",")] if publication_types else None
+
+        if query is None and query_filepath:
+            with Path(query_filepath).open("r") as f:
+                query = f.read().strip()
+
+        findpapers.search(
+            outputpath,
+            query,
+            since,
+            until,
+            limit,
+            limit_per_database,
+            databases,
+            publication_types,
+            scopus_api_token,
+            ieee_api_token,
+            proxy,
+            verbose,
+        )
+    except Exception as e:
+        if verbose:
+            logging.debug(e, exc_info=True)
+        else:
+            typer.echo(e)
+        raise typer.Exit(code=1)
+
+
+@app.command("refine")
+def refine(
+    filepath: str = typer.Argument(..., help="A valid file path for the search result file"),
+    categories: List[str] = typer.Option(
+        [],
+        "-c",
+        "--categories",
+        show_default=True,
+        help="A comma-separated list of categories to assign to the papers with their facet following the pattern: <facet>:<term_b>,<term_c>,...",
+    ),
+    highlights: str = typer.Option(
+        None,
+        "-h",
+        "--highlights",
+        show_default=True,
+        help="A comma-separated list of terms to be highlighted on the abstract",
+    ),
+    show_abstract: bool = typer.Option(
+        False,
+        "-a",
+        "--abstract",
+        show_default=True,
+        help="A flag to indicate if the paper's abstract should be shown or not",
+    ),
+    show_extra_info: bool = typer.Option(
+        False,
+        "-e",
+        "--extra-info",
+        show_default=True,
+        help="A flag to indicate if the paper's extra info should be shown or not",
+    ),
+    only_selected_papers: bool = typer.Option(
+        False,
+        "-s",
+        "--selected",
+        show_default=True,
+        help="If only the selected papers will be refined",
+    ),
+    only_removed_papers: bool = typer.Option(
+        False,
+        "-r",
+        "--removed",
+        show_default=True,
+        help="If only the removed papers will be refined",
+    ),
+    read_only: bool = typer.Option(
+        False,
+        "-l",
+        "--list",
+        show_default=True,
+        help="If this flag is present, this function call will only list the papers",
+    ),
+    verbose: bool = typer.Option(
+        False,
+        "-v",
+        "--verbose",
+        show_default=True,
+        help="If you wanna a verbose mode logging",
+    ),
+) -> None:
+    try:
+        highlights = [x.strip() for x in highlights.split(",")] if highlights else None
+
+        categories_by_facet = {} if len(categories) > 0 else None
+        for categories_string in categories:
+            string_split = categories_string.split(":")
+            facet = string_split[0].strip()
+            categories_by_facet[facet] = [x.strip() for x in string_split[1].split(",")]
+
+        findpapers.refine(
+            filepath,
+            categories_by_facet,
+            highlights,
+            show_abstract,
+            show_extra_info,
+            only_selected_papers,
+            only_removed_papers,
+            read_only,
+            verbose,
+        )
+    except Exception as e:
+        if verbose:
+            logging.debug(e, exc_info=True)
+        else:
+            typer.echo(e)
+        raise typer.Exit(code=1)
+
+
+@app.command("download")
+def download(
+    filepath: str = typer.Argument(..., help="A valid file path for the search result file"),
+    outputpath: str = typer.Argument(..., help="A valid directory path where the downloaded papers will be placed"),
+    only_selected_papers: bool = typer.Option(
+        False,
+        "-s",
+        "--selected",
+        show_default=True,
+        help="A flag to indicate if only selected papers (selections can be done on refine command) will be downloaded",
+    ),
+    categories: List[str] = typer.Option(
+        [],
+        "-c",
+        "--categories",
+        show_default=True,
+        help="A comma-separated list of categories (categorization can be done on refine command) that will be used to filter which papers will be downloaded, using the following pattern: <facet>:<term_b>,<term_c>,...",
+    ),
+    proxy: str = typer.Option(
+        None,
+        "-x",
+        "--proxy",
+        show_default=True,
+        help="proxy URL that can be used during requests",
+    ),
+    verbose: bool = typer.Option(
+        False,
+        "-v",
+        "--verbose",
+        show_default=True,
+        help="If you wanna a verbose mode logging",
+    ),
+) -> None:
+    try:
+        categories_by_facet = {} if len(categories) > 0 else None
+        for categories_string in categories:
+            string_split = categories_string.split(":")
+            facet = string_split[0].strip()
+            categories_by_facet[facet] = [x.strip() for x in string_split[1].split(",")]
+
+        findpapers.download(filepath, outputpath, only_selected_papers, categories_by_facet, proxy, verbose)
+    except Exception as e:
+        if verbose:
+            logging.debug(e, exc_info=True)
+        else:
+            typer.echo(e)
+        raise typer.Exit(code=1)
+
+
+@app.command("bibtex")
+def bibtex(
+    filepath: str = typer.Argument(..., help="A valid file path for the search result file"),
+    outputpath: str = typer.Argument(..., help="A valid directory path where the generated bibtex will be placed"),
+    only_selected_papers: bool = typer.Option(
+        False,
+        "-s",
+        "--selected",
+        show_default=True,
+        help="A flag to indicate if only selected papers (selections be done on refine command) will be used for bibtex generation",
+    ),
+    categories: List[str] = typer.Option(
+        [],
+        "-c",
+        "--categories",
+        show_default=True,
+        help="A comma-separated list of categories (categorization can be done on refine command) that will be used to filter which papers will be used for bibtex generation, using the following pattern: <facet>:<term_b>,<term_c>,...",
+    ),
+    add_findpapers_citation: bool = typer.Option(
+        False,
+        "-f",
+        "--findpapers",
+        show_default=True,
+        help="A flag to indicate if you want to add an entry for Findpapers in your BibTeX output file",
+    ),
+    verbose: bool = typer.Option(
+        False,
+        "-v",
+        "--verbose",
+        show_default=True,
+        help="If you wanna a verbose mode logging",
+    ),
+) -> None:
+    try:
+        categories_by_facet = {} if len(categories) > 0 else None
+        for categories_string in categories:
+            string_split = categories_string.split(":")
+            facet = string_split[0].strip()
+            categories_by_facet[facet] = [x.strip() for x in string_split[1].split(",")]
+
+        findpapers.generate_bibtex(
+            filepath,
+            outputpath,
+            only_selected_papers,
+            categories_by_facet,
+            add_findpapers_citation,
+            verbose,
+        )
+    except Exception as e:
+        if verbose:
+            logging.debug(e, exc_info=True)
+        else:
+            typer.echo(e)
+        raise typer.Exit(code=1)
+
+
+@app.command("version")
+def version() -> None:
+    typer.echo(f"findpapers {findpapers.__version__}")
+
+
+def main() -> None:
+    app()

pyproject.toml

@@ -13,6 +13,8 @@ streamlit-aggrid = "^0.3.0"
 rispy = "^0.7.1"
 stqdm = "^0.0.4"
 pydantic = "^1.10.7"
+typer = "^0.9.0"
+lxml = "^4.9.2"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.2.2"