Range reference handling, filling the range

pmc_open_access_xml.py

@@ -84,10 +84,10 @@ def clean_raw(xml_text):
     """
     #Some XML can't be parsed because they are not starting with the DOCTYPE declaration
     # Could be disabled if we handle the parsing error (TBD, how many files would be trashed)
-    
+
     begin_doc = begin_doc_rgx.search(xml_text)
     xml_text  = xml_text[begin_doc.start():]
-    
+
     #Some XML are poisoned with consecutive tabs and new lines
     # xml_text  = re.sub('\s+',' ',xml_text) # Commented because <code> requires those spacing
     return xml_text
@@ -116,7 +116,7 @@ def get_ref_indexes(ref_el_l, refs_pmid, refs_nonpmid_keys):
         reference_d[k] = (v, " ##REF## ", "pmid_ref")
     for i, k in enumerate(refs_nonpmid_keys):
         reference_d[k] = (i, " ##UREF## ", "unknown_pub_ref")
-        
+
     refs_key_l = []
     for el in ref_el_l:
         keyword, ref_name = TAG_DIC[el.tag]
@@ -137,20 +137,64 @@ def parseout_el_refs(el, rids):
     Extract then from the text all the references founds to the rids dictionnary,
     and replace them by keywords of the corresponding family (eg " ##FIG## " for a figure,
     " ##TAB## " for a table, or " ##MATHS## " for mathematical formulas)
-    
+
+    The range reference (e.g. 1-3 or 15-17) are replaced by their range (1,2,3 or 15,16,17)
+
     Returns the parsed text, the identifiers for the references and the references text that
     were replaced by the keywords. (eg, "Figure 2" was a hypertext reference and got replaced by " ##FIG## ")
     """
+    for xref in el.xpath(".//xref"):
+        inner_text = "".join(xref.itertext())
+        if inner_text == "":  # Removing "empty" references
+            tail    = xref.tail if xref.tail else ""
+            prev_el = xref.getprevious()
+            parent  = xref.getparent()
+            if prev_el is None:
+                parent.text  = "".join([(parent.text if parent.text else ""), tail])
+            else:
+                prev_el.tail = "".join([(prev_el.tail if prev_el.tail else ""), tail])
+            parent.remove(xref)
+
     res_rid     = defaultdict(list)
     res_reftext = defaultdict(list)
+    ref_rstart, ref_rstop = None, None
+    has_ref_range = None
     for xref in el.xpath(".//xref[not(ancestor::xref)]"): #Ignore innermost of imbricated references
+        inner_text = "".join(xref.itertext())
+        parent  = xref.getparent()
         rid = xref.get("rid")
         if rid in rids.keys():
             ref_idx, ref_kword, ref_class = rids[rid]
             res_rid[ref_class].append(ref_idx)
-            res_reftext[ref_class].append("".join(xref.itertext()))
-            parent  = xref.getparent()
+            res_reftext[ref_class].append(inner_text)
+
             tail    = xref.tail if xref.tail else ""
+            #### START HANDLING REF RANGE ########
+            try:
+                if has_ref_range is None:
+                    if ref_kword in [" ##UREF## ", " ##REF## "]:                 # Otherwise it's a year
+                        has_ref_range = res_reftext[ref_class][-1].isnumeric() and int(res_reftext[ref_class][-1]) < 500
+
+                if has_ref_range and ref_kword in [" ##UREF## ", " ##REF## "]:
+                    if tail=="-":
+                        ref_rstart = int(res_reftext[ref_class][-1])
+                        tail = ", "
+                    elif ref_rstart is not None:
+                        ref_rstop = int(res_reftext[ref_class][-1])
+                        ref_kword = [ref_kword]
+                        for i in range(ref_rstart+1, ref_rstop):
+                            new_rid = re.sub(str(ref_rstop), str(i), rid, count=1)
+                            ref_idx_, ref_kword_, ref_class_ = rids[new_rid]
+                            res_rid[ref_class_].insert(-1, ref_idx_)
+                            res_reftext[ref_class_].insert(-1, str(i))
+                            ref_kword.insert(-1, ref_kword_)
+                        ref_kword = ", ".join(ref_kword)
+                        ref_rstart = None
+            except (KeyError, ValueError):
+                ref_rstart = None
+                continue  # The substitution failed, happen when text don't match the rid
+            #### END HANDLING REF RANGE ########
+
             prev_el = xref.getprevious()
             if prev_el is None:
                 parent.text  = "".join([(parent.text if parent.text else ""), ref_kword, tail])
@@ -162,12 +206,12 @@ def parseout_el_refs(el, rids):
     #Removing the xml namespace, (otherwise they would be everywhere)
     tag_start = text.find(">")+1
     tag_txt = text[:tag_start]
-    
+
     for k, v in el.nsmap.items():
         tag_txt = tag_txt.replace(f' xmlns:{k}="{v}"', "", 1)
 
     text = "".join([tag_txt, text[tag_start:]])
-            
+
     return text, res_rid, res_reftext
 
 
@@ -207,7 +251,6 @@ def get_references(article_tree):
                     citation_d[el.tag].append(el.text)
             references_nonpmid.append(dict(citation_d))
             references_nonpmid_keys.append(ref_key)
-    
     return references_pmid, references_nonpmid, references_nonpmid_keys
 
 def construct_datadict(article_tree):
@@ -220,26 +263,25 @@ def construct_datadict(article_tree):
     - Titles are used to identify ["introduction", "methods", "results" and "discussion"]
     - The path are then used to group paragraphs and titles into corresponding content.
     - Remaining p and title are put in three other section: front, body, back
-    
+
     Returns:
         - content_d: Dictionnary with the content result
         - reference_d: The references of each kind (figure, table, ...) for each content type (intro, figure caption, ...)
         - reference_text_d: The replaced text by the keywords of the references, with keys matching reference_d.
         - reference_count: The count of unique external-document references.
-        
+
     Useful information about the tags can be found here: https://jats.nlm.nih.gov/archiving/tag-library/1.3/
     """
-
     res_content_d, res_reference_d, res_reference_text_d = {}, defaultdict(dict), defaultdict(dict)
-    
+
     refs_pmid, refs_nonpmid, refs_nonpmid_keys = get_references(article_tree)
     reference_count = len(refs_pmid)+len(refs_nonpmid)
-    
+
     res_content_d["unknown_pub"] = json.dumps(refs_nonpmid)
     refs_el = article_tree.find(".//ref-list")
     if refs_el is not None:
         refs_el.getparent().remove(refs_el)
-    
+
     # Extracts the glossary if exists, and removes it from the tree
     glossary = {}
     def search_def(el):
@@ -251,7 +293,7 @@ def construct_datadict(article_tree):
             definition = item.find(".//def")
             definition = "".join(definition.itertext()) if definition is not None else ""
             glossary[k] = definition
-            
+
     for el in article_tree.findall(".//glossary"):
         search_def(el)
         el.getparent().remove(el)
@@ -259,7 +301,7 @@ def construct_datadict(article_tree):
         search_def(el) #There may be still more def-list outside of a glossary
         el.getparent().remove(el)
     res_content_d["glossary"] = glossary
-        
+
     # After testing, no question were found in the dataset, so I commented that part
     # question_l = []
     # for el in article_tree.xpath(".//question-preamble|.//question|.//answer|.//explanation"):
@@ -268,7 +310,7 @@ def construct_datadict(article_tree):
     # res_content_d["question"] = "\n".join(question_l)
     # for el in article_tree.xpath(".//question-wrap-group|.//question-wrap|.//answer-set|.//explanation"):
         # el.getparent().remove(el)
-    
+
     # One big query is faster than multiple small ones
     ref_el_l = article_tree.xpath(".//fig|.//table-wrap|.//array|.//supplementary-material\
                                   |.//inline-supplementary-material|.//disp-formula\
@@ -292,7 +334,7 @@ def construct_datadict(article_tree):
         repl_xref.tail = el.tail
         el.addprevious(repl_xref)
         el.getparent().remove(el)
-                
+
     # Finally, the discovered references and text are added to the result
     for ref_k in REFS_KEYS[2:]: #Slicing from 2, to not add pmid and unknown ref here
         res_content_d[ref_k[:-4]] = text_l_d[ref_k]#"\n".join(text_l_d[ref_k])
@@ -312,7 +354,7 @@ def construct_datadict(article_tree):
             res_reference_d[part][ref_k] =  list(chain(*tmp_l)) 
             tmp_l = [refs_d[ref_k] for refs_d in ref_texts_l]
             res_reference_text_d[part][ref_k] =   list(chain(*tmp_l))
-            
+
     path_l, text_l, refs_l, refs_text_l = [], [], [], []
     t_paths, t_texts_lowcase  = [], []
     for part in ["front", "body", "back"]: #Iterate parts and insert first front and back
@@ -374,7 +416,7 @@ def construct_datadict(article_tree):
     
     res_reference_d      = dict(res_reference_d)
     res_reference_text_d = dict(res_reference_text_d)
-        
+
     return (res_content_d, res_reference_d, res_reference_text_d, reference_count)
 
 class OpenAccessXMLConfig(datasets.BuilderConfig):
@@ -408,7 +450,7 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
                 {
                     "accession_id":  datasets.Value("string"),
                     "pmid":          datasets.Value("string"),
-                    
+
                     "introduction":  datasets.features.Sequence(datasets.Value("string")),
                     "methods":       datasets.features.Sequence(datasets.Value("string")),
                     "results":       datasets.features.Sequence(datasets.Value("string")),
@@ -430,7 +472,7 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
                     "footnote":      datasets.features.Sequence(datasets.Value("string")),
                     "graphic":       datasets.features.Sequence(datasets.Value("string")),
                     "media":         datasets.features.Sequence(datasets.Value("string")),
-                    
+
                     "unknown_pub": datasets.Value("string"),
                     # "question":    datasets.Value("string"),
                     "glossary":    datasets.features.Sequence(
@@ -475,9 +517,9 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
             "incremental_file_lists": [],
             "incremental_archives": []
             }
-        
+
         baseline_package_list = dl_manager.download(f"{_URL_ROOT}oa_file_list.csv")
-  
+
         baseline_file_lists    = []
         baseline_archives      = []
         for subset in self.config.subsets:
@@ -494,12 +536,12 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
                     baseline_archive = dl_manager.download(baseline_archive_url)
                 except FileNotFoundError:  # non-commercial PMC000xxxxxx baseline does not exist
                     continue
-                
+
                 baseline_file_lists.append(baseline_file_list)
                 baseline_archives.append(baseline_archive)
 
             baseline_file_list_url = f"{url}{basename}{baseline}.filelist.csv"
-            
+
             # Incremental commented because some articles are already in the main parts (updates?)
             # Need to find a way to add them to the dataset without duplicating the articles.
             # Also adding them would mean that each new day the dataset is loaded, the whole dataset is recreated.
@@ -547,7 +589,7 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
                 incrementals = incrementals.join(oa_package_list).reset_index().set_index("Article File")
                 incrementals.File = incrementals.File.fillna('')
                 incrementals = incrementals.to_dict(orient="index")
-                
+
                 for path, file in incremental_archive:
                     data = incrementals.pop(path)
                     pmcid = data["AccessionID"]
@@ -563,7 +605,7 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
                         article_tree = etree.ElementTree(etree.fromstring(text))
                     except etree.XMLSyntaxError: #In some files, xml is broken
                         continue
-                        
+
                     content_d, reference_d, reference_text_d, n_ref = construct_datadict(article_tree)
                     glossary = np.array([[k,v] for k,v in content_d["glossary"].items()])
                     data = {
@@ -611,7 +653,7 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
             baselines = baselines.join(oa_package_list).reset_index().set_index("Article File")
             baselines.File = baselines.File.fillna('')
             baselines = baselines.to_dict(orient="index")
-            
+
             for path, file in baseline_archive:
                 data = baselines.pop(path)
                 pmcid = data["AccessionID"]
@@ -627,7 +669,7 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
                     article_tree = etree.ElementTree(etree.fromstring(text))
                 except etree.XMLSyntaxError: #In some files, xml is broken
                     continue
-                    
+
                 content_d, reference_d, reference_text_d, n_ref = construct_datadict(article_tree)
                 glossary = np.array([[k,v] for k,v in content_d["glossary"].items()])
                 data = {
@@ -669,5 +711,3 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
 
             #except FileNotFoundError:  # non-commercial PMC000xxxxxx baseline does not exist
             #    continue
-                
-