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Fixes coming from the openDS public review #7

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merged 3 commits into from
Oct 7, 2024
Merged

Fixes coming from the openDS public review #7

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aae685a
Fixes coming from the openDS public review
samleeflang Sep 11, 2024
76e7f4b
Fix names, add enums, improve descriptions
samleeflang Sep 20, 2024
ecaefce
Code review
samleeflang Sep 24, 2024
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94 changes: 47 additions & 47 deletions app/data/opends/annotation-termlist.csv
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48 changes: 24 additions & 24 deletions app/data/opends/create-update-tombstone-event-termlist.csv
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58 changes: 29 additions & 29 deletions app/data/opends/data-mapping-termlist.csv
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178 changes: 89 additions & 89 deletions app/data/opends/digital-media-termlist.csv
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630 changes: 319 additions & 311 deletions app/data/opends/digital-specimen-termlist.csv
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100 changes: 54 additions & 46 deletions app/data/opends/machine-annotation-service-termlist.csv
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61 changes: 31 additions & 30 deletions app/data/opends/source-system-termlist.csv
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5 changes: 3 additions & 2 deletions app/routes.py
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Expand Up @@ -476,8 +476,9 @@ def generate_terms(header_mdfile, term_file):
on=['compound_name'], how='left'
)
terms = terms_skos_df.sort_values(by=['class_name'])
terms['examples'] = terms['examples'].str.replace(r'"', '')
terms['definition'] = terms['definition'].str.replace(r'"', '')
terms['examples'] = terms['examples'].str.replace(r'"', '').replace("'", "").replace("[", "").replace("]", "")
terms['enum'] = terms['enum'].str.replace(r'"', '').replace("'", "").replace("[", "").replace("]", "")
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terms['definition'] = terms['definition'].str.replace(r'"', '').replace("'", "").replace("[", "").replace("]", "")
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Maybe make a function out of this as you are repeating the same action three times

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👍

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Removed the logic for definition as this is never an array


# Unique Class Names
opends_classes = terms_df["class_name"].dropna().unique()
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6 changes: 3 additions & 3 deletions app/templates/includes/resources/diagrams/class-diagrams/annotation-full.html
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Expand Up @@ -29,7 +29,7 @@
tombstoneDate : string
tombstoneText : string
TombstonedByAgent : object
hasRelatedPID : array
hasRelatedPID : array<object>
}
class Agent {
name : string
Expand All @@ -39,15 +39,15 @@
roleOrder : integer
email : string
url : string
hasIdentifier : array
hasIdentifier : array<ods:Identifier>
}
class AnnotationTarget {
ID : string
type : string
hasSelector : object
}
class AnnotationBody {
value : array
value : array<string>
references : string
score : number
}
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8 changes: 4 additions & 4 deletions ...plates/includes/resources/diagrams/class-diagrams/create-update-tombstone-event-full.html
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Expand Up @@ -2,14 +2,14 @@
class CreateUpdateTombstoneEvent {
ID : string
type : string
hasProvAgent : array
hasProvAgent : array<ods:Agent>
}
class Activity {
wasAssociatedWith : array
wasAssociatedWith : array<ods:Agent>
endedAtTime : string
used : string
comment : string
changeValue : array
changeValue : array<object>
}
class Entity {
value : object
Expand All @@ -24,7 +24,7 @@
roleOrder : integer
email : string
url : string
hasIdentifier : array
hasIdentifier : array<ods:Identifier>
}
CreateUpdateTombstoneEvent -- Activity
CreateUpdateTombstoneEvent -- Entity
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14 changes: 7 additions & 7 deletions app/templates/includes/resources/diagrams/class-diagrams/data-mapping-full.html
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@@ -1,5 +1,5 @@
classDiagram
class Mapping {
class DataMapping {
ID : string
type : string
status : None
Expand All @@ -9,16 +9,16 @@
dateCreated : string
dateModified : string
creator : object
DefaultMapping : array
FieldMapping : array
DefaultMapping : array<ods:DefaultMapping>
FieldMapping : array<ods:FieldMapping>
mappingDataStandard : None
TombstoneMetadata : object
}
class TombstoneMetadata {
tombstoneDate : string
tombstoneText : string
TombstonedByAgent : object
hasRelatedPID : array
hasRelatedPID : array<object>
}
class Agent {
name : string
Expand All @@ -28,7 +28,7 @@
roleOrder : integer
email : string
url : string
hasIdentifier : array
hasIdentifier : array<ods:Identifier>
}
Mapping -- TombstoneMetadata
Mapping -- Agent
DataMapping -- TombstoneMetadata
DataMapping -- Agent
14 changes: 7 additions & 7 deletions app/templates/includes/resources/diagrams/class-diagrams/digital-media-full.html
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Expand Up @@ -20,11 +20,11 @@
rightsHolder : string
source : string
creator : string
hasAssertion : array
hasCitation : array
hasIdentifier : array
hasEntityRelationship : array
hasAgent : array
hasAssertion : array<ods:Assertion>
hasCitation : array<ods:Citation>
hasIdentifier : array<ods:Identifier>
hasEntityRelationship : array<ods:EntityRelationship>
hasAgent : array<ods:Agent>
TombstoneMetadata : object
}
class Agent {
Expand All @@ -35,7 +35,7 @@
roleOrder : integer
email : string
url : string
hasIdentifier : array
hasIdentifier : array<ods:Identifier>
}
class Assertion {
measurementID : string
Expand Down Expand Up @@ -92,7 +92,7 @@
tombstoneDate : string
tombstoneText : string
TombstonedByAgent : object
hasRelatedPID : array
hasRelatedPID : array<object>
}
DigitalMedia -- Agent
DigitalMedia -- Assertion
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44 changes: 22 additions & 22 deletions app/templates/includes/resources/diagrams/class-diagrams/digital-specimen-full.html
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Expand Up @@ -19,7 +19,7 @@
sourceSystemID : string
sourceSystemName : string
livingOrPreserved : None
language : array
language : array<string>
license : string
basisOfRecord : string
preparations : string
Expand All @@ -45,15 +45,15 @@
associatedOrganisms : string
organismRemarks : string
dynamicProperties : string
hasMaterialEntity : array
hasIdentification : array
hasAssertion : array
hasEvent : array
hasEntityRelationship : array
hasCitation : array
hasIdentifier : array
hasChronometricAge : array
hasAgent : array
hasMaterialEntity : array<ods:MaterialEntity>
hasIdentification : array<ods:Identification>
hasAssertion : array<ods:Assertion>
hasEvent : array<ods:Event>
hasEntityRelationship : array<ods:EntityRelationship>
hasCitation : array<ods:Citation>
hasIdentifier : array<ods:Identifier>
hasChronometricAge : array<ods:ChronometricAge>
hasAgent : array<ods:Agent>
TombstoneMetadata : object
}
class MaterialEntity {
Expand All @@ -70,13 +70,13 @@
recordedBy : string
recordedByID : string
verbatimLabel : string
hasIdentification : array
hasAssertion : array
hasEntityRelationship : array
hasCitation : array
hasIdentifier : array
hasEvent : array
hasAgent : array
hasIdentification : array<ods:Identification>
hasAssertion : array<ods:Assertion>
hasEntityRelationship : array<ods:EntityRelationship>
hasCitation : array<ods:Citation>
hasIdentifier : array<ods:Identifier>
hasEvent : array<ods:Event>
hasAgent : array<ods:Agent>
}
class Identification {
identificationID : string
Expand All @@ -91,8 +91,8 @@
isVerifiedIdentification : boolean
identificationRemarks : string
identificationQualifier : string
hasCitation : array
hasTaxonIdentification : array
hasCitation : array<ods:Citation>
hasTaxonIdentification : array<ods:TaxonIdentification>
}
class TaxonIdentification {
taxonID : string
Expand Down Expand Up @@ -167,7 +167,7 @@
eventRemarks : string
collectorName : string
collectorID : string
hasAssertion : array
hasAssertion : array<ods:Assertion>
Location : object
}
class Location {
Expand Down Expand Up @@ -245,7 +245,7 @@
roleOrder : integer
email : string
url : string
hasIdentifier : array
hasIdentifier : array<ods:Identifier>
}
class Assertion {
measurementID : string
Expand Down Expand Up @@ -322,7 +322,7 @@
tombstoneDate : string
tombstoneText : string
TombstonedByAgent : object
hasRelatedPID : array
hasRelatedPID : array<object>
}

DigitalSpecimen -- MaterialEntity
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18 changes: 15 additions & 3 deletions ...templates/includes/resources/diagrams/class-diagrams/machine-annotation-service-full.html
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Expand Up @@ -18,13 +18,15 @@
serviceAvailability : string
maintainer : object
license : string
dependency : array
dependency : array<string>
slaDocumentation : string
topicName : string
maxReplicas : integer
batchingPermitted : boolean
timeToLive : integer
TombstoneMetadata : object
hasEnvironmentalVariable : array<ods:EnvironmentalVariable>
hasSecretVariable : array<ods:SecretVariable>
}
class ContactPoint {
description : string
Expand All @@ -36,7 +38,7 @@
tombstoneDate : string
tombstoneText : string
TombstonedByAgent : object
hasRelatedPID : array
hasRelatedPID : array<object>
}
class Agent {
name : string
Expand All @@ -46,8 +48,18 @@
roleOrder : integer
email : string
url : string
hasIdentifier : array
hasIdentifier : array<ods:Identifier>
}
class SecretVariable {
name : string
secretKeyRef : string
}
class EnvironmentalVariable {
name : string
value : ['string', 'integer', 'boolean']
}
MachineAnnotationService -- ContactPoint
MachineAnnotationService -- TombstoneMetadata
MachineAnnotationService -- Agent
MachineAnnotationService -- SecretVariable
MachineAnnotationService -- EnvironmentalVariable
5 changes: 3 additions & 2 deletions app/templates/includes/resources/diagrams/class-diagrams/source-system-full.html
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Expand Up @@ -12,14 +12,15 @@
url : string
collectionManagementSystem : string
translatorType : None
maximumRecords : integer
dataMappingID : string
TombstoneMetadata : object
}
class TombstoneMetadata {
tombstoneDate : string
tombstoneText : string
TombstonedByAgent : object
hasRelatedPID : array
hasRelatedPID : array<object>
}
class Agent {
name : string
Expand All @@ -29,7 +30,7 @@
roleOrder : integer
email : string
url : string
hasIdentifier : array
hasIdentifier : array<ods:Identifier>
}
SourceSystem -- TombstoneMetadata
SourceSystem -- Agent
20 changes: 18 additions & 2 deletions app/templates/includes/termlist/termlist-table.html
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Expand Up @@ -49,13 +49,13 @@ <h2 id="5-vocabulary">5 Vocabulary</h2>

{% if v['examples'] is number %}
{% else %}
{% set list1 = v['examples'].split('`, `') %}
{% set list1 = v['examples'].split(', ') %}
<tr>
<th scope="row">Examples</th>
<td>
<ul class="td-list">
{% for item in list1 %}
<li><span>{{ item|replace("`","") }}</span></li>
<li><span>{{ item }}</span></li>
{% endfor %}
</ul>

Expand All @@ -64,6 +64,22 @@ <h2 id="5-vocabulary">5 Vocabulary</h2>

{% endif %}

{% if v['enum'] is number %}
{% else %}
{% set list1 = v['enum'].split(', ') %}
<tr>
<th scope="row">Controlled Vocabulary</th>
<td>
<ul class="td-list">
{% for item in list1 %}
<li><span>{{ item }}</span></li>
{% endfor %}
</ul>

</td>
</tr>
Comment on lines +70 to +80
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Don't know how this should look but often and elements are stored in separate (table rows)

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Hmm took this over from Latimer Core only made some small changes to it. Would like to keep this for now

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I understand, just a generic HTML thing that is possible, but not recommended

{% endif %}

{% if v['datatype'] is number %}
{% else %}
<tr>
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