diff --git a/kirsche/command.py b/kirsche/command.py
index 760eb0a..416984c 100644
--- a/kirsche/command.py
+++ b/kirsche/command.py
@@ -3,6 +3,7 @@
import click
from loguru import logger
+from pyecharts.charts.base import default
from kirsche.download import list_unique_ids, download_metadata
from kirsche.connect import (
append_connections,
@@ -12,6 +13,7 @@
from kirsche.dataset import DataViews
from kirsche.utils.io import load_json
from kirsche.utils.bib import load_bib
+from kirsche.visalize import make_chart, PaperGraph, visualize
logger.remove()
@@ -69,7 +71,7 @@ def _metadata(paper_id, bib_file, metadata_file, sleep_time):
def kirsche(ctx):
if ctx.invoked_subcommand is None:
click.echo("Hello {}".format(os.environ.get("USER", "")))
- click.echo("Welcome to Kirsche.")
+ click.echo("Welcome to Kirsche. Use kirsche --help for help.")
else:
pass
@@ -78,7 +80,7 @@ def kirsche(ctx):
@click.option("--paper_id", "-p", help="Paper ID", multiple=True)
@click.option("--bib_file", "-b", type=click.Path(exists=True), help="Bib file path")
@click.option("--metadata_file", "-m", help="Target data file path")
-@click.option("--sleep_time", "-s", default=1, help="Sleep time between requests")
+@click.option("--sleep_time", "-st", default=1, help="Sleep time between requests")
def metadata(paper_id, bib_file, metadata_file, sleep_time):
"""Download paper data from service provides (e.g., SemanticScholar).
@@ -132,7 +134,7 @@ def connections_from_metadata(metadata_file, connected_papers_file):
help="path to data file with paper metadata",
)
@click.option("--connected_papers_file", "-c", help="path to save enhanced data file")
-@click.option("--sleep_time", "-s", default=1, help="Sleep time between requests")
+@click.option("--sleep_time", "-st", default=1, help="Sleep time between requests")
def connections(paper_id, bib_file, metadata_file, connected_papers_file, sleep_time):
"""Establish connections between the list of papers, either from a list of DOIs, bib file, or from download metadata file.
@@ -184,5 +186,73 @@ def connections(paper_id, bib_file, metadata_file, connected_papers_file, sleep_
click.echo(dv.json_simple)
+@kirsche.command()
+@click.option(
+ "--source_paper_id", "-sp", required=False, help="Source: Paper ID", multiple=True
+)
+@click.option(
+ "--source_bib_file",
+ "-sb",
+ required=False,
+ type=click.Path(exists=True),
+ help="Source: Bib file path",
+)
+@click.option(
+ "--source_metadata_file",
+ "-sm",
+ required=False,
+ type=click.Path(exists=True),
+ help="Source: path to data file with paper metadata",
+)
+@click.option(
+ "--source_connected_papers_file",
+ "-sc",
+ required=False,
+ help="Source: path to save enhanced data file",
+)
+@click.option("--title", default="Kirsche: Paper Graph", help="title of the chart")
+@click.option(
+ "--target_html_path", "-th", required=True, help="Target: path to html file"
+)
+@click.option("--sleep_time", "-st", default=1, help="Sleep time between requests")
+def visualization(
+ source_paper_id,
+ source_bib_file,
+ source_metadata_file,
+ source_connected_papers_file,
+ title,
+ target_html_path,
+ sleep_time,
+):
+ """ """
+ if source_connected_papers_file:
+ connected_papers = load_json(source_connected_papers_file)
+ else:
+ click.secho(f"Retrieving paper metadata...")
+ if not source_metadata_file:
+ if source_bib_file:
+ logger.debug(f"Using bib file: {source_bib_file}")
+ records = _metadata(source_paper_id, source_bib_file, None, sleep_time)
+ else:
+ records = load_json(source_metadata_file)
+ click.secho(f" Retrieved {len(records)} records.")
+
+ click.secho(f"Connecting papers...")
+ connected_papers = append_connections(records)
+ click.secho(f" Connected papers...")
+
+ # Filter out unnecessary keys in the dictionary
+ click.secho(f"Filtering and saving data...")
+ connected_papers = save_connected_papers(connected_papers)
+ click.secho(f" Done...")
+
+ g = PaperGraph(connected_papers, title=title)
+ nodes = g.nodes
+ edges = g.edges
+
+ click.secho(f"Saving html file...")
+ visualize(nodes, edges, g.title, target_html_path)
+
+
if __name__ == "__main__":
pass
diff --git a/kirsche/utils/graph.py b/kirsche/utils/graph.py
index ddd79d2..58ec911 100644
--- a/kirsche/utils/graph.py
+++ b/kirsche/utils/graph.py
@@ -2,16 +2,21 @@
class PaperGraph:
- """A graph object to hold graphs"""
+ """A graph object to hold graphs
- def __init__(self, paper_connections):
+ :param paper_connections: a list of dictionaries that specifies the connections between papers
+ :param title: the title of the graph
+ """
+
+ def __init__(self, paper_connections: list, title: str = None):
if not isinstance(paper_connections, list):
raise TypeError("The connections paper_connections must be a dictionary")
self.nodes, self.edges = self._extract_nodes_and_edges(paper_connections)
+ self.title = title
- def _calculate_node(self, node, schema):
+ def _calculate_node(self, node: dict, schema: dict):
"""calculate the node"""
simplified_node = {}
for k, v in schema.items():
@@ -23,30 +28,29 @@ def _calculate_node(self, node, schema):
return simplified_node
- def _extract_nodes_and_edges(self, connections, node_schema=None, edge_schema=None):
- """extract nodes and edges from connections"""
+ def _extract_nodes_and_edges(
+ self, connections: list, node_schema: dict = None, edge_schema: dict = None
+ ):
+ """extract nodes and edges from connections
+
+ :param connections: a list of dictionaries that specifies the connections between papers
+ :param node_schema: a dictionary that specifies how the nodes are extracted
+ :param edge_schema: a dictionary that specifies how the edges are built
+ """
if node_schema is None:
node_schema = {
"name": {
"key": "title",
- # "key": "doi",
- "default": "No Title"
- },
- "id": {
- # "key": "title"
- "key": "doi"
+ "default": "No Title",
},
+ "id": {"key": "doi"},
"symbolSize": {
"key": "numCitedBy",
- "transform": lambda x: 5*math.log(x+2)
- },
- "x": {
- "key": "year"
- },
- "y": {
- "key": "numCiting"
+ "transform": lambda x: 5 * math.log(x + 2),
},
+ "x": {"key": "year"},
+ "y": {"key": "numCiting"},
}
if edge_schema is None:
@@ -70,8 +74,7 @@ def _extract_nodes_and_edges(self, connections, node_schema=None, edge_schema=No
return nodes, edges
def __str__(self):
- return f"nodes: {self.nodes}\nedges: {self.edges}"
-
+ return f"Graph: {self.title}\n nodes: {self.nodes}\n edges: {self.edges}"
if __name__ == "__main__":
diff --git a/kirsche/visalize.py b/kirsche/visalize.py
index 83f7e1b..b3463f9 100644
--- a/kirsche/visalize.py
+++ b/kirsche/visalize.py
@@ -1,11 +1,40 @@
+from pathlib import Path
+from typing import Union
+
import pyecharts.options as opts
from pyecharts.charts import Graph
+from kirsche.utils.graph import PaperGraph
+from kirsche.utils.io import load_json
+
+
+def load_graph(connections_json: Union[str, Path], title: str) -> PaperGraph:
+ """Load json file that contains the paper connection information, and build a graph using it.
+
+ :param connections_json: json file that contains the paper connection information
+ :param title: title of the graph which will be shown in the top of the chart
+ """
+
+ data = load_json(connections_json)
+ if data:
+ g = PaperGraph(data, title=title)
+ else:
+ raise ValueError(f"No data in json file: {connections_json}!")
-def visualize(nodes, edges, target, title):
- """Generate interactive graphs"""
+ return g
+
+def visualize(nodes: list, edges: list, title: str, target: Union[str, Path]) -> None:
+ """Generate interactive graphs
+
+ :param nodes: nodes of the graph
+ :param edges: edges of the graph
+ :param title: title of the graph which will be shown in the top of the chart
+ :param target: target file path
+ """
+
+ # Build the graph and export it to html file
(
Graph(init_opts=opts.InitOpts(width="1600px", height="800px"))
.add(
@@ -21,3 +50,30 @@ def visualize(nodes, edges, target, title):
.set_global_opts(title_opts=opts.TitleOpts(title=title))
.render(target)
)
+
+
+def make_chart(
+ connections_json: Union[Path, str], target: Union[Path, str], title: str
+) -> None:
+ """Generate interactive graphs
+
+ :param connections_json: json file that contains the paper connection information
+ :param target: target file path
+ :param title: title of the graph which will be shown in the top of the chart
+ """
+
+ g = load_graph(connections_json, title)
+
+ nodes = g.nodes
+ edges = g.edges
+
+ visualize(nodes, edges, g.title, target)
+
+
+if __name__ == "__main__":
+ import json
+
+ paper_connections = "tests/data/io/test.json"
+ target = "tests/data/visualize/test.html"
+
+ make_chart(paper_connections, target, "This is an Experiment")
diff --git a/tests/data/visualize/test.html b/tests/data/visualize/test.html
new file mode 100644
index 0000000..236bf99
--- /dev/null
+++ b/tests/data/visualize/test.html
@@ -0,0 +1,894 @@
+
+
+
+
+ Awesome-pyecharts
+
+
+
+
+
+
+
+
diff --git a/tests/data/visualize/test_32.html b/tests/data/visualize/test_32.html
new file mode 100644
index 0000000..924ed43
--- /dev/null
+++ b/tests/data/visualize/test_32.html
@@ -0,0 +1,894 @@
+
+
+
+
+ Awesome-pyecharts
+
+
+
+
+
+
+
+
diff --git a/tests/data/visualize/test__connection_enhanced.html b/tests/data/visualize/test__connection_enhanced.html
new file mode 100644
index 0000000..4cf617a
--- /dev/null
+++ b/tests/data/visualize/test__connection_enhanced.html
@@ -0,0 +1,131 @@
+
+
+
+
+ Awesome-pyecharts
+
+
+
+
+
+
+
+