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some linting
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@cbroschinski
cbroschinski committed Aug 23, 2019
1 parent de83648 commit 615c1c0
Showing 1 changed file with 52 additions and 49 deletions.
101 changes: 52 additions & 49 deletions python/generate_apc_report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
from subprocess import run
import sys

from babel.dates import format_date
from babel.dates import format_date
import openapc_toolkit as oat

ARG_HELP_STRINGS = {
Expand All @@ -21,8 +21,8 @@
}

with open("report/strings.json") as f:
json_content = f.read()
LANG = json.loads(json_content)
json_content = f.read()
LANG = json.loads(json_content)

def mean(sample):
return reduce(lambda x, y: x + y, sample) / len(sample)
Expand Down Expand Up @@ -50,8 +50,8 @@ def get_data_dir_stats(data_dir):
"readme": False,
"orig_files": 0
}
for f in files:
lower = f.lower()
for file_name in files:
lower = file_name.lower()
if "readme" in lower:
stats["readme"] = True
continue
Expand All @@ -60,49 +60,50 @@ def get_data_dir_stats(data_dir):
stats["orig_files"] += 1
return stats

def generate_header(institution, ins_content, lang):
def generate_header(lang):
header = LANG[lang]["front"]
header += LANG[lang]["header"]
header += LANG[lang]["intro"]
return header

def generate_metadata_section(institution, ins_content, stats, lang):
md = LANG[lang]["md_header"]
markdown = LANG[lang]["md_header"]
ins_line = None
for line in ins_content:
if line[0] == institution:
ins_line = line
break
ins_line = line
break
else:
oat.print_r("ERROR: Entry " + institution + " not found in institutions file!")
sys.exit()
locale_date = format_date(date.today(), locale=lang)
md += "* " + LANG[lang]["md_date"] + ": " + locale_date + "\n"
markdown += "* " + LANG[lang]["md_date"] + ": " + locale_date + "\n"
git_rev = run(["git", "describe", "--tags", "--abbrev=0"], capture_output=True).stdout.decode()
git_rev = git_rev.replace("\n", "")
rev_url = "https://github.com/OpenAPC/openapc-de/tree/" + git_rev
md += "* " + LANG[lang]["md_rev"] + ": [" + git_rev + "](" + rev_url + ")\n"
md += "* " + LANG[lang]["md_ins"] + ": " + ins_line[2] + "\n"
md += "* " + LANG[lang]["md_ins_apc"] + ": " + ins_line[0] + "\n"
treemap_url = "<https://treemaps.intact-project.org/apcdata/" + ins_line[1].replace("_", "-") + ">"
md += "* " + LANG[lang]["md_treemap"] + ": " + treemap_url + "\n"
markdown += "* " + LANG[lang]["md_rev"] + ": [" + git_rev + "](" + rev_url + ")\n"
markdown += "* " + LANG[lang]["md_ins"] + ": " + ins_line[2] + "\n"
markdown += "* " + LANG[lang]["md_ins_apc"] + ": " + ins_line[0] + "\n"
url = "https://treemaps.intact-project.org/apcdata/"
treemap_url = "<" + url + ins_line[1].replace("_", "-") + ">"
markdown += "* " + LANG[lang]["md_treemap"] + ": " + treemap_url + "\n"
data_dir = ins_line[6]
if oat.has_value(data_dir):
stats = get_data_dir_stats(data_dir)
data_url = "https://github.com/OpenAPC/openapc-de/tree/master/data/" + data_dir
md += "* " + LANG[lang]["md_data_dir"] + ": [" + data_dir + "](" + data_url + ")\n"
md += "* " + LANG[lang]["md_num_files"] + ": " + str(stats["orig_files"]) + "\n"
md += "* " + LANG[lang]["md_readme"] + ": "
markdown += "* " + LANG[lang]["md_data_dir"] + ": [" + data_dir + "](" + data_url + ")\n"
markdown += "* " + LANG[lang]["md_num_files"] + ": " + str(stats["orig_files"]) + "\n"
markdown += "* " + LANG[lang]["md_readme"] + ": "
if stats["readme"]:
md += LANG[lang]["md_readme_yes"]
markdown += LANG[lang]["md_readme_yes"]
else:
md += LANG[lang]["md_readme_no"]
md += "\n"
markdown += LANG[lang]["md_readme_no"]
markdown += "\n"
else:
oat.print_y("WARNING: No data dir entry found for " + institution + "!")
md += "\n"
return md
markdown += "\n"
return markdown

def generate_duplicates_section(institution, dup_content, ins_content, lang):
duplicates = {}
for line in dup_content:
Expand All @@ -115,9 +116,9 @@ def generate_duplicates_section(institution, dup_content, ins_content, lang):
doi = line[3]
if doi in duplicates and line not in duplicates[doi]:
duplicates[doi].append(line)
md = LANG[lang]["dup_header"]
md += LANG[lang]["dup_intro"]
md += LANG[lang]["dup_intro_2"]
markdown = LANG[lang]["dup_header"]
markdown += LANG[lang]["dup_intro"]
markdown += LANG[lang]["dup_intro_2"]
count = 1
for doi, articles in duplicates.items():
dup_case = str(count) + ") " + LANG[lang]["dup_case"].format(articles[0][3])
Expand All @@ -129,17 +130,17 @@ def generate_duplicates_section(institution, dup_content, ins_content, lang):
pair = "* " + institution + " (" + line[2] + ")"
institutions.append(pair)
dup_case += "\n".join(institutions) + "\n\n"
md += dup_case
md += LANG[lang]["dup_th"]
markdown += dup_case
markdown += LANG[lang]["dup_th"]
for article in articles:
row = "|"
for index in [0, 1, 2, 6]:
row += article[index] + "|"
md += row + "\n"
md += "\n"
markdown += row + "\n"
markdown += "\n"
count += 1
return md
return markdown

def generate_apc_deviaton_section(institution, articles, stats, lang):
md_content = ""
journal_dict = {}
Expand Down Expand Up @@ -172,12 +173,11 @@ def generate_apc_deviaton_section(institution, articles, stats, lang):
md_content += row
md_content += "\n\n"
md_content += LANG[lang]["ad_stats_header"].format(institution)
md_content += "* " + LANG[lang]["ad_stats_articles"] + ": " + str(stats["articles"]) + "\n"
md_content += "* " + LANG[lang]["ad_stats_not_checked"] + ": " + str(stats["not_checked"]) + "\n"
md_content += "* " + LANG[lang]["ad_stats_within_limits"] + ": " + str(stats["within_limits"]) + "\n"
md_content += "* " + LANG[lang]["ad_stats_significant"] + ": " + str(stats["significant"]) + "\n"
for stat in ["articles", "not_checked", "within_limits", "significant"]:
md_content += "* " + LANG[lang]["ad_stats_" + stat]
md_content += ": " + str(stats[stat]) + "\n"
return md_content

def find_significant_apc_differences(apc_content, institution, verbose=False):
titles = {}
articles = []
Expand Down Expand Up @@ -222,7 +222,8 @@ def find_significant_apc_differences(apc_content, institution, verbose=False):
rounded_stddev = round(titles[title]["stddev"], 2)
diff = round(float(apc) - rounded_mean, 2)
if verbose:
msg = 'Article {}, journal "{}": Cost ({}€) differs more than 2 standard deviations (2 * {}€) from mean APC ({}€)'
msg = ('Article {}, journal "{}": Cost ({}€) differs more than 2 standard ' +
'deviations (2 * {}€) from mean APC ({}€)')
oat.print_y(msg.format(doi, title, apc, rounded_stddev, rounded_mean))
stats["significant"] += 1
article.append(rounded_mean)
Expand All @@ -232,29 +233,31 @@ def find_significant_apc_differences(apc_content, institution, verbose=False):
sig_articles.append(article)
else:
if verbose:
msg = 'Article {}, journal "{}": No significant cost difference ({}€, mean APC is {}€)'
msg = ('Article {}, journal "{}": No significant cost difference ({}€, mean ' +
'APC is {}€)')
oat.print_g(msg.format(doi, title, apc, round(titles[title]["mean"], 2)))
stats["within_limits"] += 1
if verbose:
oat.print_g("\nAnalysis finished, results:")
for k, v in stats.items():
oat.print_g(k + ": " + str(v))
for key, value in stats.items():
oat.print_g(key + ": " + str(value))
return sig_articles, stats

def main():
args = parse()
_, apc_content = oat.get_csv_file_content("../data/apc_de.csv", "utf-8", True)
_, ins_content = oat.get_csv_file_content("../data/institutions.csv", "utf-8", True)
_, dup_content = oat.get_csv_file_content("../data/unresolved_duplicates.csv", "utf-8", True)

sig_articles, stats = find_significant_apc_differences(apc_content, args.institution, args.verbose)


sig_articles, stats = find_significant_apc_differences(apc_content, args.institution,
args.verbose)

report = ""
report += generate_header(args.institution, ins_content, args.lang)
report += generate_header(args.lang)
report += generate_metadata_section(args.institution, ins_content, stats, args.lang)
report += generate_duplicates_section(args.institution, dup_content, ins_content, args.lang)
report += generate_apc_deviaton_section(args.institution, sig_articles, stats, args.lang)

ins = args.institution.lower().replace(" ", "_")
today = format_date(date.today(), format="dd_MM_yy")
file_name = "report_" + ins + "_" + today + ".pdf"
Expand Down

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