Merge pull request #172 from elifesciences/develop

PR for version 0.71.0 release

elifecleaner/__init__.py

@@ -1,7 +1,7 @@
 import logging
 
 
-__version__ = "0.70.0"
+__version__ = "0.71.0"
 
 
 LOGGER = logging.getLogger(__name__)

elifecleaner/prc.py

@@ -2,7 +2,6 @@
 from xml.etree.ElementTree import Element, SubElement
 from docmaptools import parse as docmap_parse
 from jatsgenerator import build as jats_build
-from elifetools.utils import doi_to_doi_uri
 from elifecleaner import LOGGER
 
 # for each ISSN, values for journal-id-type tag text
@@ -419,68 +418,3 @@ def add_history_date(root, date_type, date_struct, identifier=None):
         date_tag.set("iso-8601-date", time.strftime("%Y-%m-%d", date_struct))
     jats_build.set_dmy(date_tag, date_struct)
     return root
-
-
-EVENT_DESC_PREPRINT = "This manuscript was published as a preprint."
-EVENT_DESC_REVIEWED_PREPRINT = "This manuscript was published as a reviewed preprint."
-EVENT_DESC_REVISED_PREPRINT = "The reviewed preprint was revised."
-
-
-def add_pub_history(root, history_data, identifier=None):
-    "add the pub-history tag and add event data to it"
-    if not history_data:
-        return root
-    article_meta_tag = root.find(".//front/article-meta")
-    if article_meta_tag is None:
-        LOGGER.warning(
-            "%s article-meta tag not found",
-            identifier,
-        )
-        return root
-    # look for an existing pub-history tag
-    pub_history_tag = article_meta_tag.find("./pub-history")
-    # if no pub-history tag, add one
-    if pub_history_tag is None:
-        # insert the new tag into the XML after the history or elocation-id tag
-        insert_index = 1
-        for tag_index, tag in enumerate(article_meta_tag.findall("*")):
-            if tag.tag in "history":
-                insert_index = tag_index + 1
-                break
-            if tag.tag == "elocation-id":
-                insert_index = tag_index + 1
-        pub_history_tag = Element("pub-history")
-        article_meta_tag.insert(insert_index, pub_history_tag)
-    # add event tags to the pub-history tag
-    added_reviewed_preprint = None
-    for history_event_data in history_data:
-        event_tag = SubElement(pub_history_tag, "event")
-        if history_event_data.get("type"):
-            if history_event_data.get("type") == "preprint":
-                event_desc_tag = SubElement(event_tag, "event-desc")
-                event_desc_tag.text = EVENT_DESC_PREPRINT
-            elif history_event_data.get("type") == "reviewed-preprint":
-                event_desc_tag = SubElement(event_tag, "event-desc")
-                if added_reviewed_preprint:
-                    # already added one reviewed-preprint
-                    event_desc_tag.text = EVENT_DESC_REVISED_PREPRINT
-                else:
-                    # adding the first reviewed-preprint
-                    event_desc_tag.text = EVENT_DESC_REVIEWED_PREPRINT
-                added_reviewed_preprint = True
-        if history_event_data.get("date"):
-            date_struct = date_struct_from_string(history_event_data.get("date"))
-            date_tag = SubElement(event_tag, "date")
-            if history_event_data.get("type"):
-                date_tag.set("date-type", history_event_data.get("type"))
-            jats_build.set_dmy(date_tag, date_struct)
-            date_tag.set("iso-8601-date", time.strftime("%Y-%m-%d", date_struct))
-            if history_event_data.get("doi"):
-                self_uri_tag = SubElement(event_tag, "self-uri")
-                if history_event_data.get("type"):
-                    self_uri_tag.set("content-type", history_event_data.get("type"))
-                self_uri_tag.set(
-                    "{http://www.w3.org/1999/xlink}href",
-                    doi_to_doi_uri(history_event_data.get("doi")),
-                )
-    return root

elifecleaner/pub_history.py

@@ -0,0 +1,220 @@
+import time
+from xml.etree.ElementTree import Element, SubElement
+from docmaptools import parse as docmap_parse
+from jatsgenerator import build as jats_build
+from elifetools.utils import doi_to_doi_uri
+from elifecleaner import sub_article, LOGGER
+from elifecleaner.prc import date_struct_from_string
+
+
+def find_pub_history_tag(root, identifier=None):
+    "find pub-history tag in the article-meta tag"
+    article_meta_tag = root.find(".//front/article-meta")
+    if article_meta_tag is None:
+        LOGGER.warning(
+            "%s article-meta tag not found",
+            identifier,
+        )
+        return None
+    # look for an existing pub-history tag
+    pub_history_tag = article_meta_tag.find("./pub-history")
+    # if no pub-history tag, add one
+    if pub_history_tag is None:
+        # insert the new tag into the XML after the history or elocation-id tag
+        insert_index = 1
+        for tag_index, tag in enumerate(article_meta_tag.findall("*")):
+            if tag.tag in "history":
+                insert_index = tag_index + 1
+                break
+            if tag.tag == "elocation-id":
+                insert_index = tag_index + 1
+        pub_history_tag = Element("pub-history")
+        article_meta_tag.insert(insert_index, pub_history_tag)
+    return pub_history_tag
+
+
+def add_self_uri_tag(parent, article_type, uri, title):
+    "add self-uri tag for each peer review in event tag"
+    self_uri_tag = SubElement(parent, "self-uri")
+    if article_type:
+        self_uri_tag.set("content-type", article_type)
+    self_uri_tag.set(
+        "{http://www.w3.org/1999/xlink}href",
+        uri,
+    )
+    self_uri_tag.text = str(title)
+
+
+def add_history_event_tag(parent, event_data):
+    "add event tag to pub-history"
+    event_tag = SubElement(parent, "event")
+    if event_data.get("event_desc"):
+        event_desc_tag = SubElement(event_tag, "event-desc")
+        event_desc_tag.text = event_data.get("event_desc")
+    if event_data.get("date"):
+        date_struct = date_struct_from_string(event_data.get("date"))
+        date_tag = SubElement(event_tag, "date")
+        if event_data.get("type"):
+            date_tag.set("date-type", event_data.get("type"))
+        jats_build.set_dmy(date_tag, date_struct)
+        date_tag.set("iso-8601-date", time.strftime("%Y-%m-%d", date_struct))
+        if event_data.get("doi"):
+            self_uri_tag = SubElement(event_tag, "self-uri")
+            if event_data.get("type"):
+                self_uri_tag.set("content-type", event_data.get("type"))
+            self_uri_tag.set(
+                "{http://www.w3.org/1999/xlink}href",
+                doi_to_doi_uri(event_data.get("doi")),
+            )
+    if event_data.get("self_uri_list"):
+        for self_uri_data in event_data.get("self_uri_list"):
+            add_self_uri_tag(
+                event_tag,
+                self_uri_data.get("content_type"),
+                self_uri_data.get("uri"),
+                self_uri_data.get("title"),
+            )
+
+
+EVENT_DESC_PREPRINT = "This manuscript was published as a preprint."
+EVENT_DESC_REVIEWED_PREPRINT = "This manuscript was published as a reviewed preprint."
+EVENT_DESC_REVISED_PREPRINT = "The reviewed preprint was revised."
+
+MECA_EVENT_DESC_PREPRINT = "Preprint posted"
+MECA_EVENT_DESC_REVIEWED_PREPRINT = "Reviewed preprint"
+MECA_EVENT_DESC_REVISED_PREPRINT = "Reviewed preprint"
+
+
+def preprint_event_desc(style):
+    "generate event event-desc tag text for a preprint history event"
+    event_description = None
+    if style == "accepted":
+        event_description = EVENT_DESC_PREPRINT
+    elif style == "meca":
+        event_description = MECA_EVENT_DESC_PREPRINT
+    return event_description
+
+
+def reviewed_preprint_event_desc(style, first_review_event, version):
+    "generate event event-desc tag text for a reviewed preprint history event"
+    event_description = None
+    extra = ""
+    if style == "meca" and version:
+        extra = " v%s" % version
+    if first_review_event:
+        # adding the first reviewed-preprint
+        if style == "accepted":
+            event_description = "%s%s" % (
+                EVENT_DESC_REVIEWED_PREPRINT,
+                extra,
+            )
+        elif style == "meca":
+            event_description = "%s%s" % (
+                MECA_EVENT_DESC_REVIEWED_PREPRINT,
+                extra,
+            )
+    else:
+        # already added one reviewed-preprint
+        if style == "accepted":
+            event_description = "%s%s" % (
+                EVENT_DESC_REVISED_PREPRINT,
+                extra,
+            )
+        elif style == "meca":
+            event_description = "%s%s" % (
+                MECA_EVENT_DESC_REVISED_PREPRINT,
+                extra,
+            )
+    return event_description
+
+
+def history_event_self_uri_list(docmap_string, version_doi):
+    "a list of self-uri tag data for a history event"
+    self_uri_list = []
+    d_json = docmap_parse.docmap_json(docmap_string)
+    step_map = docmap_parse.preprint_version_doi_step_map(d_json)
+    if step_map.get(version_doi):
+        generate_dois = False
+        data = sub_article.sub_article_data(
+            docmap_string,
+            version_doi=version_doi,
+            generate_dois=generate_dois,
+        )
+        for data_item in data:
+            self_uri_data = {}
+            if data_item.get("article").article_type:
+                self_uri_data["content_type"] = data_item.get("article").article_type
+            self_uri_data["uri"] = doi_to_doi_uri(data_item.get("article").doi)
+            self_uri_data["title"] = str(data_item.get("article").title)
+            self_uri_list.append(self_uri_data)
+    return self_uri_list
+
+
+def collect_history_event_data(
+    history_data, style, docmap_string=None, add_self_uri=False
+):
+    "populate a list of history event data"
+    history_event_data = []
+    if not history_data:
+        return history_event_data
+    first_review_event = True
+    for data in history_data:
+        event_data = {}
+        event_data["type"] = data.get("type")
+        event_data["date"] = data.get("date")
+        event_data["doi"] = data.get("doi")
+        event_data["versionIdentifier"] = data.get("versionIdentifier")
+        # event description
+        if event_data.get("type") == "preprint":
+            event_data["event_desc"] = preprint_event_desc(style)
+        elif event_data.get("type") == "reviewed-preprint":
+            event_data["event_desc"] = reviewed_preprint_event_desc(
+                style, first_review_event, event_data.get("versionIdentifier")
+            )
+            first_review_event = False
+        # self-uri values
+        if add_self_uri and docmap_string:
+            event_data["self_uri_list"] = history_event_self_uri_list(
+                docmap_string, version_doi=event_data.get("doi")
+            )
+        # append the event data to the list
+        history_event_data.append(event_data)
+    return history_event_data
+
+
+def add_pub_history_tag(root, history_event_data, identifier=None):
+    "set event data in pub-history tag"
+    if not history_event_data:
+        return root
+    pub_history_tag = find_pub_history_tag(root, identifier)
+    if pub_history_tag is None:
+        return root
+    # add event tags to the pub-history tag
+    for event_data in history_event_data:
+        add_history_event_tag(
+            pub_history_tag,
+            event_data,
+        )
+    return root
+
+
+def add_pub_history(root, history_data, docmap_string=None, identifier=None):
+    "add the pub-history tag and add event data to it"
+    style = "accepted"
+    add_self_uri = False
+    # collect history event data
+    history_event_data = collect_history_event_data(
+        history_data, style, docmap_string, add_self_uri
+    )
+    return add_pub_history_tag(root, history_event_data, identifier)
+
+
+def add_pub_history_meca(root, history_data, docmap_string=None, identifier=None):
+    "add the MECA style pub-history tag and add event data to it"
+    style = "meca"
+    add_self_uri = True
+    # collect history event data
+    history_event_data = collect_history_event_data(
+        history_data, style, docmap_string, add_self_uri
+    )
+    return add_pub_history_tag(root, history_event_data, identifier)

tests/helpers.py

@@ -61,3 +61,22 @@ def sub_article_xml_fixture(
         b'article-type="%s" id="%s">%s%s</sub-article>'
         % (article_type, sub_article_id, front_stub_xml_string, body_xml_string)
     )
+
+
+class FakeRequest:
+    def __init__(self):
+        self.headers = {}
+        self.body = None
+
+
+class FakeResponse:
+    def __init__(self, status_code, response_json=None, text="", content=None):
+        self.status_code = status_code
+        self.response_json = response_json
+        self.content = content
+        self.text = text
+        self.request = FakeRequest()
+        self.headers = {}
+
+    def json(self):
+        return self.response_json