Merge pull request #134 from CBIIT/dev-1.1.0

Dev 1.1.0

graphql/bento-extended.graphql

@@ -208,33 +208,6 @@ type ProgramDetail {
     projects: [ProjectInfo]
 }
 
-type ProjectDetail {
-    project_id: String
-    application_id: String
-    fiscal_year: String
-    project_title: String
-    project_type: String
-    abstract_text: String
-    keywords: String
-    org_name: String
-    org_city: String
-    org_state: String
-    org_country: String
-    principal_investigators: String
-    lead_doc: String
-    program_officers: String
-    award_amount: String
-    nci_funded_amount: String
-    award_notice_date: String
-    project_start_date: String
-    project_end_date: String
-    full_foa: String
-    num_publications: Int
-    num_datasets: Int
-    num_clinical_trials: Int
-    num_patents: Int
-}
-
 type ProjectOverview {
     program: String
     project_id: String
@@ -332,15 +305,6 @@ schema {
 type QueryType {
     schemaVersion: String @cypher(statement: "RETURN '1.1.0'")
 
-    "Simple counts"
-    numberOfPrograms: Int @cypher(statement: "MATCH (n:program) return count(n)")
-    numberOfProjects: Int @cypher(statement: "MATCH (n:project) return count(n)")
-    numberOfPublications: Int @cypher(statement: "MATCH (n:publication) return count(n)")
-    numberOfGEOs: Int @cypher(statement: "MATCH (n:geo) return count(n)")
-    numberOfSRAs: Int @cypher(statement: "MATCH (n:sra) return count(n)")
-    numberOfDBGaps: Int @cypher(statement: "MATCH (n:dbgap) return count(n)")
-    numberOfClinicalTrials: Int @cypher(statement: "MATCH (n:clinical_trial) return count(n)")
-
     programInfo: [ProgramInfo] @cypher(statement: """
         MATCH (p:program)
         OPTIONAL MATCH (p)<--(pr:project)
@@ -354,13 +318,6 @@ type QueryType {
         }
     """, passThrough: true)
 
-    programPublicationCount(program_id: String): Int @cypher(statement: """
-        MATCH (p:program {program_id: $program_id})
-        OPTIONAL MATCH (p)<--(pr:project)
-        OPTIONAL MATCH (pr)<--(pub:publication)
-        RETURN count(DISTINCT pub)
-    """, passThrough: true)
-
     programGEOCount(program_id: String): Int @cypher(statement: """
         MATCH (p:program {program_id: $program_id})
         OPTIONAL MATCH (p)<--(pr:project)
@@ -382,28 +339,6 @@ type QueryType {
         RETURN count(DISTINCT d)
     """, passThrough: true)
 
-    programDatasetCount(program_id: String): Int @cypher(statement: """
-        MATCH (p:program {program_id: $program_id})
-        OPTIONAL MATCH (p)<--(:project)<--(:publication)<--(ds)
-        WHERE ds:geo OR ds:sra OR ds:dbgap
-        RETURN COUNT(DISTINCT ds)
-    """, passThrough: true)
-
-    programClinicalTrialCount(program_id: String): Int @cypher(statement: """
-        MATCH (p:program {program_id: $program_id})
-        OPTIONAL MATCH (p)<--(pr:project)
-        OPTIONAL MATCH (ct:clinical_trial)
-            WHERE (pr)<--(:publication)<--(ct) OR (pr)<--(ct)
-        RETURN COUNT(DISTINCT ct)
-    """, passThrough: true)
-
-    programPatentCount(program_id: String): Int @cypher(statement: """
-        MATCH (p:program {program_id: $program_id})
-        OPTIONAL MATCH (p)<--(:project)<--(pat)
-        WHERE pat:granted_patent OR pat:patent_application
-        RETURN COUNT(DISTINCT pat)
-    """, passThrough: true)
-
     "Group counts"
     projectCountInProgramByDOC(program_id: String): [GroupCount] @cypher(statement: """
         MATCH (p:program {program_id: $program_id})
@@ -511,24 +446,6 @@ type QueryType {
         return  COUNT(DISTINCT d.accession)
     """, passThrough: true)
 
-    numberOfDatasets(project_ids: [String] = []): Int @cypher(statement: """
-        MATCH (pr:project)
-            WHERE (size($project_ids) = 0 OR pr.project_id IN $project_ids)
-        OPTIONAL MATCH (pr)<--(:publication)<--(dt)
-        WITH dt
-            WHERE (dt:geo OR dt:sra OR dt:dbgap)
-        RETURN COUNT(DISTINCT dt.accession)
-    """, passThrough: true)
-
-    numberOfPatents(project_ids: [String] = []): Int @cypher(statement: """
-        MATCH (pr:project)
-            WHERE (size($project_ids) = 0 OR pr.project_id IN $project_ids)
-        OPTIONAL MATCH (pr)<--(p)
-        WITH p
-            WHERE (p:patent_application OR p:granted_patent)
-        return  COUNT(DISTINCT p.patent_id)
-    """, passThrough: true)
-
     numberOfClinicalTrialsByProjects(project_ids: [String] = []): Int @cypher(statement: """
         MATCH (pr:project)
             WHERE (size($project_ids) = 0 OR pr.project_id IN $project_ids)
@@ -1044,41 +961,4 @@ type QueryType {
         }
     """, passThrough: true)
 
-    projectDetail(project_id: String): ProjectDetail @cypher(statement:  """
-        MATCH (pr:project {project_id: $project_id})
-        OPTIONAL MATCH (pr)<--(pub:publication)
-        OPTIONAL MATCH (pub)<--(dt)
-            WHERE (dt:geo) OR (dt:sra) OR (dt:dbgap)
-        OPTIONAL MATCH (pr)<-[*1..2]-(c:clinical_trial)
-        OPTIONAL MATCH (pr)<--(pat)
-            WHERE (pat:granted_patent) OR (pat:patent_application)
-        WITH DISTINCt pr, pub, dt, c, pat
-        RETURN {
-            project_id: pr.project_id,
-            application_id: pr.application_id,
-            fiscal_year: pr.fiscal_year,
-            project_title: pr.project_title,
-            project_type: pr.project_type,
-            abstract_text: pr.abstract_text,
-            keywords: pr.keywords,
-            org_name: pr.org_name,
-            org_city: pr.org_city,
-            org_state: pr.org_state,
-            org_country: pr.org_country,
-            principal_investigators: pr.principal_investigators,
-            lead_doc: pr.lead_doc,
-            program_officers: pr.program_officers,
-            award_amount: pr.award_amount,
-            nci_funded_amount: pr.nci_funded_amount,
-            award_notice_date: pr.award_notice_date,
-            project_start_date: pr.project_start_date,
-            project_end_date: pr.project_end_date,
-            full_foa: pr.full_foa,
-            num_publications: COUNT(DISTINCT pub),
-            num_datasets: COUNT(DISTINCT dt),
-            num_clinical_trials: COUNT(DISTINCT c),
-            num_patents: COUNT(DISTINCT pat)
-        }
-    """, passThrough: true)
-
 }

src/bento/caseDetailData.js

@@ -243,7 +243,7 @@ export const tabContainers = [
       },
       {
         dataField: 'publish_date',
-        header: 'Publish Date',
+        header: 'Publication Date',
         sort: 'asc',
         display: true,
         headerStyles: {

src/bento/dashboardTabData.js

@@ -264,7 +264,7 @@ export const tabContainers = [
       },
       {
         dataField: 'publish_date',
-        header: 'Publish Date',
+        header: 'Publication Date',
         sort: 'asc',
         display: true,
         headerStyles: {

src/bento/tableDownloadCSV.js

@@ -198,7 +198,7 @@ export const customPublicationsTabDownloadCSV = {
     'Authors',
     'Citation Count',
     'Relative Citation Ratio',
-    'Publish Date',
+    'Publication Date',
   ],
   query: GET_PUBLICATIONS_TAB,
   apiVariable: 'publicationOverView',
@@ -408,7 +408,7 @@ export const customCaseDetailPublicationsTabDownloadCSV = {
     'Authors',
     'Citation Count',
     'Relative Citation Ratio',
-    'Publish Date',
+    'Publication Date',
   ],
   query: GET_CASE_DETAIL_PUBLICATIONS_TAB,
   apiVariable: 'publicationOverViewByProject',

src/components/NavBar/CustomizedNavBar.js

@@ -143,7 +143,8 @@ const NavBar = () => {
             <MenuDropDown className="dropdown-block">
               <ul className="dropdown-list">
                 <li><NavLink to="/about" style={path === '/about' ? subMenuActiveStyle : null}>About INS</NavLink></li>
-                <li><a href="/INS_Release_Note.pdf" target="_blank" rel="noreferrer">Release Note</a></li>
+                <li><a href="/INS_glossary.pdf" target="_blank" rel="noreferrer">Glossary (PDF)</a></li>
+                <li><a href="/Release_v1.1.0.pdf" target="_blank" rel="noreferrer">Release Notes (PDF)</a></li>
               </ul>
             </MenuDropDown>
           </LiSection>

src/pages/about/aboutBody.js

@@ -25,7 +25,7 @@ const AboutBody = () => {
                   GATHERING RESEARCH OUTPUTS: A CONTINUOUS CHALLENGE
                 </h2>
                 <p>
-                  The National Cancer Institute (NCI) is excited to release initial phase of the Index of NCI Studies (INS) to tackle the challenge of assembling grants information from various publicly available resources into one place. Building connections between NCI programs, grants, and outputs is a complex task usually addressed through manual curation by portfolio analysis experts. As we work to automate the process and share this resource with the public, we would like to inform you the known limitations within the data gathering process and information displayed by the INS. We are working on improving data gathering process and will periodically release updates which allows us to iteratively improve the INS site.
+                  The National Cancer Institute (NCI) is excited to release initial phase of the Index of NCI Studies (INS) to tackle the challenge of assembling grants information from various publicly available resources into one place. Building connections between NCI programs, grants, and outputs is a complex task usually addressed through manual curation by portfolio analysis experts. As we work to automate the process and share this resource with the public, we would like to inform users of the known limitations within the data gathering process and information displayed by the INS. We are working on improving the data gathering process and will periodically release updates. This workflow allows us to improve the INS site in an iterative way.
                 </p>
                 <ul className="aboutPageDisclaimerItems">
                   <li>

src/pages/caseDetail/caseDetailTabThemeConfig.js

@@ -21,8 +21,9 @@ export default ({
     overridesObj.MUIDataTableToolbar = {
       root: {
         minHeight: '15px',
-        position: 'absolute',
-        top: '5px',
+        top: '-40px',
+        right: '375px',
+        marginBottom: '-35px',
       },
     };
     overridesObj.MuiTablePagination.toolbar.paddingTop = '11px';

src/pages/dashboardTab/components/tabThemeConfig.js

@@ -21,8 +21,9 @@ export default ({
     overridesObj.MUIDataTableToolbar = {
       root: {
         minHeight: '15px',
-        position: 'absolute',
-        top: '5px',
+        top: '-40px',
+        right: '375px',
+        marginBottom: '-35px',
       },
     };
     overridesObj.MuiTablePagination.toolbar.paddingTop = '11px';

src/themes/light.js

@@ -434,7 +434,7 @@ export default {
         minHeight: '15px',
         position: 'absolute',
         top: '-40px',
-        left: '25px',
+        right: '400px',
       },
       titleText: {
         color: tableHeaderFontColor,