updated user journey test to include visualisation

MRCIEU · Sep 20, 2023 · e9b17b9 · e9b17b9
1 parent 9347448
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diff --git a/cypress/integration/user-journey.js b/cypress/integration/user-journey.js
@@ -73,10 +73,11 @@ describe('User journey of login and upload abstracts, visualise then delete uplo
                 .invoke('text')
                 .should('equal', 'TeMMPo: Select exposure MeSH® terms')
 
-        // Lets tick some exposure terms in the checkbox tree then move on to mediators
+        // Lets add some exposure terms in the textarea, click add, then move on to mediators
 
-            cy.get('a')
-                .contains('Organisms', { matchCase: false })
+            cy.get('#term_names').type('Public Health Systems Research;Humans');
+
+            cy.contains('Add', { matchCase: false })
                 .click()
 
             cy.contains('Save and move on to select mediators', { matchCase: false })
@@ -88,10 +89,11 @@ describe('User journey of login and upload abstracts, visualise then delete uplo
                 .invoke('text')
                 .should('equal', 'TeMMPo: Select mediator MeSH® terms')
 
-        // Lets tick mediator terms in the checkbox tree then move on to outcomes
+        // Lets add terms in the textarea, click add, then move on to outcomes
+
+            cy.get('#term_names').type('Genetic Markers; Penetrance');
 
-            cy.get('a')
-                .contains('Diseases', { matchCase: false })
+            cy.contains('Add', { matchCase: false })
                 .click()
 
             cy.contains('Save and move on to select outcomes', { matchCase: false })
@@ -103,10 +105,11 @@ describe('User journey of login and upload abstracts, visualise then delete uplo
                 .invoke('text')
                 .should('equal', 'TeMMPo: Select outcome MeSH® terms')
 
-        // Lets tick an outcome term in the checkbox
+        // Lets add outcome term in the textarea, click add, move on to genes
+
+            cy.get('#term_names').type('Neoplasm Metastasis;Eryptosis');
 
-            cy.get('a')
-                .contains('Humanities', { matchCase: false })
+            cy.contains('Add', { matchCase: false })
                 .click()
 
             cy.contains('Save and move on to select Genes and Filters', { matchCase: false })
@@ -118,15 +121,7 @@ describe('User journey of login and upload abstracts, visualise then delete uplo
                 .invoke('text')
                 .should('equal', 'TeMMPo: Select genes and filter')
 
-        // Lets click on the dropdown filter
-
-            cy.get('.selection')
-                .click()
-            cy.get('li')
-                .contains('Body Regions > Breast', { matchCase: false })
-                .click()
-
-        // Lets click on the search button...
+        // click the button to continue and get some results
 
             cy.get('button.btn.btn-primary')
                 .contains('Search', { matchCase: false })
@@ -146,7 +141,7 @@ describe('User journey of login and upload abstracts, visualise then delete uplo
                 .eq(1)
                 .should('not.be.empty')
 
-        // now we are gonna wait a minute
+        // now we are gonna wait a minute...
 
             cy.wait(60000)
 
@@ -157,15 +152,45 @@ describe('User journey of login and upload abstracts, visualise then delete uplo
         // this is where we will do the visualiations...
 
 
+        // select sankey chart
 
+            cy.get('tbody')
+                .contains('View Sankey diagram')
+                .click()
 
 
+        // check sankey chart contains human....etc
 
+            cy.get('#sankey_multiple')
+                .should('include.text', 'Humans')
+                .and('include.text', 'Genetic Markers')
+                .and('include.text', 'Public Health Systems Research')
 
 
-        // now lets delete the file we uploaded
+        // go back to results tab
 
-        // goto results tab and check its empty
+            cy.get('#side-menu')
+                .contains('Results')
+                .click()
+
+            cy.get('.page-header')
+                .should('have.text', 'Results')
+
+        // select bubble chart
+
+            cy.get('tbody')
+                .contains('View bubble chart')
+                .click()
+
+        // should contain Genetic Markers on the page
+
+            cy.get('#bubble_chart')
+                .should('include.text', 'Genetic Markers')
+
+
+        // thats the end of visualiations test, now lets delete the file we uploaded...
+
+        // goto results tab...
 
             cy.get('#side-menu')
                 .contains('Results')
@@ -179,8 +204,6 @@ describe('User journey of login and upload abstracts, visualise then delete uplo
             cy.get('.controls')
                 .find('a.btn.btn-danger.btn-sm')
                 .contains('Delete', { matchCase: false })
-
-        // have to force because possible bug where delete button is sometimes hidden in the table?
                 .click({force:true})
 
         // now check we go the the delete search page

diff --git a/test-abstract-ovid-test-sample-5.txt b/test-abstract-ovid-test-sample-5.txt
@@ -0,0 +1,242 @@
+<1>
+Unique Identifier
+  999991
+Record Owner
+  From MEDLINE, a database of the U.S. National Library of Medicine.
+Status
+  MEDLINE
+Authors
+  Smith J, Chang Y
+Authors Full Name
+  Smith, Jane. Chang, Yi.
+Institution
+  College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
+Title
+  Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways.
+Source
+  Nucleic Acids Research.  41(9):e101, 2013 May.
+Other ID
+  Source: NLM. PMC3643575
+MeSH Subject Headings
+    Cells
+    Colorectal Neoplasms/ge [Genetics]
+    Colorectal Neoplasms/me [Metabolism]
+    Eryptosis
+    Fictional MeSH Term AA
+    Fictional MeSH Term B
+    Genetic Markers
+    Genetic Pleiotropy
+    Histamine/me [Metabolism]
+    Humans
+    Male
+    *Metabolic Networks and Pathways/ge [Genetics]
+    *Metabolomics
+    Neoplasm Metastasis
+    Prostatic Neoplasms/ge [Genetics]
+    Prostatic Neoplasms/me [Metabolism]
+    Prostatic Neoplasms/pa [Pathology]
+    Public Health Systems Research
+    Serogroup
+    *Transcriptome
+Abstract
+  Example Gene B, A1BG is in this absctrast, A2M, A2MP1; NAT2 Lorem ipsum LBM180, ABCA3 dolor sit amet, consectetur adipiscing elit. Duis in turpis aliquet, cursus nisi id, mattis augue. Pellentesque vehicula at ligula vel porta. Fusce suscipit malesuada justo. Cras convallis odio nec dolor elementum facilisis. Donec vel lobortis felis, ut gravida risus. Vivamus interdum ex libero. Phasellus id pharetra tortor. Mauris euismod convallis augue, sit amet aliquet metus hendrerit ac. Duis mattis leo maximus nisi sagittis, a pulvinar turpis fringilla. Ut pellentesque ligula purus, ut iaculis metus finibus nec. Suspendisse diam felis, aliquam sed nisl at, luctus rhoncus magna. Nullam porttitor neque eget sem sagittis rhoncus. Praesent accumsan fermentum odio, ac pellentesque dui feugiat at. In metus nisl, scelerisque eget velit at, pulvinar placerat ex.
+Registry Number/Name of Substance
+  51-45-6 (Histamine).
+Publication Type
+  Journal Article.  Research Support, Non-U.S. Gov't.
+Date Created
+  20130506
+Year of Publication
+  2013
+Link to the Ovid Full Text or citation
+ http://ovidsp.ovid.com/ovidweb.cgi?T=JS&CSC=Y&NEWS=N&PAGE=fulltext&D=medl&AN=23482392
+Link to the External Link Resolver
+ http://linkserver.bristol.ac.uk:9003/prod?sid=OVID:medline&id=pmid:23482392&id=doi:10.1093%2Fnar%2Fgkt161&issn=0305-1048&isbn=&volume=41&issue=9&spage=e101&pages=e101&date=2013&title=Nucleic+Acids+Research&atitle=Subpathway-GM%3A+identification+of+metabolic+subpathways+via+joint+power+of+interesting+genes+and+metabolites+and+their+topologies+within+pathways.&aulast=Li&pid=%3Cauthor%3ELi+C%3C%2Fauthor%3E%3CAN%3E23482392%3C%2FAN%3E%3CDT%3EJournal+Article%3C%2FDT%3E
+
+<2>
+Unique Identifier
+  999992
+Record Owner
+  From MEDLINE, a database of the U.S. National Library of Medicine.
+Status
+  MEDLINE
+Authors
+  Smith J, Chang Y
+Authors Full Name
+  Smith, Jane. Chang, Yi.
+Institution
+  College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
+Title
+  Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways.
+Source
+  Nucleic Acids Research.  41(9):e101, 2013 May.
+Other ID
+  Source: NLM. PMC3643575
+MeSH Subject Headings
+    Colorectal Neoplasms/ge [Genetics]
+    Colorectal Neoplasms/me [Metabolism]
+    Genetic Pleiotropy
+    Histamine/me [Metabolism]
+    Humans
+    Male
+    *Metabolic Networks and Pathways/ge [Genetics]
+    *Metabolomics
+    Neoplasm Metastasis
+    Prostatic Neoplasms/ge [Genetics]
+    Prostatic Neoplasms/me [Metabolism]
+    Prostatic Neoplasms/pa [Pathology]
+    Pyroptosis
+    Serogroup
+    *Transcriptome
+Abstract
+  Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis in turpis aliquet, cursus nisi id, mattis augue. Pellentesque vehicula at ligula vel porta. Fusce suscipit malesuada justo. Cras convallis odio nec dolor elementum facilisis. Donec vel lobortis felis, ut gravida risus. Vivamus interdum ex libero. Phasellus id pharetra tortor. Mauris euismod convallis augue, sit amet aliquet metus hendrerit ac. Duis mattis leo maximus nisi sagittis, a pulvinar turpis fringilla. Ut pellentesque ligula purus, ut iaculis metus finibus nec. Suspendisse diam felis, aliquam sed nisl at, luctus rhoncus magna. Nullam porttitor neque eget sem sagittis rhoncus. Praesent accumsan fermentum odio, ac pellentesque dui feugiat at. In metus nisl, scelerisque eget velit at, pulvinar placerat exexex.
+Registry Number/Name of Substance
+  51-45-6 (Histamine).
+Publication Type
+  Journal Article.  Research Support, Non-U.S. Gov't.
+Date Created
+  20130506
+Year of Publication
+  2013
+Link to the Ovid Full Text or citation
+ http://ovidsp.ovid.com/ovidweb.cgi?T=JS&CSC=Y&NEWS=N&PAGE=fulltext&D=medl&AN=23482392
+Link to the External Link Resolver
+ http://linkserver.bristol.ac.uk:9003/prod?sid=OVID:medline&id=pmid:23482392&id=doi:10.1093%2Fnar%2Fgkt161&issn=0305-1048&isbn=&volume=41&issue=9&spage=e101&pages=e101&date=2013&title=Nucleic+Acids+Research&atitle=Subpathway-GM%3A+identification+of+metabolic+subpathways+via+joint+power+of+interesting+genes+and+metabolites+and+their+topologies+within+pathways.&aulast=Li&pid=%3Cauthor%3ELi+C%3C%2Fauthor%3E%3CAN%3E23482392%3C%2FAN%3E%3CDT%3EJournal+Article%3C%2FDT%3E
+
+<3>
+Unique Identifier
+  999993
+Record Owner
+  From MEDLINE, a database of the U.S. National Library of Medicine.
+Status
+  MEDLINE
+Authors
+  Smith J, Chang Y
+Authors Full Name
+  Smith, Jane. Chang, Yi.
+Institution
+  College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
+Title
+  Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways.
+Source
+  Nucleic Acids Research.  41(9):e101, 2013 May.
+Other ID
+  Source: NLM. PMC3643575
+MeSH Subject Headings
+    Colorectal Neoplasms/ge [Genetics]
+    Colorectal Neoplasms/me [Metabolism]
+    Genetic Markers
+    Histamine/me [Metabolism]
+    Humans
+    Male
+    *Metabolic Networks and Pathways/ge [Genetics]
+    *Metabolomics
+    Neoplasm Metastasis
+    Prostatic Neoplasms/ge [Genetics]
+    Prostatic Neoplasms/me [Metabolism]
+    Prostatic Neoplasms/pa [Pathology]
+    Serogroup
+    *Transcriptome
+Abstract
+  Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis in turpis aliquet, cursus nisi id, mattis augue. Pellentesque vehicula at ligula vel porta. Fusce suscipit malesuada justo. Cras convallis odio nec dolor elementum facilisis. Donec vel lobortis felis, ut gravida risus. Vivamus interdum ex libero. Phasellus id pharetra tortor. Mauris euismod convallis augue, sit amet aliquet metus hendrerit ac. Duis mattis leo maximus nisi sagittis, a pulvinar turpis fringilla. Ut pellentesque ligula purus, ut iaculis metus finibus nec. Suspendisse diam felis, aliquam sed nisl at, luctus rhoncus magna. Nullam porttitor neque eget sem sagittis rhoncus. Praesent accumsan fermentum odio, ac pellentesque dui feugiat at. In metus nisl, scelerisque eget velit at, pulvinar placerat ex.
+Registry Number/Name of Substance
+  51-45-6 (Histamine).
+Publication Type
+  Journal Article.  Research Support, Non-U.S. Gov't.
+Date Created
+  20130506
+Year of Publication
+  2013
+Link to the Ovid Full Text or citation
+ http://ovidsp.ovid.com/ovidweb.cgi?T=JS&CSC=Y&NEWS=N&PAGE=fulltext&D=medl&AN=23482392
+Link to the External Link Resolver
+ http://linkserver.bristol.ac.uk:9003/prod?sid=OVID:medline&id=pmid:23482392&id=doi:10.1093%2Fnar%2Fgkt161&issn=0305-1048&isbn=&volume=41&issue=9&spage=e101&pages=e101&date=2013&title=Nucleic+Acids+Research&atitle=Subpathway-GM%3A+identification+of+metabolic+subpathways+via+joint+power+of+interesting+genes+and+metabolites+and+their+topologies+within+pathways.&aulast=Li&pid=%3Cauthor%3ELi+C%3C%2Fauthor%3E%3CAN%3E23482392%3C%2FAN%3E%3CDT%3EJournal+Article%3C%2FDT%3E
+
+<4>
+Unique Identifier
+  999994
+Record Owner
+  From MEDLINE, a database of the U.S. National Library of Medicine.
+Status
+  MEDLINE
+Authors
+  Smith J, Chang Y
+Authors Full Name
+  Smith, Jane. Chang, Yi.
+Institution
+  College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
+Title
+  Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways.
+Source
+  Nucleic Acids Research.  41(9):e101, 2013 May.
+Other ID
+  Source: NLM. PMC3643575
+MeSH Subject Headings
+    Fictional MeSH Term A
+    Fictional MeSH Term B
+    Fictional MeSH Term C
+Abstract
+  Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis in turpis aliquet, cursus nisi id, mattis augue. Pellentesque vehicula at ligula vel porta. Fusce suscipit malesuada justo. Cras convallis odio nec dolor elementum facilisis. Donec vel lobortis felis, ut gravida risus. Vivamus interdum ex libero. Phasellus id pharetra tortor. Mauris euismod convallis augue, sit amet aliquet metus hendrerit ac. Duis mattis leo maximus nisi sagittis, a pulvinar turpis fringilla. Ut pellentesque ligula purus, ut iaculis metus finibus nec. Suspendisse diam felis, aliquam sed nisl at, luctus rhoncus magna. Nullam porttitor neque eget sem sagittis rhoncus. Praesent accumsan fermentum odio, ac pellentesque dui feugiat at. In metus nisl, scelerisque eget velit at, pulvinar placerat ex. Example Gene X, Example Gene B2, Example Gene A, Example Gene Sym C
+Registry Number/Name of Substance
+  51-45-6 (Histamine).
+Publication Type
+  Journal Article.  Research Support, Non-U.S. Gov't.
+Date Created
+  20130506
+Year of Publication
+  2013
+Link to the Ovid Full Text or citation
+ http://ovidsp.ovid.com/ovidweb.cgi?T=JS&CSC=Y&NEWS=N&PAGE=fulltext&D=medl&AN=23482392
+Link to the External Link Resolver
+ http://linkserver.bristol.ac.uk:9003/prod?sid=OVID:medline&id=pmid:23482392&id=doi:10.1093%2Fnar%2Fgkt161&issn=0305-1048&isbn=&volume=41&issue=9&spage=e101&pages=e101&date=2013&title=Nucleic+Acids+Research&atitle=Subpathway-GM%3A+identification+of+metabolic+subpathways+via+joint+power+of+interesting+genes+and+metabolites+and+their+topologies+within+pathways.&aulast=Li&pid=%3Cauthor%3ELi+C%3C%2Fauthor%3E%3CAN%3E23482392%3C%2FAN%3E%3CDT%3EJournal+Article%3C%2FDT%3E
+
+<5>
+Unique Identifier
+  999995
+Record Owner
+  From MEDLINE, a database of the U.S. National Library of Medicine.
+Status
+  MEDLINE
+Authors
+  Smith J, Chang Y
+Authors Full Name
+  Smith, Jane. Chang, Yi.
+Institution
+  College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
+Title
+  Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways.
+Source
+  Nucleic Acids Research.  41(9):e101, 2013 May.
+Other ID
+  Source: NLM. PMC3643575
+MeSH Subject Headings
+    Colorectal Neoplasms/ge [Genetics]
+    Colorectal Neoplasms/me [Metabolism]
+    Eryptosis
+    Genetic Markers
+    Histamine/me [Metabolism]
+    Humans
+    Male
+    *Metabolic Networks and Pathways/ge [Genetics]
+    *Metabolomics
+    Neoplasm Metastasis
+    Penetrance
+    Prostatic Neoplasms/ge [Genetics]
+    Prostatic Neoplasms/me [Metabolism]
+    Prostatic Neoplasms/pa [Pathology]
+    Serogroup
+    *Transcriptome
+Abstract
+  Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis in turpis aliquet, cursus nisi id, mattis augue. Pellentesque vehicula at ligula vel porta. Fusce suscipit malesuada justo. Cras convallis odio nec dolor elementum facilisis. Donec vel lobortis felis, ut gravida risus. Vivamus interdum ex libero. Phasellus id pharetra tortor. Mauris euismod convallis augue, sit amet aliquet metus hendrerit ac. Duis mattis leo maximus nisi sagittis, a pulvinar turpis fringilla. Ut pellentesque ligula purus, ut iaculis metus finibus nec. Suspendisse diam felis, aliquam sed nisl at, luctus rhoncus magna. Nullam porttitor neque eget sem sagittis rhoncus. Praesent accumsan fermentum odio, ac pellentesque dui feugiat at. In metus nisl, scelerisque eget velit at, pulvinar placerat ex.
+Registry Number/Name of Substance
+  51-45-6 (Histamine).
+Publication Type
+  Journal Article.  Research Support, Non-U.S. Gov't.
+Date Created
+  20130506
+Year of Publication
+  2013
+Link to the Ovid Full Text or citation
+ http://ovidsp.ovid.com/ovidweb.cgi?T=JS&CSC=Y&NEWS=N&PAGE=fulltext&D=medl&AN=23482392
+Link to the External Link Resolver
+ http://linkserver.bristol.ac.uk:9003/prod?sid=OVID:medline&id=pmid:23482392&id=doi:10.1093%2Fnar%2Fgkt161&issn=0305-1048&isbn=&volume=41&issue=9&spage=e101&pages=e101&date=2013&title=Nucleic+Acids+Research&atitle=Subpathway-GM%3A+identification+of+metabolic+subpathways+via+joint+power+of+interesting+genes+and+metabolites+and+their+topologies+within+pathways.&aulast=Li&pid=%3Cauthor%3ELi+C%3C%2Fauthor%3E%3CAN%3E23482392%3C%2FAN%3E%3CDT%3EJournal+Article%3C%2FDT%3E