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Results of running ruff format and ruff check #119

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221 changes: 129 additions & 92 deletions api/dis_plots.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
''' dis_plots.py
Plot functions for the DIS UI
'''
"""dis_plots.py
Plot functions for the DIS UI
"""

from math import pi
import pandas as pd
Expand All @@ -13,86 +13,101 @@
SOURCE3_PALETTE = ["mediumblue", "darkorange", "wheat"]
TYPE_PALETTE = ["mediumblue", "darkorange", "wheat", "darkgray"]


# ******************************************************************************
# * Utility functions *
# ******************************************************************************
def _preprint_type_piechart(coll, year):
''' Create a preprint type pie chart
Keyword arguments:
coll: dois collection
year: year or "All"
Returns:
Chart components
'''
"""Create a preprint type pie chart
Keyword arguments:
coll: dois collection
year: year or "All"
Returns:
Chart components
"""
match = {"type": "posted-content"}
if year != 'All':
match['jrc_publishing_date'] = {"$regex": "^"+ year}
payload = [{"$match": match},
{"$group": {"_id": {"institution": "$institution"},"count": {"$sum": 1}}}]
if year != "All":
match["jrc_publishing_date"] = {"$regex": "^" + year}
payload = [
{"$match": match},
{"$group": {"_id": {"institution": "$institution"}, "count": {"$sum": 1}}},
]
try:
rows = coll.aggregate(payload)
except Exception as err:
raise err
data = {}
for row in rows:
if not row['_id']['institution']:
data['No institution'] = row['count']
if not row["_id"]["institution"]:
data["No institution"] = row["count"]
else:
data[row['_id']['institution'][0]['name']] = row['count']
data[row["_id"]["institution"][0]["name"]] = row["count"]
if not data:
return None, None
title = "Preprint DOI institutions"
if year != 'All':
if year != "All":
title += f" ({year})"
return pie_chart(dict(sorted(data.items())), title,
"source", width=600, height=400, location='bottom_right')
return pie_chart(
dict(sorted(data.items())),
title,
"source",
width=600,
height=400,
location="bottom_right",
)


def _preprint_capture_piechart(coll, year):
''' Create a preprint capture pie chart
Keyword arguments:
coll: dois collection
year: year or "All"
Returns:
Chart components
'''
"""Create a preprint capture pie chart
Keyword arguments:
coll: dois collection
year: year or "All"
Returns:
Chart components
"""
data = {}
payload = {"subtype": "preprint", "jrc_preprint": {"$exists": 1},
"relation.is-preprint-of": {"$exists": 0}}
if year != 'All':
payload['jrc_publishing_date'] = {"$regex": "^"+ year}
payload = {
"subtype": "preprint",
"jrc_preprint": {"$exists": 1},
"relation.is-preprint-of": {"$exists": 0},
}
if year != "All":
payload["jrc_publishing_date"] = {"$regex": "^" + year}
try:
data['Fuzzy matching'] = coll.count_documents(payload)
data["Fuzzy matching"] = coll.count_documents(payload)
except Exception as err:
raise err
del payload['relation.is-preprint-of']
del payload["relation.is-preprint-of"]
try:
data['Crossref relation'] = coll.count_documents(payload)
data["Crossref relation"] = coll.count_documents(payload)
except Exception as err:
raise err
data['Crossref relation'] = data['Crossref relation'] - data['Fuzzy matching']
if not data['Crossref relation'] and not data['Fuzzy matching']:
data["Crossref relation"] = data["Crossref relation"] - data["Fuzzy matching"]
if not data["Crossref relation"] and not data["Fuzzy matching"]:
return None, None
title = "Preprint capture method"
if year != 'All':
if year != "All":
title += f" ({year})"
return pie_chart(data, title, "source", colors=SOURCE_PALETTE, width=600, height=400)
return pie_chart(
data, title, "source", colors=SOURCE_PALETTE, width=600, height=400
)


def preprint_pie_charts(data, year, coll):
''' Create a preprint capture pie chart
Keyword arguments:
data: dictionary of data
year: year or "All"
coll: dois collection
Returns:
Chart components
'''
"""Create a preprint capture pie chart
Keyword arguments:
data: dictionary of data
year: year or "All"
coll: dois collection
Returns:
Chart components
"""
title = "DOIs by preprint status"
if year != 'All':
if year != "All":
title += f" ({year})"
chartscript, chartdiv = pie_chart(data, title, "source",
colors=SOURCE_PALETTE, width=600, height=400)
chartscript, chartdiv = pie_chart(
data, title, "source", colors=SOURCE_PALETTE, width=600, height=400
)
# Preprint types
try:
script2, div2 = _preprint_type_piechart(coll, year)
Expand All @@ -111,41 +126,60 @@ def preprint_pie_charts(data, year, coll):
raise err
return chartscript, chartdiv


# ******************************************************************************
# * Basic charts *
# ******************************************************************************

def pie_chart(data, title, legend, height=300, width=400, location="right", colors=None):
''' Create a pie chart
Keyword arguments:
data: dictionary of data
title: chart title
legend: data key name
height: height of the chart (optional)
width: width of the chart (optional)
colors: list of colors (optional)
Returns:
Figure components
'''

def pie_chart(
data, title, legend, height=300, width=400, location="right", colors=None
):
"""Create a pie chart
Keyword arguments:
data: dictionary of data
title: chart title
legend: data key name
height: height of the chart (optional)
width: width of the chart (optional)
colors: list of colors (optional)
Returns:
Figure components
"""
if len(data) == 1:
colors = ["mediumblue"]
elif len(data) == 2:
colors = SOURCE_PALETTE
if not colors:
colors = all_palettes['Category10'][len(data)]
colors = all_palettes["Category10"][len(data)]
elif isinstance(colors, str):
print(colors)
colors = all_palettes[colors][len(data)]
pdata = pd.Series(data).reset_index(name='value').rename(columns={'index': legend})
pdata['angle'] = pdata['value']/pdata['value'].sum() * 2*pi
pdata['percentage'] = pdata['value']/pdata['value'].sum()*100
pdata['color'] = colors
pdata = pd.Series(data).reset_index(name="value").rename(columns={"index": legend})
pdata["angle"] = pdata["value"] / pdata["value"].sum() * 2 * pi
pdata["percentage"] = pdata["value"] / pdata["value"].sum() * 100
pdata["color"] = colors
tooltips = f"@{legend}: @value (@percentage%)"
plt = figure(title=title, toolbar_location=None, height=height, width=width,
tools="hover", tooltips=tooltips, x_range=(-0.5, 1.0))
plt.wedge(x=0, y=1, radius=0.4,
start_angle=cumsum('angle', include_zero=True), end_angle=cumsum('angle'),
line_color="white", fill_color='color', legend_field=legend, source=pdata)
plt = figure(
title=title,
toolbar_location=None,
height=height,
width=width,
tools="hover",
tooltips=tooltips,
x_range=(-0.5, 1.0),
)
plt.wedge(
x=0,
y=1,
radius=0.4,
start_angle=cumsum("angle", include_zero=True),
end_angle=cumsum("angle"),
line_color="white",
fill_color="color",
legend_field=legend,
source=pdata,
)
plt.axis.axis_label = None
plt.axis.visible = False
plt.grid.grid_line_color = None
Expand All @@ -154,33 +188,36 @@ def pie_chart(data, title, legend, height=300, width=400, location="right", colo


def stacked_bar_chart(data, title, xaxis, yaxis, colors=None, width=None, height=None):
''' Create a stacked bar chart
Keyword arguments:
data: dictionary of data
title: chart title
xaxis: x-axis column name
yaxis: list of y-axis column names
colors: list of colors (optional)
width: width of chart (optional)
height: height of chart (optional)
Returns:
Figure components
'''
"""Create a stacked bar chart
Keyword arguments:
data: dictionary of data
title: chart title
xaxis: x-axis column name
yaxis: list of y-axis column names
colors: list of colors (optional)
width: width of chart (optional)
height: height of chart (optional)
Returns:
Figure components
"""
if not colors:
colors = plasma(len(yaxis))
plt = figure(x_range=data[xaxis], title=title,
toolbar_location=None, tools="hover",
tooltips=f"$name @{xaxis}: @$name")
plt = figure(
x_range=data[xaxis],
title=title,
toolbar_location=None,
tools="hover",
tooltips=f"$name @{xaxis}: @$name",
)
if width and height:
plt.width = width
plt.height = height
plt.vbar_stack(yaxis, x=xaxis, width=0.9,
color=colors, source=data,
legend_label=yaxis
)
plt.legend.location = 'top_left'
plt.vbar_stack(
yaxis, x=xaxis, width=0.9, color=colors, source=data, legend_label=yaxis
)
plt.legend.location = "top_left"
if width and height:
plt.add_layout(plt.legend[0], 'right')
plt.add_layout(plt.legend[0], "right")
plt.xgrid.grid_line_color = None
plt.y_range.start = 0
plt.background_fill_color = "ghostwhite"
Expand Down
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