copy report to html tree

OllyButters · Jul 25, 2024 · 2459fb1 · 2459fb1
1 parent f54dc1d
commit 2459fb1
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Showing 5 changed files with 32 additions and 15 deletions.
diff --git a/source/analyse/analyse.py b/source/analyse/analyse.py
@@ -514,59 +514,59 @@ def mesh(papers):
 ################################################################################
 # output a csv file with some general info in
 ################################################################################
-def output_csv(papers):
+def output_summary(papers):
 
     print('\n###Outputting CSV file###')
-    with open(config.data_dir + '/all.csv', 'w') as csvfile:
+    with open(config.data_dir + '/summary.csv', 'w') as csvfile:
         all_file = csv.writer(csvfile)
         all_file.writerow(['year', 'authors', 'title', 'first_author', 'journal', 'citations', 'tags'])
 
         for this_paper in papers:
             try:
                 title = this_paper['clean']['title']
-            except:
+            except Exception:
                 title = '???'
 
             try:
                 first_author = this_paper['clean']['full_author_list'][0]['family']
-            except:
+            except Exception:
                 first_author = '???'
 
             try:
                 all_authors = this_paper['clean']['full_author_list']
                 author_string = ''
                 for this_author in all_authors:
                     author_string = author_string + this_author['family'] + ', '
-            except:
+            except Exception:
                 author_string = '???'
 
             try:
                 journal = this_paper['clean']['journal']['journal_name']
-            except:
+            except Exception:
                 journal = '???'
 
             try:
                 citations = this_paper['clean']['citations']['scopus']['count']
-            except:
+            except Exception:
                 citations = '???'
 
             try:
                 year = this_paper['clean']['clean_date']['year']
-            except:
+            except Exception:
                 year = '???'
 
             try:
                 tags = []
                 tag_string = ''
                 for this_tag in this_paper['clean']['zotero_tags']:
                     tags.append(this_tag['tag'])
-                tag_string = ', '.join(tags)
-            except:
+                tag_string = ' | '.join(tags)
+            except Exception:
                 tag_string = '???'
 
             try:
                 all_file.writerow([year, author_string, title, first_author, journal, citations, tag_string])
-            except:
+            except Exception:
                 pass
 
 

diff --git a/source/config/config.py b/source/config/config.py
@@ -67,14 +67,15 @@
     logging_loglevel = config.get('logging', 'loglevel', fallback = 'DEBUG')
 
     # Metrics
-    metrics_study_start_year = int(config.get('metrics', 'metrics_study_start_year'))
-    metrics_study_current_year = int(config.get('metrics', 'metrics_study_current_year'))
+    #metrics_study_start_year = int(config.get('metrics', 'metrics_study_start_year'))
+    #metrics_study_current_year = int(config.get('metrics', 'metrics_study_current_year'))
 
     # Pages
     WEB_PAGE_SHOW_INSTITUTE_UK_MAP = config.getboolean('pages', 'web_page_show_institute_UK_map', fallback = True)
     WEB_PAGE_SHOW_INSTITUTE_COUNTRY_MAP = config.getboolean('pages', 'web_page_show_institute_country_map', fallback = True)
     WEB_PAGE_SHOW_ZOTERO_TAGS = config.getboolean('pages', 'web_page_show_zotero_tags', fallback = True)
     web_page_is_in_iframe = config.getboolean('pages', 'web_page_is_in_iframe', fallback = False)
+    WEB_PAGE_REPORTS = config.get('pages', 'web_page_reports', fallback = None)
 
 except Exception as e:
     print('Problem with the settings file')

diff --git a/source/papers.py b/source/papers.py
@@ -25,6 +25,7 @@
 from analyse import analyse
 from analyse import coverage_report
 from config import config
+import web_pages.reports
 
 __author__ = "Olly Butters, Hugh Garner, Tom Burton, Becca Wilson"
 __date__ = 16/4/2024
@@ -125,7 +126,7 @@
 analyse.first_authors(papers)
 analyse.inst(papers)
 # analyse.mesh(papers)
-analyse.output_csv(papers)
+analyse.output_summary(papers)
 analyse.dates(papers)
 
 ###########################################################
@@ -141,6 +142,7 @@
 #web_pages.build_htmlv2.build_search(papers)
 
 web_pages.build_htmlv2.build_all(papers, papers_with_keywords, papers_with_abstract_text)
+web_pages.reports.copy_reports()
 
 #if config.WEB_PAGE_SHOW_ZOTERO_TAGS:
 #    web_pages.build_htmlv2.build_zotero_tags(papers)

diff --git a/source/setup/setup.py b/source/setup/setup.py
@@ -156,7 +156,7 @@ def build_file_tree():
     if not os.path.exists(config.html_dir):
         os.makedirs(config.html_dir)
 
-    html_directories = {"/mesh", "/css", "/papers", "/tags", "/keywords", "/country", "/institute", "/metrics", "/keyword_wordcloud", "/abstractwordcloud", "/authornetwork", "/help", "/search", "/status"}
+    html_directories = {"/mesh", "/css", "/papers", "/tags", "/keywords", "/country", "/institute", "/metrics", "/keyword_wordcloud", "/abstractwordcloud", "/help", "/search", "/reports"}
 
     for direct in html_directories:
         if not os.path.exists(config.html_dir + direct):

diff --git a/source/web_pages/reports.py b/source/web_pages/reports.py
@@ -0,0 +1,14 @@
+import os
+import shutil
+from config import config
+
+# Copy specified reports to the html directory
+def copy_reports():
+    print('Copying reports to html directory.')
+
+    if config.WEB_PAGE_REPORTS:
+        print('Copying ', config.WEB_PAGE_REPORTS, ' to html directory.')
+
+        if os.path.exists(config.data_dir + '/' + config.WEB_PAGE_REPORTS):
+
+            shutil.copy(config.data_dir + '/' + config.WEB_PAGE_REPORTS, config.html_dir + '/reports/')