Data links
-
+
@@ -15,16 +14,24 @@
diff --git a/app/javascript/vue/tasks/content/editor/components/Otu/OtuModal.vue b/app/javascript/vue/tasks/content/editor/components/Otu/OtuModal.vue
index 60aac37094..f806dfe52c 100644
--- a/app/javascript/vue/tasks/content/editor/components/Otu/OtuModal.vue
+++ b/app/javascript/vue/tasks/content/editor/components/Otu/OtuModal.vue
@@ -13,7 +13,7 @@
:containerStyle="{ width: '600px', height: '70vh' }"
>
-
-
Select Topic
+Select OTU
-
--
-
- - {{ item.source.author_year }} - - -
+
-
-
{{ item.text }}
-
+ {{ item.text }}
@@ -54,41 +52,43 @@ export default {
},
computed: {
- disabled () {
- return !this.$store.getters[GetterNames.GetContentSelected]
- },
-
topic () {
return this.$store.getters[GetterNames.GetTopicSelected]
},
- content () {
- return this.$store.getters[GetterNames.GetContentSelected]
- },
-
otu () {
return this.$store.getters[GetterNames.GetOtuSelected]
+ },
+
+ content () {
+ return this.$store.getters[GetterNames.GetContentSelected]
}
},
watch: {
- content (val, oldVal) {
- if (val) {
- if (JSON.stringify(val) !== JSON.stringify(oldVal)) {
- this.loadContent()
- }
- } else {
+ topic (newVal, oldVal) {
+ if (newVal?.id && newVal.id !== oldVal?.id) {
+ this.loadContent()
+ }
+
+ if (!newVal?.id) {
this.contents = []
}
+ },
+
+ otu (newVal) {
+ if (newVal?.id) {
+ this.loadContent()
+ }
}
},
methods: {
loadContent () {
- if (this.disabled) return
-
- Content.where({ topic_id: this.topic.id }).then(response => {
- this.contents = response.body.filter(c => c.id !== this.content.id)
+ Content.where({ topic_id: this.topic.id }).then(({ body }) => {
+ this.contents = this.content?.id
+ ? body.filter(c => c.id !== this.content.id)
+ : body
})
},
diff --git a/app/javascript/vue/tasks/content/editor/editor/compare.vue b/app/javascript/vue/tasks/content/editor/editor/compare.vue
index 1a1043c72e..9c206b9695 100644
--- a/app/javascript/vue/tasks/content/editor/editor/compare.vue
+++ b/app/javascript/vue/tasks/content/editor/editor/compare.vue
@@ -1,8 +1,8 @@
-
+
+ />
Save
0) {
@@ -233,44 +217,6 @@ export default {
}
},
- addCitation (cursorPosition) {
- this.record.content.text = [this.record.content.text.slice(0, cursorPosition),
- document.querySelector('[data-panel-name="pinboard"]').getAttribute('data-clipboard'),
- this.record.content.text.slice(cursorPosition)].join('')
-
- if (this.newRecord) {
- if (!this.record.content.id) {
- Content.find(this.record.content.id).then(response => {
- this.record.content.id = response.body.id
- this.newRecord = false
- this.createCitation()
- })
- }
- } else {
- this.update()
- this.createCitation()
- }
- },
-
- createCitation () {
- const sourcePDF = document.querySelector('[data-pdf-source-id]').getAttribute('data-pdf-source-id')
-
- if (sourcePDF === undefined) return
- this.currentSourceID = Number(sourcePDF)
-
- const citation = {
- pages: '',
- citation_object_type: 'Content',
- citation_object_id: this.record.content.id,
- source_id: this.currentSourceID
- }
- if (this.existCitation(citation)) return
-
- Citation.create({ citation }).then(response => {
- this.$store.commit(MutationNames.AddCitationToList, response.body)
- })
- },
-
handleInput () {
if (this.firstInput) {
this.firstInput = false
@@ -318,6 +264,7 @@ export default {
this.firstInput = true
this.resetAutoSave()
+
Content.where(params).then(response => {
if (response.body.length > 0) {
const record = response.body[0]
@@ -331,15 +278,18 @@ export default {
this.newRecord = false
this.$store.commit(MutationNames.SetContentSelected, response.body[0])
+ this.$refs.contentText.setFocus()
} else {
- const content = this.initContent()
-
- content.topic_id = this.topic.id
- content.otu_id = this.otu.id
+ const content = {
+ ...this.initContent(),
+ topic_id: this.topic.id,
+ otu_id: this.otu.id
+ }
this.record.content = content
this.$store.commit(MutationNames.SetContent, undefined)
this.newRecord = true
+ this.$refs.contentText.setFocus()
}
})
this.loadMarkwdown = false
diff --git a/app/javascript/vue/tasks/content/editor/editor/figureItem.vue b/app/javascript/vue/tasks/content/editor/editor/figureItem.vue
index c02c56818e..5633c1b16a 100644
--- a/app/javascript/vue/tasks/content/editor/editor/figureItem.vue
+++ b/app/javascript/vue/tasks/content/editor/editor/figureItem.vue
@@ -4,13 +4,51 @@
:class="{ 'card-handle' : !edit }">
![]()
-
-
+
+
+
+
+
+
+
+
+
+
{
TW.workbench.alert.create('Depiction was successfully updated.', 'notice')
})
+ },
+
+ linkDepiction () {
+ this.$emit('link', this.depiction)
}
}
}
diff --git a/app/javascript/vue/tasks/content/editor/editor/figuresPanel.vue b/app/javascript/vue/tasks/content/editor/editor/figuresPanel.vue
index 88ff4f2ca3..78b05fc243 100644
--- a/app/javascript/vue/tasks/content/editor/editor/figuresPanel.vue
+++ b/app/javascript/vue/tasks/content/editor/editor/figuresPanel.vue
@@ -11,7 +11,10 @@
item-key="id"
>
- depiction.id) })
+ Depiction.sort({ depiction_ids: this.depictions.map(depiction => depiction.id) })
}
}
}
diff --git a/app/javascript/vue/tasks/content/editor/editor/selectTopicOtu.vue b/app/javascript/vue/tasks/content/editor/editor/selectTopicOtu.vue
index 48240c80d6..acb91fd0b1 100644
--- a/app/javascript/vue/tasks/content/editor/editor/selectTopicOtu.vue
+++ b/app/javascript/vue/tasks/content/editor/editor/selectTopicOtu.vue
@@ -41,6 +41,8 @@ export default {
OtuModal
},
+ emits: ['close'],
+
data () {
return {
showModal: true,
@@ -76,6 +78,7 @@ export default {
closeModal () {
if (this.otu && this.topic) {
this.showModal = false
+ this.$emit('close')
}
}
}
diff --git a/app/models/source.rb b/app/models/source.rb
index 17b388df97..d30294322e 100644
--- a/app/models/source.rb
+++ b/app/models/source.rb
@@ -295,7 +295,6 @@ def self.batch_create(file)
# @param used_on [String] a model name
# @return [Scope]
- # the max 10 most recently used (1 week, could parameterize) TaxonName, as used
def self.used_recently(user_id, project_id, used_on = 'TaxonName')
Source.select('sources.id').
joins(:citations)
diff --git a/app/views/tasks/accessions/breakdown/sqed_depiction/_form.html.erb b/app/views/tasks/accessions/breakdown/sqed_depiction/_form.html.erb
index 5efa0e973b..eebdb11f0c 100644
--- a/app/views/tasks/accessions/breakdown/sqed_depiction/_form.html.erb
+++ b/app/views/tasks/accessions/breakdown/sqed_depiction/_form.html.erb
@@ -3,9 +3,13 @@
Identifiers
- <%= f.fields_for(:identifiers, @result.depiction.depiction_object.identifiers.where(identifiers: {type: 'Identifier::Local::CatalogNumber'})) do |i| -%> + <% identifiers = @result.depiction.depiction_object.identifiers.where("identifiers.type ilike '%Local%'") + [ + Identifier::Local::CatalogNumber.new( + identifier_object: @result.depiction.depiction_object, + namespace_id: (@result.namespace_locked? ? @result.namespace_id : nil) + ) ] %> + <%= f.fields_for(:identifiers, identifiers) do |i| -%> <%= i.hidden_field :type -%> -
@@ -22,7 +26,7 @@
fields_for_object: i})
%>
- <% if @result.depiction.depiction_object.identifiers.size == 1 %>
+ <% if identifiers.first == i.object %>
<%= check_box_tag(:lock_namespace, '1', @result.namespace_locked?) -%>lock
<% end %>
diff --git a/docker-compose.yml b/docker-compose.yml
index 8f1f157f55..40c80358d9 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -15,14 +15,21 @@ services:
- "127.0.0.1:3000:3000" # local:docker
links:
- db
+ - postgres10_legacy
stdin_open: true
tty: true
- db:
+ postgres10_legacy:
image: mdillon/postgis:10
+ volumes:
+ - pg:/var/lib/postgresql/data
+ db:
+ image: postgis/postgis:12-3.0
+ environment:
+ - POSTGRES_HOST_AUTH_METHOD=trust
ports:
- "0.0.0.0:15432:5432"
volumes:
- - pg:/var/lib/postgresql/data
+ - pg12:/var/lib/postgresql/data
webpack:
build:
context: .
@@ -40,4 +47,6 @@ services:
volumes:
pg:
external: false
+ pg12:
+ external: false
diff --git a/exe/docker_compose_start.sh b/exe/docker_compose_start.sh
index 2296d300f2..aad8cf03f2 100755
--- a/exe/docker_compose_start.sh
+++ b/exe/docker_compose_start.sh
@@ -4,18 +4,26 @@ IFS=$'\n\t'
# This script is run within the app container!
-function wait_for_db {
+function wait_for_db() {
sleep 3
- until pg_isready -h "db" -U "postgres"; do
- echo "Waiting for postgresql to start..."
+ until pg_isready -h "$1" -U "postgres"; do
+ echo "Waiting for postgresql at $1 to start..."
sleep 2
done
}
# Could do sanity check of environment here
# * Raise a warning of the database.yml file looks like it is setup for docker-compose
-wait_for_db
+wait_for_db "postgres10_legacy"
+wait_for_db "db"
+
+# If database is empty migrate data over from legacy postgres 10 postgres
+if psql -h db -U postgres -tAc "SELECT '<'||COUNT(*)||'>' FROM pg_database WHERE datname NOT LIKE 'template%'" | grep -q "<1>"; then
+ echo "Migrating from legacy postgres 10 to postgres 12"
+ pg_dumpall -h postgres10_legacy -U postgres | psql -h db -U "postgres" -f-
+fi
+
if [ ! -f /app/config/database.yml ]; then
cp /app/config/database.yml.docker.compose.example /app/config/database.yml
@@ -38,35 +46,15 @@ else
printf "\n Found config/application_settings.yml \n"
fi
-# 1) Ensure that we can connect to the database first from within the app container (where this is being run). That is build into this script script the
-# connection string, likely based on the database.yml? Check available environment variables.
-
-# 2) Raise a warning if we can not, and exit, shutting down as cleanly as possible
-
-# 3) Only then do the following (`psql` likely needs to change to something more reflective of the database.yml config for those using non-default settings):
-
-if echo "\c db; \dt" | psql | grep schema_migrations 2>&1 >/dev/null
-then
- bundle exec rake db:migrate
- echo "Done migration successfully"
-else
- printf "\n\n !!!!!!!!!! Building a new taxonworks_development database !!!!!!!!!! \n\n "
- bundle exec rake db:create
- printf "\n\n Starting migration process \n\n"
- bundle exec rake db:migrate
- echo "Done migration successfully"
-fi
+printf "\n\n Creating databases (if not exist already) \n\n "
+bundle exec rake db:create
+printf "\n\n Starting migration process \n\n"
+bundle exec rake db:migrate
+echo "Done migration successfully"
if [ -f /app/tmp/pids/server.pid ]; then
rm /app/tmp/pids/server.pid
fi
-# Why this sleep? Errors we hit at this point are
-# likely because webpack has not finished compiling, we
-# should create a more specific check here
-#
-# sleep 60s;
-
-
bundle exec rails s -p 3000 -b '0.0.0.0'
diff --git a/lib/taxonworks/version.rb b/lib/taxonworks/version.rb
index 7af04f9712..c14d7646a7 100644
--- a/lib/taxonworks/version.rb
+++ b/lib/taxonworks/version.rb
@@ -1,3 +1,3 @@
module Taxonworks
- VERSION = "0.22.2"
+ VERSION = "0.22.3"
end