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ae68fca
fix authors get filtered out by person table dates
rickjohnson Jul 16, 2021
fcbdc40
partially done getnormedpubs in PubMedDataSource
rickjohnson Jul 16, 2021
ab213e4
fix pubmed handling of person dates to include
rickjohnson Jul 16, 2021
11aaac6
pubmed write source_metadata to normed pub files
rickjohnson Jul 16, 2021
a1818cd
added missing semantic scholar id to center query
rickjohnson Jul 16, 2021
994e44c
convert to multiple semantic ids per person
rickjohnson Jul 20, 2021
ea36033
Merge pull request #200 from share-research/multiple_semantic_scholar…
rickjohnson Jul 20, 2021
6e6a984
add given name mismatch confidence checking
rickjohnson Jul 20, 2021
241d408
Merge pull request #201 from share-research/lower_confidence_if_given…
rickjohnson Jul 20, 2021
d81f603
remove mentions of singular semantic_scholar_id
rickjohnson Jul 20, 2021
cd60ee1
Merge pull request #202 from share-research/multiple_semantic_scholar…
rickjohnson Jul 20, 2021
d56a461
add'l semantic_scholar_id fixes
rickjohnson Jul 20, 2021
d44526c
Merge pull request #203 from share-research/lower_confidence_if_given…
rickjohnson Jul 20, 2021
53fe0bf
fix recheck_pubs
rickjohnson Jul 20, 2021
dc43290
Merge pull request #204 from share-research/lower_confidence_if_given…
rickjohnson Jul 20, 2021
9247044
add tedst code 1 author for rechecking pub matches
rickjohnson Jul 21, 2021
22d7510
Merge pull request #205 from share-research/lower_confidence_if_given…
rickjohnson Jul 21, 2021
934f891
update min confidence to 0.4
rickjohnson Jul 22, 2021
05b3da1
Merge pull request #206 from share-research/flex_no_nd_filter
rickjohnson Jul 22, 2021
b6ea819
change crossref use nd filter only if result >300
rickjohnson Jul 22, 2021
776dc7d
Merge pull request #207 from share-research/flex_no_nd_filter
rickjohnson Jul 22, 2021
5355161
remove ND from center review list, ui sync fixes
rickjohnson Jul 22, 2021
c9d93b8
fix for adding review_org level
rickjohnson Jul 22, 2021
9f238b7
Merge pull request #208 from share-research/ui_fixes
rickjohnson Jul 22, 2021
2a7b68f
remove broken migrations
rickjohnson Jul 22, 2021
9c334f6
Merge pull request #209 from share-research/add_missing_doi_support
rickjohnson Jul 22, 2021
823467d
add metadata SemanticScholar for pubs w/out dois
rickjohnson Jul 23, 2021
92417fc
add get bibtex properties from WoS
rickjohnson Jul 23, 2021
05c865c
insert pubs without dois to DB
rickjohnson Jul 27, 2021
b6194e5
skip syncing review when pub has doi as null
rickjohnson Jul 27, 2021
a08d520
make author review group by title instead of doi
rickjohnson Jul 27, 2021
7591926
change synchronize reviews to sync on title
rickjohnson Jul 28, 2021
18a33ec
center review group pubs by title instead of doi
rickjohnson Jul 28, 2021
575a03b
Merge pull request #210 from share-research/add_missing_doi_support
rickjohnson Jul 28, 2021
91c7e96
accepted only in center screen, perf improvements
rickjohnson Jul 30, 2021
583a132
add conf set for any person pubs missing conf sets
rickjohnson Aug 2, 2021
61cd63a
Merge pull request #211 from share-research/add_missing_doi_support
rickjohnson Aug 2, 2021
f54fd5d
fix counts off when new conf value goes under 0.5
rickjohnson Aug 3, 2021
e9c2ece
Merge pull request #212 from share-research/add_missing_doi_support
rickjohnson Aug 3, 2021
a6c5ef1
force pending count to zero if ends up being neg #
rickjohnson Aug 3, 2021
5a0cd8c
Merge pull request #213 from share-research/add_missing_doi_support
rickjohnson Aug 3, 2021
6caa734
fix spacing in index.vue
rickjohnson Aug 3, 2021
da79e75
Merge pull request #214 from share-research/add_missing_doi_support
rickjohnson Aug 3, 2021
194d81d
update synchronize reviews to use normalized title
rickjohnson Aug 5, 2021
bc96675
Merge pull request #215 from share-research/add_missing_doi_support
rickjohnson Aug 5, 2021
e29cc78
group publications into sets by doi and title
rickjohnson Aug 9, 2021
951368d
updated author review to work for pub sets
rickjohnson Aug 9, 2021
94505da
fix pub load bugs and flicker of sourcename chip
rickjohnson Aug 10, 2021
400756a
add grouping by pubsets to center review
rickjohnson Aug 12, 2021
3987829
remove temp log message
rickjohnson Aug 12, 2021
d4261e1
fix clear author selected if change center review
rickjohnson Aug 12, 2021
9c30c82
update_synchronize_reviews use publication graph
rickjohnson Aug 13, 2021
80d5e57
Merge pull request #219 from share-research/add_missing_doi_support
rickjohnson Aug 13, 2021
17de7d4
fix bug where pubsets were not getting cleared
rickjohnson Aug 13, 2021
7b75104
Merge pull request #220 from share-research/add_missing_doi_support
rickjohnson Aug 13, 2021
e3eb5f5
fix bugreview sync with pubs with undefined doi
rickjohnson Aug 13, 2021
5d030ef
Merge pull request #221 from share-research/add_missing_doi_support
rickjohnson Aug 13, 2021
8abe2c5
remove comment
rickjohnson Aug 13, 2021
69e7cc4
add source_id to query for center review pubs
rickjohnson Aug 13, 2021
827de3b
updated readme for setup
rickjohnson Aug 13, 2021
a247ac6
Merge pull request #222 from share-research/add_missing_doi_support
rickjohnson Aug 13, 2021
f1302d3
added toggle center in dashboard
rickjohnson Aug 17, 2021
29c42d6
Merge pull request #225 from share-research/add_missing_doi_support
rickjohnson Aug 17, 2021
e2a8705
moved person sort and other UI tweaks
rickjohnson Aug 18, 2021
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14 changes: 12 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,20 @@ This pilot project will prototype a new process that automates data collection f

## Starting from scratch

clone from git into target machine
cd pace-admin
cp .env.template .env
curl -o- https://raw.githubusercontent.com/creationix/nvm/v0.33.2/install.sh | bash
Logout of terminal and log back in
nvm install 13.14.0
nvm use 13.14.0

Follow steps here to install docker: https://docs.docker.com/compose/install/

make install
make cleardb
make start_docker
sudo snap install docker
sudo make cleardb
sudo make start_docker
make migrate
make newdb

Expand Down
5 changes: 2 additions & 3 deletions client/src/components/CenterReviewPubFilter.vue
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
<q-icon name="search" />
</template>
</q-input>
<q-select
<!--<q-select
name="institution_review"
v-model="selectedInstitutionReviewState"
:options="institutionReviewStateOptions"
Expand All @@ -27,7 +27,7 @@
style="width:325px"
label="ND Author Review:"
class="fullSelect"
/>
/>-->
<q-select
name="sort_center_pub"
v-model="selectedCenterPubSort"
Expand Down Expand Up @@ -61,7 +61,6 @@ export default {
data () {
return {
sortCenterPubOptions: [
'Confidence',
'Title',
'Authors'
],
Expand Down
137 changes: 0 additions & 137 deletions client/src/components/MainAuthorReviewFilter.vue

This file was deleted.

33 changes: 30 additions & 3 deletions client/src/components/MainFilter.vue
Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,6 @@
<div>
<YearFilter />
</div>
</div>
<div class="row">
<div>
<PeopleFilter />
</div>
Expand Down Expand Up @@ -97,7 +95,20 @@ export default {
selectedCenterPubSort: sync('filter/selectedCenterPubSort'),
selectedCenterAuthor: sync('filter/selectedCenterAuthor'),
centerAuthorOptions: sync('filter/centerAuthorOptions'),
pubSearch: sync('filter/pubSearch')
selectedMemberYears: sync('filter/selectedMemberYears'),
selectedInstitutions: sync('filter/selectedInstitutions'),
institutionOptions: sync('filter/institutionOptions'),
selectedPubYears: sync('filter/selectedPubYears'),
selectedPersonConfidence: sync('filter/selectedPersonConfidence'),
pubSearch: sync('filter/pubSearch'),
preferredPersonTotal: sync('filter/preferredPersonTotal'),
preferredPersonConfidence: sync('filter/preferredPersonConfidence'),
yearPubStaticMin: sync('filter/yearPubStaticMin'),
yearPubStaticMax: sync('filter/yearPubStaticMax'),
yearMemberStaticMin: sync('filter/yearMemberStaticMin'),
yearMemberStaticMax: sync('filter/yearMemberStaticMax'),
changedPubYears: sync('filter/changedPubYears'),
changedMemberYears: sync('filter/changedMemberYears')
},
async created () {
this.fetchData()
Expand All @@ -123,6 +134,22 @@ export default {
// console.log(`Current type review is: ${JSON.stringify(typeReview, null, 2)}`)
return typeReview.value
})
},
resetFilters () {
this.selectedPersonPubSort = this.preferredPersonPubSort
this.selectedCenterPubSort = this.selectedCenterPubSort
this.selectedPersonSort = this.preferredPersonSort
this.selectedPersonTotal = this.preferredPersonTotal
this.selectedPersonConfidence = this.preferredPersonConfidence
this.selectedPubYears = {
min: this.yearPubStaticMin,
max: this.yearPubStaticMax
}
this.selectedInstitutions = _.clone(this.institutionOptions)
this.selectedMemberYears = {
min: this.yearMemberStaticMin,
max: this.yearMemberStaticMax
}
}
}
}
Expand Down
Original file line number Diff line number Diff line change
@@ -1,15 +1,6 @@
<template>
<div class="row">
<div class="q-pa-md" style="min-width:200px">
<q-select
filled
v-model="selectedInstitutions"
multiple
:options="institutionOptions"
use-chips
stack-label
label="Institutions"
/>
<q-select
name="sort_person"
:key="personSortKey"
Expand All @@ -20,7 +11,7 @@
label="Sort Person By:"
/>
</div>
<div class="q-pa-md" style="min-width:250px">
<div class="q-pa-md" style="min-width:200px">
<q-select
name="person_total"
v-model="selectedPersonTotal"
Expand All @@ -30,38 +21,22 @@
label="Show Total Counts:"
class="fullSelect"
/>
<q-select
name="person_confidence"
v-model="selectedPersonConfidence"
:options="personConfidenceOptions"
color="primary"
filled
label="Minimum Confidence:"
class="fullSelect"
/>
</div>
</div>
</template>

<script>
import { sync } from 'vuex-pathify'
import _ from 'lodash'

import readInstitutions from '../../../gql/readInstitutions.gql'

export default {
data () {
return {
sortPersonOptions: [
'Total',
'Total Counts',
'Name'
],
personTotalOptions: [
'Pending',
'All'
],
personConfidenceOptions: [
'50%',
'Pending Only',
'All'
],
filterMenuIcons: {
Expand All @@ -76,13 +51,10 @@ export default {
},
computed: {
personSortKey: sync('filter/personSortKey'),
institutionOptions: sync('filter/institutionOptions'),
preferredPersonTotal: sync('filter/preferredPersonTotal'),
preferredPersonSort: sync('filter/preferredPersonSort'),
selectedInstitutions: sync('filter/selectedInstitutions'),
selectedPersonSort: sync('filter/selectedPersonSort'),
selectedPersonTotal: sync('filter/selectedPersonTotal'),
selectedPersonConfidence: sync('filter/selectedPersonConfidence')
selectedPersonTotal: sync('filter/selectedPersonTotal')
},
async created () {
this.fetchData()
Expand All @@ -92,14 +64,8 @@ export default {
},
methods: {
async fetchData () {
const results = await this.$apollo.query({
query: readInstitutions
})
this.institutionOptions = _.compact(_.map(results.data.institutions, 'name'))
this.selectedInstitutions = (this.selectedInstitutions && this.selectedInstitutions.length > 0) ? this.selectedInstitutions : _.clone(this.institutionOptions)
this.selectedPersonSort = (this.selectedPersonSort) ? this.selectedPersonSort : this.preferredPersonSort
this.selectedPersonTotal = (this.selectedPersonTotal) ? this.selectedPersonTotal : this.preferredPersonTotal
this.selectedPersonConfidence = (this.selectedPersonConfidence) ? this.selectedPersonConfidence : this.preferredPersonConfidence
}
}
}
Expand Down
14 changes: 14 additions & 0 deletions client/src/gql/readAllPublicationsCSL.js
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
import gql from 'graphql-tag'
import _ from 'lodash'

export default function readAllPublicationsCSL () {
return gql`
query MyQuery {
publications {
id
doi
csl
}
}
`
}
1 change: 1 addition & 0 deletions client/src/gql/readAuthorsByPublications.js
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ export default function readAuthorsByPublications (publicationIds) {
){
id
doi
title
authors: csl(path: "author")
}
}
Expand Down
2 changes: 1 addition & 1 deletion client/src/gql/readCenterMembers.js
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ export default function readCenterMembers () {
family_name
start_date
end_date
semantic_scholar_id
semantic_scholar_ids
institution {
name
}
Expand Down
1 change: 1 addition & 0 deletions client/src/gql/readPersonPublicationsConfSets.js
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ export default function readPersonPublicationsConfSets (personPubIds) {
person_id
publication_id
doi
title
value
datetime
}
Expand Down
1 change: 1 addition & 0 deletions client/src/gql/readPersonPublicationsReviews.js
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ export default function readPersonPublicationsReviews (personPubIds, reviewOrgVa
person_id
publication_id
doi
title
review_type
datetime
}
Expand Down
2 changes: 1 addition & 1 deletion client/src/gql/readPersons.js
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ export default function readPersons () {
family_name
start_date
end_date
semantic_scholar_id
semantic_scholar_ids
institution {
name
}
Expand Down
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