Merge branch 'main' of ssh://gitlab.igem.org/2024/bielefeld-cebitec

code/cit.py

-import argparse
-import bibtexparser
-import re
+# Voraussetzungen
+#- Python 3.x
+#- bibtexparser (Installieren Sie es mit `pip install bibtexparser`)
 
 
 problemlist = []
 
 def main(): 
+
     print("Starting program...")
+    try:
+        import bibtexparser
+    except ImportError:
+        print("The package 'bibtexparser' is not installed. Install with: pip install bibtexparser")
+        exit(1)
+    try:
+        import argparse
+    except ImportError:
+        print("The package  'argparse' is not installed.")
+        exit(1)
+     try:
+        import re
+    except ImportError:
+        print("The package  're' is not installed.")
+        exit(1)
+
+
     try:
         #reading command line input and parsing it 
         parser = argparse.ArgumentParser(
                             prog='HTML Citations',
                             description='create acessible HTML Citations from bib files')
-        parser.add_argument('-i','--input')
+        parser.add_argument('-i','--input', required=True, help="path to source bib")
+        parser.add_argument('-s','--startnumber', required=True, help="number from which to start numbering") 
+        
         args = parser.parse_args()
         print("Source: " + args.input)
     except argparse.ArgumentError as e:
@@ -21,6 +41,7 @@ def main():
         print(f"An unexpected error occurred: {e}")
     print("Reading file...")
     #reading and parsing the file
+
     try:
         with open(args.input, 'r') as file:
             file_content = file.read()
@@ -33,12 +54,15 @@ def main():
                     length = len(library.entries)
                     print("found " + str(length) + " entries")
                     ran = range(length)
+                    startnum = int(args.startnumber); 
+                    count = 0; 
                     #processing every entry and writing the dictionary for it 
                     for x in ran:
-                        print("\n Initializing empty dictionary for entry "+ str(x+1) + "...")
+
+                        print("\n Initializing empty dictionary for entry "+ str(startnum+count) + "...")
                         dictio = {}
                         en_x = library.entries[x]
-                        print("Filling dictionary for entry "+ str(x+1) + "")
+                        print("Filling dictionary for entry "+ str(startnum+count) + "")
                         
                         # Direkt auf die Einträge zugreifen, da es sich um ein Dictionary handelt
                         for key, value in en_x.items(): 
@@ -47,9 +71,9 @@ def main():
                         
                         # Überprüfung auf den Typ des Eintrags über 'ENTRYTYPE'
                         if en_x['ENTRYTYPE'] == "article":
-                            articleHTML(dictio, x, out)
+                            articleHTML(dictio, (startnum+count), out)
                         elif en_x['ENTRYTYPE'] == "misc":
-                            miscHTML(dictio, x, out)
+                            miscHTML(dictio, (startnum+count), out)
 
 
             except Exception as e:
@@ -71,9 +95,9 @@ def main():
 
 
 def articleHTML(dictio, x, out):
-    print("Writing html code for entry "+ str(x+1) + "...")
-    out.write("{/*<!-- Citation num " + str(x+1) + "--> */}" + "\n")
-    out.write("<li typeof=\"schema:ScolarlyArticle\" role=\"doc-biblioentry\" property=\"schema:citation\" id=\"desc-" + str(x+1) + "\">"+ "\n")
+    print("Writing html code for entry "+ str(x) + "...")
+    out.write("{/*<!-- Citation num " + str(x) + "--> */}" + "\n")
+    out.write("<li typeof=\"schema:ScolarlyArticle\" role=\"doc-biblioentry\" property=\"schema:citation\" id=\"desc-" + str(x) + "\">"+ "\n")
     out.write("\t" + "<span property=\"schema:author\" typeof=\"schema:Person\">"+ "\n")
     
     print("Just a sec, seperating authors...")
@@ -137,16 +161,16 @@ def articleHTML(dictio, x, out):
                     out.write("\t" + "<span property=\"schema:pageBegin\">"+ pages +"</span>"+ "\n")
                 else:
                     print("Sorry, no readable page information")
-                    problemlist.append("Check for missing page info at " + str (x+1))
+                    problemlist.append("Check for missing page info at " + str (x))
             else: 
                 print("Sorry, no page information")
-                problemlist.append("Check for missing page info at " + str (x+1))
+                problemlist.append("Check for missing page info at " + str (x))
         else:
             print("Sorry, no page information")
-            problemlist.append("Check for missing page info at " + str (x+1))
+            problemlist.append("Check for missing page info at " + str (x))
     except KeyError as e:
         print("Sorry, no page information")
-        problemlist.append("Check for missing page info at " + str (x+1))
+        problemlist.append("Check for missing page info at " + str (x))
 
     year = dictio['year']
     out.write("\t" +"(<time property=\"schema:datePublished\" datatype=\"xsd:gYear\" dateTime=\" " + year + "\">"+year+"</time>)."+ "\n")
@@ -156,15 +180,15 @@ def articleHTML(dictio, x, out):
         out.write("\t" +"<a className=\"doi\" href=\"https://doi.org/"+doi+"\"> doi: "+doi+"</a>"+ "\n")
     except KeyError as e:
         print("Sorry, no doi information")
-        problemlist.append("Check for missing doi info at " + str (x+1))
+        problemlist.append("Check for missing doi info at " + str (x))
 
     out.write("</li>" + "\n"+ "\n")
 
 
 def miscHTML(dictio, x, out):
-    print("Writing html code for entry "+ str(x+1) + "...")
-    out.write("#<!-- Citation num " + str(x+1) + "-->" + "\n")
-    out.write("<li typeof=\"schema:WebPage\" role=\"doc-biblioentry\" property=\"schema:citation\" id=\"desc-" + str(x+1) + "\">"+ "\n")
+    print("Writing html code for entry "+ str(x) + "...")
+    out.write("#<!-- Citation num " + str(x) + "-->" + "\n")
+    out.write("<li typeof=\"schema:WebPage\" role=\"doc-biblioentry\" property=\"schema:citation\" id=\"desc-" + str(x) + "\">"+ "\n")
     out.write("\t" + "<span property=\"schema:author\" typeof=\"schema:Organisation\">"+ "\n")
     aut = dictio['author']
     out.write("\t" + "\t" +"<span property=\"schema:Name\">" +aut + "</span>."+ "\n")

code/output.txt

-{/*<!-- Citation num 1--> */}
-<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-1">
+{/*<!-- Citation num 3--> */}
+<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-3">
 	<span property="schema:author" typeof="schema:Person">
 		<span property="schema:Name"> Roth, F.</span>;
 		<span property="schema:Name"> Draguhn, A.</span>