switch over the creation of links in pub-hash from http to https; mov…

…e the base URLs to config

README.md

@@ -4,8 +4,8 @@
 
 # SUL Bibliographic Management System
 
-[*SUL Bibliographic Management System*](http://sulcap.stanford.edu/)
-by [Stanford University Libraries](http://library.stanford.edu).
+[*SUL Bibliographic Management System*](https://sulcap.stanford.edu/)
+by [Stanford University Libraries](https://library.stanford.edu).
 
 ## Configuration
 

app/data/bibtex_to_ingest/August19 17 Batch/aydin.txt

@@ -27,7 +27,7 @@ journal = {Geological Society, London,},
 title = {Fluid flow through porous sandstone with overprinting and intersecting geological structures of various types},
 year = {2012},
 doi = {10.1144/SP374.11},
-url = {http://dx.doi.org/10.1144/SP374.11},
+url = {https://dx.doi.org/10.1144/SP374.11},
 comment = {Special Paper on Advances in the Study of Fractured Reservoirs},
 }
 
@@ -53,7 +53,7 @@ journal = {Journal of Structural Geology},
 title = {Growth processes, dimensional parameters and scaling relationships of two conjugate sets of compactive shear bands in porous carbonate grainstones, Favignana Island, Italy},
 year = {2012},
 doi = {10.1016/j.bbr.2011.03.031},
-url = {http://dx.doi.org/10.1016/j.bbr.2011.03.031},
+url = {https://dx.doi.org/10.1016/j.bbr.2011.03.031},
 }
 
 @article{na110,

app/data/bibtex_to_ingest/August19 17 Batch/elambin.txt

@@ -10,7 +10,7 @@ author = {Lambin E. F. and Gibbs H. and Ferreira L. and Grau R. and Mayaux P. an
 journal = {Global Environmental Change},
 title = {Estimating the world's potentially available cropland using a bottom-up approach},
 year = {2013},
-url = {http://dx.doi.org/10.1016/j.gloenvcha.2013.05.005},
+url = {https://dx.doi.org/10.1016/j.gloenvcha.2013.05.005},
 }
 
 @article{jvmrtfwcfsawfrra13,
@@ -39,7 +39,7 @@ journal = {Current Opinion in Environmental Sustainability},
 title = {Globalization of land use: Displacement and distant drivers},
 volume = {5},
 year = {2013},
-url = {http://dx.doi.org/10.1016/j.cosust.2013.04.003},
+url = {https://dx.doi.org/10.1016/j.cosust.2013.04.003},
 }
 
 @incollection{fp13,

app/data/bibtex_to_ingest/August23 8 Batch/mjgrove.txt

@@ -46,7 +46,7 @@ author = {J. C. Fosdick and M. Grove and J. K. Hourigan and M. Calderón},
 journal = {Earth and Planetary Science Letters},
 title = {Retroarc deformation and exhumation near the end of the Andes, southern Patagonia},
 year = {2013},
-url = {http://dx.doi.org/10.1016/j.epsl.2012.12.007},
+url = {https://dx.doi.org/10.1016/j.epsl.2012.12.007},
 }
 
 @article{yfiwwlg13,
@@ -56,7 +56,7 @@ pages = {268-282},
 title = {Is Myanmar jadeitite of Jurassic age? A result from incompletely recrystallized inherited zircon},
 volume = {160-161},
 year = {2013},
-url = {http://dx.doi.org/10.1016/j.lithos.2012.12.011},
+url = {https://dx.doi.org/10.1016/j.lithos.2012.12.011},
 }
 
 @article{zlcgoit13,
@@ -75,7 +75,7 @@ pages = {TC6006},
 title = {Paleozoic-to-early Cenozoic cooling and exhumation of the basement underlying the eastern Puna plateau margin},
 volume = {31},
 year = {2013},
-url = {http://dx.doi.org/10.1029/2012TC003168},
+url = {https://dx.doi.org/10.1029/2012TC003168},
 }
 
 @article{fgsbi12,
@@ -156,7 +156,7 @@ pages = {75-87},
 title = {Calibration of Nu-Instruments Noblesse multicollector mass spectrometers for argon isotopic measurements using a newly developed reference gas},
 volume = {290},
 year = {2011},
-url = {http://dx.doi.org/10.1016/j.chemgeo.2011.09.003},
+url = {https://dx.doi.org/10.1016/j.chemgeo.2011.09.003},
 }
 
 @article{gtiwgsm11,
@@ -247,7 +247,7 @@ number = {20-30},
 title = {Decoupling of U-Pb dates from chemical and crystallographic domains in granulite facies zircon},
 volume = {270},
 year = {2010},
-url = {http://dx.doi.org/10.1016/j.chemgeo.2009.11.002},
+url = {https://dx.doi.org/10.1016/j.chemgeo.2009.11.002},
 }
 
 @article{kelwg10,
@@ -257,7 +257,7 @@ pages = {22-32},
 title = {First Paleoproterozoic ophiolite from Gondwana: Geochronologic-geochemical documentation of ancient oceanic crust from Kandra, SE India},
 volume = {487},
 year = {2010},
-url = {http://dx.doi.org/10.1016/j.tecto.2010.03.005},
+url = {https://dx.doi.org/10.1016/j.tecto.2010.03.005},
 }
 
 @article{cygdslkgf09,

app/data/bibtex_to_ingest/August23 8 Batch/mmac.txt

@@ -64,7 +64,7 @@ title = {Provenance of north Gondwana Cambrian-Ordovician sandstone: U-Pb SHRIMP
 volume = {143},
 year = {2006},
 doi = {10.1017/S0016756805001640},
-url = {http://dx.doi.org/10.1017/S0016756805001640},
+url = {https://dx.doi.org/10.1017/S0016756805001640},
 }
 
 @article{vmdgm05,

app/data/bibtex_to_ingest/August23 8 Batch/zoback.txt

@@ -94,7 +94,7 @@ title = {Intraplate Earthquakes, Regional Stress and Fault Mechanics in the Cent
 volume = {581},
 year = {2012},
 doi = {10.1016/j.tecto.2012.04.002},
-url = {http://dx.doi.org/10.1016/j.tecto.2012.04.002},
+url = {https://dx.doi.org/10.1016/j.tecto.2012.04.002},
 }
 
 @article{dz11,
@@ -330,7 +330,7 @@ title = {Viscous creep in room-dried unconsolidated Gulf of Mexico shale (II): D
 volume = {72},
 year = {2010},
 doi = {0.2118/110542-PA},
-url = {http://dx.doi.org/10.2118/110542-PA},
+url = {https://dx.doi.org/10.2118/110542-PA},
 }
 
 @article{cz09,

app/models/pubmed_source_record.rb

@@ -148,11 +148,11 @@ def convert_pubmed_publication_doc_to_hash(publication)
     journal_hash[:identifier] = journal_identifiers
     record_as_hash[:journal] = journal_hash
 
-    record_as_hash[:identifier] = [{ type: 'PMID', id: pmid, url: 'http://www.ncbi.nlm.nih.gov/pubmed/' + pmid }]
+    record_as_hash[:identifier] = [{ type: 'PMID', id: pmid, url: "#{Settings.PUBMED.ARTICLE_BASE_URI}#{pmid}"}]
     # the DOI can be in one of two places: ArticleId or ELocationID
     doi = publication.at_xpath('//ArticleId[@IdType="doi"]')
     doi = publication.at_xpath('//ELocationID[@EIdType="doi"]') unless doi.present? && doi.text.present?
-    record_as_hash[:identifier] << { type: 'doi', id: doi.text, url: 'http://dx.doi.org/' + doi.text } if doi.present? && doi.text.present?
+    record_as_hash[:identifier] << { type: 'doi', id: doi.text, url: "#{Settings.SCIENCEWIRE.DOI_BASE_URL}#{doi.text}" } if doi.present? && doi.text.present?
 
     record_as_hash
   end

app/models/sciencewire_source_record.rb

@@ -188,12 +188,12 @@ def self.convert_sw_publication_doc_to_hash(publication)
     swid = extract_swid(publication)
     wosid = extract_wosid(publication)
 
-    doi_identifier = { type: 'doi', id: doi, url: 'http://dx.doi.org/' + doi } unless doi.blank?
+    doi_identifier = { type: 'doi', id: doi, url: "#{Settings.SCIENCEWIRE.DOI_BASE_URL}#{doi}" } unless doi.blank?
     issn_identifier = { type: 'issn', id: issn, url: Settings.SULPUB_ID.SEARCHWORKS_URI + issn } unless issn.blank?
 
     identifiers = []
-    identifiers << { type: 'PMID', id: pmid, url: 'http://www.ncbi.nlm.nih.gov/pubmed/' + pmid } unless pmid.blank?
-    identifiers << { type: 'WoSItemID', id: wosid, url: 'http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/' + wosid } unless wosid.blank?
+    identifiers << { type: 'PMID', id: pmid, url: "#{Settings.PUBMED.ARTICLE_BASE_URI}#{pmid}" } unless pmid.blank?
+    identifiers << { type: 'WoSItemID', id: wosid, url: "#{Settings.SCIENCEWIRE.ARTICLE_BASE_URI}#{wosid}" } unless wosid.blank?
     identifiers << { type: 'PublicationItemID', id: swid } unless swid.blank?
     identifiers << doi_identifier unless doi.blank?
 

app/views/layouts/_header.html.erb

@@ -8,7 +8,7 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <%= link_to image_tag("sul-logo.png", alt: "SUL"), 'http://library.stanford.edu/' %>
+      <%= link_to image_tag("sul-logo.png", alt: "SUL"), 'https://library.stanford.edu/' %>
     </div>
       <!-- <%= link_to "SUL Publications Server", '#', id: "logo" %> -->
      <!-- <nav>

app/views/pages/api_samples/get_pub_out.json

@@ -3,12 +3,12 @@
         {
             "id": "7692670",
             "type": "PMID",
-            "url": "http://www.ncbi.nlm.nih.gov/pubmed/7692670"
+            "url": "https://www.ncbi.nlm.nih.gov/pubmed/7692670"
         },
         {
             "id": "A1993MB62100041",
             "type": "WoSItemID",
-            "url": "http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/A1993MB62100041"
+            "url": "https://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/A1993MB62100041"
         },
         {
             "id": "24151039",
@@ -17,7 +17,7 @@
         {
             "id": "1702",
             "type": "SULPubId",
-            "url": "http://sulcap.stanford.edu/publications/1702"
+            "url": "https://sulcap.stanford.edu/publications/1702"
         }
     ],
     "title": "IDENTIFICATION OF A NEW NEUTRALIZATION EPITOPE ON VP7 OF HUMAN SEROTYPE-2 ROTAVIRUS AND EVIDENCE FOR ELECTROPHEROTYPE DIFFERENCES CAUSED BY SINGLE NUCLEOTIDE SUBSTITUTIONS",
@@ -295,12 +295,12 @@
             {
                 "id": "0042-6822",
                 "type": "issn",
-                "url": "http://searchworks.stanford.edu/?search_field=advanced&number=0042-6822"
+                "url": "https://searchworks.stanford.edu/?search_field=advanced&number=0042-6822"
             },
             {
                 "id": "",
                 "type": "doi",
-                "url": "http://dx.doi.org/"
+                "url": "https://dx.doi.org/"
             }
         ],
         "conferencestartdate": "",

app/views/pages/api_samples/get_pubs_out.json

@@ -14,12 +14,12 @@
                 {
                     "id": "15262723",
                     "type": "PMID",
-                    "url": "http://www.ncbi.nlm.nih.gov/pubmed/15262723"
+                    "url": "https://www.ncbi.nlm.nih.gov/pubmed/15262723"
                 },
                 {
                     "id": "",
                     "type": "WoSItemID",
-                    "url": "http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/"
+                    "url": "https://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/"
                 },
                 {
                     "id": "45435892",
@@ -28,7 +28,7 @@
                 {
                     "id": "1573",
                     "type": "SULPubId",
-                    "url": "http://sulcap.stanford.edu/publications/1573"
+                    "url": "https://sulcap.stanford.edu/publications/1573"
                 }
             ],
             "title": "Use of a dual-mode erbium:YAG laser for the surgical correction of rhinophyma.",
@@ -162,12 +162,12 @@
                     {
                         "id": "1521-2491",
                         "type": "issn",
-                        "url": "http://searchworks.stanford.edu/?search_field=advanced&number=1521-2491"
+                        "url": "https://searchworks.stanford.edu/?search_field=advanced&number=1521-2491"
                     },
                     {
                         "id": "",
                         "type": "doi",
-                        "url": "http://dx.doi.org/"
+                        "url": "https://dx.doi.org/"
                     }
                 ],
                 "conferencestartdate": "",
@@ -191,12 +191,12 @@
                 {
                     "id": "15137956",
                     "type": "PMID",
-                    "url": "http://www.ncbi.nlm.nih.gov/pubmed/15137956"
+                    "url": "https://www.ncbi.nlm.nih.gov/pubmed/15137956"
                 },
                 {
                     "id": "",
                     "type": "WoSItemID",
-                    "url": "http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/"
+                    "url": "https://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/"
                 },
                 {
                     "id": "45408384",
@@ -205,7 +205,7 @@
                 {
                     "id": "1574",
                     "type": "SULPubId",
-                    "url": "http://sulcap.stanford.edu/publications/1574"
+                    "url": "https://sulcap.stanford.edu/publications/1574"
                 }
             ],
             "title": "The etiology and epidemiology of anal cancer.",
@@ -397,12 +397,12 @@
                     {
                         "id": "1055-3207",
                         "type": "issn",
-                        "url": "http://searchworks.stanford.edu/?search_field=advanced&number=1055-3207"
+                        "url": "https://searchworks.stanford.edu/?search_field=advanced&number=1055-3207"
                     },
                     {
                         "id": "",
                         "type": "doi",
-                        "url": "http://dx.doi.org/"
+                        "url": "https://dx.doi.org/"
                     }
                 ],
                 "conferencestartdate": "",

config/settings.yml

@@ -30,7 +30,8 @@ PUBMED:
   LOG: log/pubmed.log
   FETCH_PATH: /entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml
   BASE_URI: https://eutils.ncbi.nlm.nih.gov
-
+  ARTICLE_BASE_URI: https://www.ncbi.nlm.nih.gov/pubmed/
+
 ## Sciencewire Auth Config
 SCIENCEWIRE:
   LOG: log/sciencewire.log
@@ -39,6 +40,8 @@ SCIENCEWIRE:
   LICENSE_ID: some-license-id
   RECOMMENDATION_PATH: /PublicationCatalog/MatchedPublicationItemIdsForAuthor?format=xml
   TMPDIR: /tmp
+  ARTICLE_BASE_URI: https://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:ut/
+  DOI_BASE_URL: https://dx.doi.org/
 
 HARVESTER:
   USE_MIDDLE_NAME: true

lib/bibtex_ingester.rb

@@ -226,7 +226,7 @@ def convert_bibtex_record_to_pub_hash(record, author)
       identifiers << isbn_for_id_array
     end
     unless doi.blank?
-      doi_for_id_array = { type: 'doi', id: doi, url: 'http://dx.doi.org/' + doi }
+      doi_for_id_array = { type: 'doi', id: doi, url: "#{Settings.SCIENCEWIRE.DOI_BASE_URL}#{doi}" }
       identifiers << doi_for_id_array
       record_as_hash[:doi] = doi
     end

spec/api/sul_bib/authorship_api_spec.rb

@@ -226,15 +226,15 @@
       it 'adds proper identifiers section' do
         pub_ids = result['identifier']
         # Check the PMID, e.g.
-        # {"type"=>"PMID", "id"=>"23684686", "url"=>"http://www.ncbi.nlm.nih.gov/pubmed/23684686"}
+        # {"type"=>"PMID", "id"=>"23684686", "url"=>"https://www.ncbi.nlm.nih.gov/pubmed/23684686"}
         pmid_hash = pub_ids.find {|id| id['type'] == 'PMID'}
         expect(pmid_hash).to be_instance_of Hash
         pmid = request_data[:pmid]
         expect(pmid_hash['type']).to eq('PMID')
         expect(pmid_hash['id']).to eq(pmid)
-        expect(pmid_hash['url']).to eq("http://www.ncbi.nlm.nih.gov/pubmed/#{pmid}")
+        expect(pmid_hash['url']).to eq("https://www.ncbi.nlm.nih.gov/pubmed/#{pmid}")
         # Check the SULPubId, e.g.
-        # {:type=>"SULPubId", :id=>"2355", :url=>"http://sulcap.stanford.edu/publications/2355"}],
+        # {:type=>"SULPubId", :id=>"2355", :url=>"https://sulcap.stanford.edu/publications/2355"}],
         sul_hash = pub_ids.find {|id| id['type'] == 'SULPubId'}
         expect(sul_hash).to be_instance_of Hash
         sul_pub_id = Publication.last.id.to_s

spec/api/sul_bib/sourcelookup_spec.rb

@@ -64,7 +64,7 @@
             {
               type: 'doi',
               id: test_doi,
-              url: "http://dx.doi.org/#{test_doi}"
+              url: "https://dx.doi.org/#{test_doi}"
             }
           ]
         }

spec/factories/pub_hash.rb

@@ -46,7 +46,7 @@
                                                       url: Settings.SULPUB_ID.SEARCHWORKS_URI + '0165-0173' },
                                                     { type: 'doi',
                                                       id: '10.1016/j.brainresrev.2004.05.006',
-                                                      url: 'http://dx.doi.org/10.1016/j.brainresrev.2004.05.006' }] },
+                                                      url: 'https://dx.doi.org/10.1016/j.brainresrev.2004.05.006' }] },
           abstract:         'Gap junctions represent direct intercellular conduits between contacting cells. The subunit proteins of these conduits are called connexins. To date, 20 and 21 connexin genes have been described in the mouse and human genome, respectiv',
           last_updated: '2013-07-23 22:06:49 UTC',
           authorship:         [{ cap_profile_id: 8804,
@@ -89,7 +89,7 @@
                                                           url: Settings.SULPUB_ID.SEARCHWORKS_URI + '0165-0173' },
                                                         { type: 'doi',
                                                           id: '10.1016/j.brainresrev.2004.05.006',
-                                                          url: 'http://dx.doi.org/10.1016/j.brainresrev.2004.05.006' }] },
+                                                          url: 'https://dx.doi.org/10.1016/j.brainresrev.2004.05.006' }] },
           abstract:           'Gap junctions represent direct intercellular conduits between contacting cells. The subunit proteins of these conduits are called connexins. To date, 20 and 21 connexin genes have been described in the mouse and human genome, respectiv',
           last_updated: '2013-07-23 22:06:49 UTC',
           authorship:           [{ cap_profile_id: 8804,

spec/factories/user_submitted_source_records.rb

@@ -15,7 +15,7 @@
         {
           "id": "10.1016/j.petrol.2016.02.026",
           "type": "doi",
-          "url": "http://dx.doi.org/10.1016/j.petrol.2016.02.026",
+          "url": "https://dx.doi.org/10.1016/j.petrol.2016.02.026",
           "additionalProperties": {}
         }
       ],

spec/lib/doi_search_spec.rb

@@ -23,7 +23,7 @@
       VCR.use_cassette('doi_search_manual_doi_local') do
         publication.pub_hash = {
           provenance: 'cap',
-          identifier: [{ type: 'doi', id: '10.1111/j.1444-0938.2010.00524.x', url: 'http://dx.doi.org/10.1111/j.1444-0938.2010.00524.x' }]
+          identifier: [{ type: 'doi', id: '10.1111/j.1444-0938.2010.00524.x', url: 'https://dx.doi.org/10.1111/j.1444-0938.2010.00524.x' }]
         }
         publication.sync_identifiers_in_pub_hash_to_db
         publication.save

spec/lib/pubmed_harvester_spec.rb

@@ -42,7 +42,7 @@
       # /publications/sourcelookup?pmid=
       h = PubmedHarvester.search_all_sources_by_pmid 24_930_130
       expect(h.first[:provenance]).to eq('pubmed')
-      expect(h.first[:identifier]).to include(type: 'doi', id: '10.1038/nmeth.2999', url: 'http://dx.doi.org/10.1038/nmeth.2999')
+      expect(h.first[:identifier]).to include(type: 'doi', id: '10.1038/nmeth.2999', url: 'https://dx.doi.org/10.1038/nmeth.2999')
       expect(h.first[:chicago_citation]).to match(/Chemically Defined Generation/)
     end