From 8084e37e328e8e280507cc402538dc44801ecf65 Mon Sep 17 00:00:00 2001 From: tsande16 Date: Mon, 8 Jul 2024 16:49:17 -0400 Subject: [PATCH] Cleanup --- pass-nihms-loader/nihms-data-harvest/pom.xml | 2 +- .../pass/loader/nihms/entrez/PmidLookup.java | 2 - .../nihms/entrez/EntrezPmidLookupTest.java | 4 - .../src/test/resources/pmid_record_ascii.json | 190 ------------------ 4 files changed, 1 insertion(+), 197 deletions(-) delete mode 100644 pass-nihms-loader/nihms-data-transform-load/src/test/resources/pmid_record_ascii.json diff --git a/pass-nihms-loader/nihms-data-harvest/pom.xml b/pass-nihms-loader/nihms-data-harvest/pom.xml index 279649ca..3262599c 100644 --- a/pass-nihms-loader/nihms-data-harvest/pom.xml +++ b/pass-nihms-loader/nihms-data-harvest/pom.xml @@ -90,13 +90,13 @@ - nihms-data-harvest-cli org.springframework.boot spring-boot-maven-plugin org.eclipse.pass.loader.nihms.NihmsHarvesterCLI + nihms-data-harvest-cli exec diff --git a/pass-nihms-loader/nihms-data-transform-load/src/main/java/org/eclipse/pass/loader/nihms/entrez/PmidLookup.java b/pass-nihms-loader/nihms-data-transform-load/src/main/java/org/eclipse/pass/loader/nihms/entrez/PmidLookup.java index a02e5a6e..1265a103 100644 --- a/pass-nihms-loader/nihms-data-transform-load/src/main/java/org/eclipse/pass/loader/nihms/entrez/PmidLookup.java +++ b/pass-nihms-loader/nihms-data-transform-load/src/main/java/org/eclipse/pass/loader/nihms/entrez/PmidLookup.java @@ -55,8 +55,6 @@ public class PmidLookup { * delayed responses. * https://www.ncbi.nlm.nih.gov/books/NBK25497/ */ - /*private static final String DEFAULT_ENTREZ_PATH = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary" + - ".fcgi?db=pubmed&retmode=json&rettype=abstract&id=%s";*/ @Value("${pmc.entrez.service.url}") private String ENTREZ_PATH; diff --git a/pass-nihms-loader/nihms-data-transform-load/src/test/java/org/eclipse/pass/loader/nihms/entrez/EntrezPmidLookupTest.java b/pass-nihms-loader/nihms-data-transform-load/src/test/java/org/eclipse/pass/loader/nihms/entrez/EntrezPmidLookupTest.java index 9d137bac..6958bb47 100644 --- a/pass-nihms-loader/nihms-data-transform-load/src/test/java/org/eclipse/pass/loader/nihms/entrez/EntrezPmidLookupTest.java +++ b/pass-nihms-loader/nihms-data-transform-load/src/test/java/org/eclipse/pass/loader/nihms/entrez/EntrezPmidLookupTest.java @@ -33,7 +33,6 @@ import org.json.JSONObject; import org.junit.jupiter.api.Test; import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.test.context.SpringBootTest; import org.springframework.boot.test.mock.mockito.MockBean; import org.springframework.test.context.TestPropertySource; @@ -52,9 +51,6 @@ public class EntrezPmidLookupTest { // Needed so tests can run after application starts @MockBean private NihmsTransformLoadCLIRunner nihmsTransformLoadCLIRunner; - @Value("${pmc.entrez.service.url}") - private String ENTREZ_PATH; - @Test public void testGetEntrezRecordJson() throws IOException, URISyntaxException { String entrez = IOUtils.toString(getClass().getClassLoader(). diff --git a/pass-nihms-loader/nihms-data-transform-load/src/test/resources/pmid_record_ascii.json b/pass-nihms-loader/nihms-data-transform-load/src/test/resources/pmid_record_ascii.json deleted file mode 100644 index a515cb37..00000000 --- a/pass-nihms-loader/nihms-data-transform-load/src/test/resources/pmid_record_ascii.json +++ /dev/null @@ -1,190 +0,0 @@ -{ - "uid": "27648456", - "pubdate": "2016 Sep", - "epubdate": "2016 Aug 26", - "source": "Ann Clin Transl Neurol", - "authors": [ - { - "name": "Bonham LW", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Geier EG", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Fan CC", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Leong JK", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Besser L", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Kukull WA", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Kornak J", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Andreassen OA", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Schellenberg GD", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Rosen HJ", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Dillon WP", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Hess CP", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Miller BL", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Dale AM", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Desikan RS", - "authtype": "Author", - "clusterid": "" - }, - { - "name": "Yokoyama JS", - "authtype": "Author", - "clusterid": "" - } - ], - "lastauthor": "Yokoyama JS", - "title": "Age-dependent effects of APOE ε4 in preclinical Alzheimer's disease.", - "sorttitle": "age dependent effects of apoe 4 in preclinical alzheimer s disease", - "volume": "3", - "issue": "9", - "pages": "668-77", - "lang": [ - "eng" - ], - "nlmuniqueid": "101623278", - "issn": "2328-9503", - "essn": "2328-9503", - "pubtype": [ - "Journal Article" - ], - "recordstatus": "PubMed", - "pubstatus": "258", - "articleids": [ - { - "idtype": "pubmed", - "idtypen": 1, - "value": "27648456" - }, - { - "idtype": "pmc", - "idtypen": 8, - "value": "PMC5018579" - }, - { - "idtype": "pmcid", - "idtypen": 5, - "value": "pmc-id: PMC5018579;" - }, - { - "idtype": "doi", - "idtypen": 3, - "value": "10.1002/acn3.333" - }, - { - "idtype": "pii", - "idtypen": 4, - "value": "ACN3333" - } - ], - "history": [ - { - "pubstatus": "received", - "date": "2016/05/06 00:00" - }, - { - "pubstatus": "revised", - "date": "2016/06/03 00:00" - }, - { - "pubstatus": "accepted", - "date": "2016/06/14 00:00" - }, - { - "pubstatus": "entrez", - "date": "2016/09/21 06:00" - }, - { - "pubstatus": "pubmed", - "date": "2016/09/21 06:00" - }, - { - "pubstatus": "medline", - "date": "2016/09/21 06:01" - }, - { - "pubstatus": "pmc-release", - "date": "2016/08/26 00:00" - } - ], - "references": [ - ], - "attributes": [ - "Has Abstract" - ], - "pmcrefcount": 33, - "fulljournalname": "Annals of clinical and translational neurology", - "elocationid": "doi: 10.1002/acn3.333", - "doctype": "citation", - "srccontriblist": [ - ], - "booktitle": "", - "medium": "", - "edition": "", - "publisherlocation": "", - "publishername": "", - "srcdate": "", - "reportnumber": "", - "availablefromurl": "", - "locationlabel": "", - "doccontriblist": [ - ], - "docdate": "", - "bookname": "", - "chapter": "", - "sortpubdate": "2016/08/26 00:00", - "sortfirstauthor": "Bonham LW", - "vernaculartitle": "" -} \ No newline at end of file