improve handling of invalid identifiers

6 files changed, 45 insertions, 5 deletions

diff --git a/python/fatcat/importer_common.py b/python/fatcat/importer_common.py
index 9d495aa7..e084d8c4 100644
--- a/python/fatcat/importer_common.py
+++ b/python/fatcat/importer_common.py
@@ -1,4 +1,5 @@
 
+import re
 import sys
 import csv
 import json
@@ -22,6 +23,7 @@ class FatcatImporter:
         self._orcid_id_map = dict()
         self._doi_id_map = dict()
         self._issn_issnl_map = None
+        self._orcid_regex = re.compile("^\\d{4}-\\d{4}-\\d{4}-\\d{4}$")
         if issn_map_file:
             self.read_issn_map_file(issn_map_file)
 
@@ -54,9 +56,11 @@ class FatcatImporter:
         reader = csv.DictReader(source, delimiter=delimiter)
         self.process_batch(reader, size)
 
+    def is_issnl(self, issnl):
+        return len(issnl) == 9 and issnl[4] == '-'
+
     def lookup_issnl(self, issnl):
         """Caches calls to the ISSN-L lookup API endpoint in a local dict"""
-        assert len(issnl) == 9 and issnl[4] == '-'
         if issnl in self._issnl_id_map:
             return self._issnl_id_map[issnl]
         container_id = None
@@ -69,9 +73,13 @@ class FatcatImporter:
         self._issnl_id_map[issnl] = container_id # might be None
         return container_id
 
+    def is_orcid(self, orcid):
+        return self._orcid_regex.match(orcid) != None
+
     def lookup_orcid(self, orcid):
         """Caches calls to the Orcid lookup API endpoint in a local dict"""
-        assert len(orcid) == 19 and orcid[4] == '-'
+        if not self.is_orcid(orcid):
+            return None
         if orcid in self._orcid_id_map:
             return self._orcid_id_map[orcid]
         creator_id = None
@@ -84,9 +92,12 @@ class FatcatImporter:
         self._orcid_id_map[orcid] = creator_id # might be None
         return creator_id
 
+    def is_doi(self, doi):
+        return doi.startswith("10.") and doi.count("/") >= 1
+
     def lookup_doi(self, doi):
         """Caches calls to the doi lookup API endpoint in a local dict"""
-        assert doi.startswith('10.')
+        assert self.is_doi(doi)
         doi = doi.lower()
         if doi in self._doi_id_map:
             return self._doi_id_map[doi]
diff --git a/python/fatcat/orcid_importer.py b/python/fatcat/orcid_importer.py
index 69b184d5..e57703d5 100644
--- a/python/fatcat/orcid_importer.py
+++ b/python/fatcat/orcid_importer.py
@@ -5,7 +5,6 @@ import itertools
 import fatcat_client
 from fatcat.importer_common import FatcatImporter
 
-
 def value_or_none(e):
     if type(e) == dict:
         e = e.get('value')
@@ -46,8 +45,12 @@ class FatcatOrcidImporter(FatcatImporter):
             else:
                 # must have *some* name
                 return None
+        orcid = obj['orcid-identifier']['path']
+        if not self.is_orcid(orcid):
+            sys.stderr.write("Bad ORCID: {}\n".format(orcid))
+            return None
         ce = fatcat_client.CreatorEntity(
-            orcid=obj['orcid-identifier']['path'],
+            orcid=orcid,
             given_name=given,
             surname=sur,
             display_name=display,
diff --git a/python/tests/files/0000-0001-8254-710X.json b/python/tests/files/0000-0001-8254-710X.json
new file mode 100644
index 00000000..094cae67
--- /dev/null
+++ b/python/tests/files/0000-0001-8254-710X.json
@@ -0,0 +1 @@
+{"orcid-identifier":{"uri":"http://orcid.org/0000-0001-8254-710X","path":"0000-0001-8254-710X","host":"orcid.org"},"preferences":{"locale":"en"},"history":{"creation-method":"Member-referred","completion-date":null,"submission-date":{"value":1407501041999},"last-modified-date":{"value":1465949566770},"claimed":true,"source":null,"deactivation-date":null,"verified-email":true,"verified-primary-email":true},"person":{"last-modified-date":null,"name":{"created-date":{"value":1460755375159},"last-modified-date":{"value":1460755375159},"given-names":{"value":"Man-Hui"},"family-name":{"value":"Li"},"credit-name":null,"source":null,"visibility":"public","path":"0000-0001-8254-710X"},"other-names":{"last-modified-date":null,"other-name":null,"path":"/0000-0001-8254-710X/other-names"},"biography":{"created-date":{"value":1460755375161},"last-modified-date":{"value":1460755375161},"content":null,"visibility":"public","path":"/0000-0001-8254-710X/biography"},"researcher-urls":{"last-modified-date":null,"researcher-url":null,"path":"/0000-0001-8254-710X/researcher-urls"},"emails":{"last-modified-date":null,"email":null,"path":"/0000-0001-8254-710X/email"},"addresses":{"last-modified-date":null,"address":null,"path":"/0000-0001-8254-710X/address"},"keywords":{"last-modified-date":null,"keyword":null,"path":"/0000-0001-8254-710X/keywords"},"external-identifiers":{"last-modified-date":null,"external-identifier":null,"path":"/0000-0001-8254-710X/external-identifiers"},"path":"/0000-0001-8254-710X/person"},"activities-summary":{"last-modified-date":null,"educations":{"last-modified-date":null,"education-summary":null,"path":"/0000-0001-8254-710X/educations"},"employments":{"last-modified-date":null,"employment-summary":null,"path":"/0000-0001-8254-710X/employments"},"fundings":{"last-modified-date":null,"group":null,"path":"/0000-0001-8254-710X/fundings"},"peer-reviews":{"last-modified-date":null,"group":null,"path":"/0000-0001-8254-710X/peer-reviews"},"works":{"last-modified-date":null,"group":null,"path":"/0000-0001-8254-710X/works"},"path":"/0000-0001-8254-710X/activities"},"path":"/0000-0001-8254-710X"}
diff --git a/python/tests/files/crossref-works.2018-01-21.badsample.json b/python/tests/files/crossref-works.2018-01-21.badsample.json
index d0ce191f..931da7a7 100644
--- a/python/tests/files/crossref-works.2018-01-21.badsample.json
+++ b/python/tests/files/crossref-works.2018-01-21.badsample.json
@@ -9,5 +9,6 @@
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Displaced tobacco workers, public health, and tobacco policy: moving beyond jobs versus health. Doctoral thesis, Department of Work Environment, University of Massachusetts, Lowell." }, { "key" : "BIB2", "author" : "Berberian", "volume" : "37", "first-page" : "126", "year" : "1987", "journal-title" : "J Occup Environ Med" }, { "key" : "BIB3", "author" : "Bignami", "volume" : "80", "first-page" : "265", "year" : "1981", "journal-title" : "Mutat Res", "DOI" : "10.1016/0027-5107(81)90099-3", "doi-asserted-by" : "crossref" }, { "key" : "BIB4", "author" : "Britton", "year" : "1989", "unstructured" : "1989. The post-Alar era dawns chilly for apple growers. Boston Globe. Oct. 25, p. 34." }, { "key" : "BIB5", "author" : "Brusick", "year" : "1976", "unstructured" : "1976. Mutagen and oncogen Study on 1,1-dimethylhydrazine. Prepared for the Aerospace Med. Res. Lab., Aeropsace Med. Div. Airforce Systems Command, Wright- Patterson A.F.B., Dayton OH Litton Bionetics, Inc., Kensington, MD. NTIS AD-A035475." }, { "key" : "BIB6", "author" : "Chemical Marketing Reporter", "year" : "1984", "unstructured" : "Chemical Marketing Reporter. 1984. Uniroyal pesticide to be reviewed by EPA: regulatory action prompted by its toxicity. July 23." }, { "key" : "BIB7", "author" : "Chemical Marketing Reporter", "year" : "1989", "unstructured" : "Chemical Marketing Reporter. 1989. Uniroyal pulls apple pesticide from market, citing controversy. June 5." }, { "key" : "BIB8", "year" : "1990", "unstructured" : "Du Pont Chemical Company. 1990. MSDS No. M0000057, p. 2." }, { "key" : "BIB9", "year" : "1993", "unstructured" : "Farm Chemicals Handbook '93. 1993. Willoughby, OH: Meister.", "volume-title" : "Farm Chemicals Handbook '93" }, { "key" : "BIB10", "year" : "1985", "unstructured" : "Farm Chemicals Handbook '85. 1985. Willoughby, OH: Meister.", "volume-title" : "Farm Chemicals Handbook '85" }, { "key" : "BIB11", "author" : "Federal Register", "year" : "1989", "unstructured" : "Federal Register. 1989. Daminozide: termination of special review of food uses. Vol. 54, No. 216, p. 47482, November 14." }, { "key" : "BIB12", "author" : "Fenske", "first-page" : "729", "year" : "2000", "unstructured" : "2000. Agricultural workers. In: editors. Occupational health: recognizing and preventing work-related disease and injury. 4th ed. Philadelphia: Lippincott Williams and Wilkins, p. 729-748.", "volume-title" : "Occupational health: recognizing and preventing work-related disease and injury" }, { "key" : "BIB13", "author" : "Gibson", "volume" : "5", "first-page" : "24", "year" : "1994", "journal-title" : "New Solutions", "DOI" : "10.2190/NS5.1.g", "doi-asserted-by" : "crossref" }, { "key" : "BIB14", "author" : "Goldenhar", "volume" : "29", "first-page" : "289", "year" : "1996", "journal-title" : "Am J Ind Med", "DOI" : "10.1002/(SICI)1097-0274(199604)29:4<289::AID-AJIM2>3.0.CO;2-K", "doi-asserted-by" : "crossref" }, { "key" : "BIB15", "author" : "Haun", "year" : "1984", "unstructured" : "1984. Inhalation studies of UDMH. Air Force Aerospace Medical Res Lab, TR-85-020." }, { "key" : "BIB16", "author" : "International Agency for Research on Cancer (IARC)", "year" : "1997", "unstructured" : "International Agency for Research on Cancer (IARC). 1997. Evaluation of carcinogen risks to humans: man-made mineral fibres and radon. Lyons, France." }, { "key" : "BIB17", "author" : "Lord", "year" : "1969", "unstructured" : "1969 (May-June). Thoughts on the apple harvest problem. Fruit Notes. U. S. Department of Agriculture, Massachusetts Extension Service." }, { "key" : "BIB18", "author" : "Manning", "first-page" : "34", "year" : "1989", "unstructured" : "Sales Agent for J. P. Sullivan and Co., of Ayer, MA, an apple commission house. In 1989. The post-Alar era dawns chilly for apple growers. Boston Globe Oct. 25 p. 34.", "volume-title" : "The post-Alar era dawns chilly for apple growers" }, { "key" : "BIB19", "author" : "National Cancer Institute", "year" : "1978", "unstructured" : "National Cancer Institute. 1978. Bioassay of daminozide for possible carcinogenicity. Washington, D.C., United State Department of Health, Education and Welfare, Public Health Service (NIC Carcinogenesis Technical Report Series No. 83; DHEW Publication No (NIH 78-1333)." }, { "key" : "BIB20", "author" : "Rogers", "volume" : "89", "first-page" : "321", "year" : "1981", "journal-title" : "Mutat Res", "DOI" : "10.1016/0165-1218(81)90113-0", "doi-asserted-by" : "crossref" }, { "key" : "BIB21", "author" : "Rosenberg", "year" : "1995", "unstructured" : "1995. The best laid bans: the impact of pesticide bans on workers. 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diff --git a/python/tests/importer.py b/python/tests/importer.py
index 190acbed..4d49e794 100644
--- a/python/tests/importer.py
+++ b/python/tests/importer.py
@@ -13,3 +13,23 @@ def test_issnl_mapping_lookup():
     assert fi.issn2issnl('9999-0027') == None
 
     assert fi.lookup_issnl('9999-9999') == None
+
+def test_identifiers():
+
+    with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file:
+        fi = FatcatImporter("http://localhost:9411/v0", issn_file)
+
+    assert fi.is_issnl("1234-5678") == True
+    assert fi.is_issnl("1234-5678.") == False
+    assert fi.is_issnl("12345678") == False
+    assert fi.is_issnl("1-2345678") == False
+
+    assert fi.is_doi("10.1234/56789") == True
+    assert fi.is_doi("101234/56789") == False
+    assert fi.is_doi("10.1234_56789") == False
+
+    assert fi.is_orcid("0000-0003-3118-6591") == True
+    assert fi.is_orcid("0000-00x3-3118-659") == False
+    assert fi.is_orcid("0000-00033118-659") == False
+    assert fi.is_orcid("0000-0003-3118-659.") == False
+
diff --git a/python/tests/orcid.py b/python/tests/orcid.py
index 00748972..e07583ac 100644
--- a/python/tests/orcid.py
+++ b/python/tests/orcid.py
@@ -13,6 +13,10 @@ def test_orcid_importer_batch(orcid_importer):
     with open('tests/files/0000-0001-8254-7103.json', 'r') as f:
         orcid_importer.process_batch(f)
 
+def test_orcid_importer_badid(orcid_importer):
+    with open('tests/files/0000-0001-8254-710X.json', 'r') as f:
+        orcid_importer.process_batch(f)
+
 def test_orcid_importer(orcid_importer):
     with open('tests/files/0000-0001-8254-7103.json', 'r') as f:
         orcid_importer.process_source(f)