Merge branch 'master' into serve

6 files changed, 162 insertions, 21 deletions

diff --git a/AUTHORS b/AUTHORS
index 21d56173..67455718 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -1,8 +1,9 @@
-894  Alejandro Gallo <aamsgallo@gmail.com>
-11  Nicolò Balzarotti <anothersms@gmail.com>
+1037  Alejandro Gallo <aamsgallo@gmail.com>
+38  Nicolò Balzarotti <anothersms@gmail.com>
+12  michaelplews <michael.plews@gmail.com>
 9  alejandrogallo <alejandrogallo@users.noreply.github.com>
-8  michaelplews <michael.plews@gmail.com>
-4  Michael R. Plews <michael.plews@gmail.com>
+5  Michael R. Plews <michael.plews@gmail.com>
+1  Dennis Bruggner <dennis@bruggner.net>
 1  Felix Hummel <felix.hummel@tuwien.ac.at>
 1  Katrin Leinweber <9948149+katrinleinweber@users.noreply.github.com>
 1  Theo Tsatsoulis <T.Tsatsoulis@fkf.mpg.de>
diff --git a/examples/scripts/papis-hubation b/examples/scripts/papis-hubation
index 68b0484e..6d8dbb6d 100755
--- a/examples/scripts/papis-hubation
+++ b/examples/scripts/papis-hubation
@@ -43,15 +43,19 @@ if 'citations' not in doc.keys():
 dois = [d.get('doi') for d in doc['citations']]
 
 print("%s citations found" % len(dois))
-print("Fetching citations' information online")
+print("Fetching citations'")
 dois_with_data = []
 for j,doi in enumerate(dois):
     progress = "%s/%s (doi: %s)" % (j+1, len(dois), doi)
     sys.stdout.write(progress)
     sys.stdout.flush()
-    dois_with_data.append(
-        papis.crossref.doi_to_data(doi)
-    )
+    citation = papis.api.get_documents_in_lib(papis.api.get_lib(),search='doi = "%s"' % doi)
+    if citation:
+        dois_with_data.append(papis.api.pick_doc(citation))
+    else:
+        dois_with_data.append(
+            papis.crossref.doi_to_data(doi)
+        )
     sys.stdout.write("\b" * (len(progress)))
     sys.stdout.write(" " * (len(progress)))
     sys.stdout.flush()
@@ -65,9 +69,32 @@ doi or sys.exit(0)
 
 print('DOI %s selected' % doi)
 
-papis.commands.main(
-    [
-        'scihub', doi
-    ] + add_flags
-)
+# set citation as the doc if it's already in the library
+citation = papis.api.get_documents_in_lib(papis.api.get_lib(),search='doi = "%s"' % doi)
+
+# get hubation options
+config_options = papis.config.get('hubation')
+
+# if open in config_options...
+if 'open' in config_options:
+    # Check if the citation is already in your library
+    if citation:
+        # and open the associated file
+        papis.commands.main(
+            [
+                'open', "ref=%s" % doc['ref']
+            ]
+        )
+    else:
+        # if it isn't, open in a browser
+        papis.document.open_in_browser(doc)
 
+elif 'browse' in config_options:
+    papis.document.open_in_browser(doc)
+
+else:
+    papis.commands.main(
+        [
+            papis.config.get('hubation'), "ref=%s" % doc['ref']
+        ] + add_flags
+    )
diff --git a/examples/scripts/papis-zotero b/examples/scripts/papis-zotero
index b5aef651..3a786450 100755
--- a/examples/scripts/papis-zotero
+++ b/examples/scripts/papis-zotero
@@ -42,6 +42,7 @@ def add(entry, pdf_file=None):
     fd.close()
     papis.commands.main(
         [
+            '-l', papis.api.get_lib(),
             'add', pdf_file or '--no-document', '--from-yaml', temp
         ] + add_flags
     )
diff --git a/papis/config.py b/papis/config.py
index 8c24dd06..ab7c2236 100644
--- a/papis/config.py
+++ b/papis/config.py
@@ -168,6 +168,15 @@ Tools options
 Bibtex options
 ^^^^^^^^^^^^^^
 
+.. papis-config:: bibtex-journal-key
+
+    Journal publishers may request abbreviated journal titles. This
+    option allows the user to set the key for the journal entry when using
+    ``papis export --bibtex``.
+
+    Set as ``full_journal_title`` or ``abbrev_journal_title`` for
+    whichever style required. Default is ``journal``.
+
 .. papis-config:: extra-bibtex-keys
 
     When exporting documents in bibtex format, you might want to add
@@ -280,6 +289,22 @@ Add command options
 
         papis add doc.pdf --author 'Bohm' --title 'Super book' --year 1928
 
+Browse command options
+^^^^^^^^^^^^^^^^^^^^^^
+
+.. papis-config:: browse-key
+
+    This command provides the key that is used to generate the
+    url. For users that ``papis add --from-doi``, setting browse-key
+    to ``doi`` constructs the url from dx.doi.org/DOI, providing a
+    much more accurate url.
+
+    Default value is set to ``url``. If the user needs functionality
+    with the ``search-engine`` option, set the option to an empty
+    string e.g.  ::
+
+        browse-key = ''
+
 .. _check-command-options:
 
 Check command options
@@ -430,6 +455,25 @@ Databases
     `the documentation <https://whoosh.readthedocs.io/en/latest/schema.html/>`_
     for more information.
 
+Other
+=====
+
+.. papis-config:: hubation
+
+   This allows the operation after picking be set when using the
+   script papis-hubation. Running ``papis hubation`` provides a list
+   of citations, which once picked, can undergo the operation
+   'e.g. open, browse, scihub' that is set. Current tested options are
+   ``open``, ``browse``, ``export``, and ``scihub``.
+
+   Default behaviour is set to scihub.
+
+.. papis-config:: citation-string
+
+    string that can be displayed in header if the reference has a
+    citation
+
+    Default set to '*'
 
 """
 import logging
@@ -493,6 +537,7 @@ general_settings = {
     "add-default-fields": '["title", "author"]',
 
     "check-keys": '["files"]',
+    "browse-key": '"url"',
     "browse-query-format": "{doc[title]} {doc[author]}",
     "search-engine": "https://duckduckgo.com",
     "user-agent": 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3)',
@@ -509,6 +554,7 @@ general_settings = {
     "mark-opener-format": get_default_opener(),
 
     "file-browser": get_default_opener(),
+    "bibtex-journal-key": 'journal',
     "extra-bibtex-keys": "",
     "extra-bibtex-types": "",
     "default-library": "papers",
@@ -537,6 +583,8 @@ general_settings = {
     '"tags": TEXT(stored=True),\n'
     '}',
 
+    "hubation": "scihub",
+    "citation-string": "*"
 }
 
 
diff --git a/papis/crossref.py b/papis/crossref.py
index cfa8a71c..b93f2018 100644
--- a/papis/crossref.py
+++ b/papis/crossref.py
@@ -150,6 +150,15 @@ latex_accents = {
     "\xa0": " ",     # Unprintable characters
 }
 
+def collapse_whitespace(s):
+    """Removes whitespace from string and returns the result. Useful
+    when whitespace causes errors (e.g. Bibtex)
+
+    :param s: string
+    :type s: str
+    """
+    logger.debug("Removing whitespace...")
+    return s.replace(" ","")
 
 def crossref_data_to_papis_data(data):
     if "author" in data.keys():
@@ -379,7 +388,7 @@ def get_cross_ref(doi):
     res.update(get_citation_info_from_results(record))
 
     # REFERENCE BUILDING
-    res['ref'] = papis.utils.format_doc(papis.config.get("ref-format"), res)
+    res['ref'] = collapse_whitespace(papis.utils.format_doc(papis.config.get("ref-format"), res))
 
     # Check if reference field with the same tag already exists
     documents = papis.api.get_documents_in_lib(
diff --git a/papis/document.py b/papis/document.py
index b2c019df..f209be71 100644
--- a/papis/document.py
+++ b/papis/document.py
@@ -16,12 +16,18 @@ def open_in_browser(document):
     """
     global logger
     url = None
-    if "url" in document.keys():
+    key = papis.config.get("browse-key")
+
+    if "url" in key:
         url = document["url"]
-    elif 'doi' in document.keys():
+    elif "doc-url" in key:
+        url = document["doc-url"]
+    elif "doi" in key:
         url = 'https://doi.org/' + document['doi']
-    elif papis.config.get('doc-url-key-name') in document.keys():
-        url = document[papis.config.get('doc-url-key-name')]
+    elif "isbn" in key:
+        url = 'https://isbnsearch.org/isbn/' + document['isbn']
+    elif key in document.keys():
+        url = document[key]
     else:
         from urllib.parse import urlencode
         params = {
@@ -88,9 +94,33 @@ def to_bibtex(document):
     bibtexString += "@%s{%s,\n" % (bibtexType, ref)
     for bibKey in papis.bibtex.bibtex_keys:
         if bibKey in document.keys():
-            bibtexString += "  %s = { %s },\n" % (
-                bibKey, papis.bibtex.unicode_to_latex(str(document[bibKey]))
-            )
+            if bibKey == 'journal' and papis.config.get('bibtex-journal-key') in document.keys():
+                bibtexString += "  %s = { %s },\n" % (
+                    'journal',
+                    papis.bibtex.unicode_to_latex(
+                        str(document[papis.config.get('bibtex-journal-key')])
+                    )
+                )
+            elif bibKey == 'journal' and papis.config.get('bibtex-journal-key') not in document.keys():
+                logger.warning(
+                    "Key '%s' is not present for ref=%s" % (
+                        papis.config.get('bibtex-journal-key'),
+                        document["ref"]
+                    )
+                )
+                bibtexString += "  %s = { %s },\n" % (
+                    'journal',
+                    papis.bibtex.unicode_to_latex(
+                        str(document['journal'])
+                    )
+                )
+            else:
+                bibtexString += "  %s = { %s },\n" % (
+                    bibKey,
+                    papis.bibtex.unicode_to_latex(
+                        str(document[bibKey])
+                    )
+                )
     bibtexString += "}\n"
     return bibtexString
 
@@ -356,6 +386,31 @@ class Document(object):
         """
         return self._keys
 
+    @property
+    def has_citations(self):
+        """Returns string defined in config if keys contains citations
+        else returns None.
+
+        :returns: String or None
+        :rtype: str OR None
+        """
+
+        if 'citations' in self.keys():
+            return papis.config.get('citation-string')
+        else:
+            return ''
+
+    def dump(self):
+        """Return information string without any obvious format
+        :returns: String with document's information
+        :rtype:  str
+
+        """
+        string = ""
+        for i in self.keys():
+            string += str(i)+":   "+str(self[i])+"\n"
+        return string
+
     def load(self):
         """Load information from info file
         """