From e57bb775b2c689d904239d4bdcb99d44c93dda8d Mon Sep 17 00:00:00 2001 From: Kirk DeLisle Date: Tue, 24 Oct 2023 10:56:38 -0600 Subject: [PATCH 1/7] Color option for Sequence Region Annotation --- csharp/local/SequenceRegionAnnotation.yaml | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/csharp/local/SequenceRegionAnnotation.yaml b/csharp/local/SequenceRegionAnnotation.yaml index bb5c9d6..ec47d60 100644 --- a/csharp/local/SequenceRegionAnnotation.yaml +++ b/csharp/local/SequenceRegionAnnotation.yaml @@ -79,6 +79,14 @@ inputFields: request: id: end dataType: integer +- control: + id: uictrlColor + label: Select color + type: color + request: + id: uictrlColor + dataType: string + data: '#afc9e1' tags: - color: '#337abc' text: sequence @@ -109,10 +117,14 @@ outputFields: name: Region end location source: inputField type: default +- id: uictrlColor + name: Color + source: inputField + type: color allowedClients: - Analyst - WebPlayer demoUrl: limitBy: none -minimumChartsVersion: 4.4.0.0 -confirmSubmit: \ No newline at end of file +minimumChartsVersion: 4.4.0.0 +confirmSubmit: From 9060d2bfa678883b12dbc5cafa00ac4e644d6f74 Mon Sep 17 00:00:00 2001 From: Kirk DeLisle Date: Tue, 24 Oct 2023 11:27:39 -0600 Subject: [PATCH 2/7] Add color option to Ab Seq Liab and Seq Motif Search --- csharp/local/AntibodySequenceLiabilities.yaml | 17 ++++++++++++-- csharp/local/SequenceMotifSearch.yaml | 23 +++++++++++++++---- 2 files changed, 33 insertions(+), 7 deletions(-) diff --git a/csharp/local/AntibodySequenceLiabilities.yaml b/csharp/local/AntibodySequenceLiabilities.yaml index c838ca4..024f4bf 100644 --- a/csharp/local/AntibodySequenceLiabilities.yaml +++ b/csharp/local/AntibodySequenceLiabilities.yaml @@ -70,18 +70,31 @@ inputFields: - N-glycosylation,N[^P][TS] - N-terminal Glutamic Acid,^E - Oxidation,[MW] +- control: + id: ctrlColor + label: Select color + type: color + request: + id: ctrlColor + dataType: string + data: '#ff0000' assembly: PublisherCore tags: - color: '#dddddd' text: MAB +- color: '#AFC9E1' + text: annotation - color: '#337abc' text: sequence -- color: '#f1f72d' - text: filter updateBehavior: automatic maximumOutputColumns: !!int 10 maximumOutputTables: !!int 0 chemistryFunction: !!bool false +outputFields: +- id: ctrlColor + name: Color + source: inputField + type: color allowedClients: - Analyst - WebPlayer diff --git a/csharp/local/SequenceMotifSearch.yaml b/csharp/local/SequenceMotifSearch.yaml index 1b7d6c4..6975d6d 100644 --- a/csharp/local/SequenceMotifSearch.yaml +++ b/csharp/local/SequenceMotifSearch.yaml @@ -29,7 +29,7 @@ inputFields: type: text validationRules: - type: required - message: 'Enter a name for the output boolean column.' + message: Enter a name for the output boolean column. request: id: columnName dataType: string @@ -39,7 +39,7 @@ inputFields: type: text validationRules: - type: required - message: 'Enter a name to be used in annotating the motif.' + message: Enter a name to be used in annotating the motif. request: id: featureName dataType: string @@ -50,19 +50,32 @@ inputFields: rows: !!int 1 validationRules: - type: required - message: 'A query sequence or regular expression must be entered.' + message: A query sequence or regular expression must be entered. request: id: expression dataType: string +- control: + id: ctrlColor + label: Select color + type: color + request: + id: ctrlColor + dataType: string + data: '#ffa500' tags: +- color: '#AFC9E1' + text: annotation - color: '#337abc' text: sequence -- color: '#f1f72d' - text: filter updateBehavior: automatic maximumOutputColumns: !!int 2 maximumOutputTables: !!int 0 chemistryFunction: !!bool false +outputFields: +- id: ctrlColor + name: Color + source: inputField + type: color allowedClients: - Analyst - WebPlayer From 3f1783a9ab200f6c03651089c76c6dc60fc79491 Mon Sep 17 00:00:00 2001 From: Kirk DeLisle Date: Tue, 24 Oct 2023 11:37:34 -0600 Subject: [PATCH 3/7] Remove outputFileds (rely on defaults) --- csharp/local/AntibodySequenceLiabilities.yaml | 5 ----- csharp/local/SequenceMotifSearch.yaml | 5 ----- 2 files changed, 10 deletions(-) diff --git a/csharp/local/AntibodySequenceLiabilities.yaml b/csharp/local/AntibodySequenceLiabilities.yaml index 024f4bf..93a6023 100644 --- a/csharp/local/AntibodySequenceLiabilities.yaml +++ b/csharp/local/AntibodySequenceLiabilities.yaml @@ -90,11 +90,6 @@ updateBehavior: automatic maximumOutputColumns: !!int 10 maximumOutputTables: !!int 0 chemistryFunction: !!bool false -outputFields: -- id: ctrlColor - name: Color - source: inputField - type: color allowedClients: - Analyst - WebPlayer diff --git a/csharp/local/SequenceMotifSearch.yaml b/csharp/local/SequenceMotifSearch.yaml index 6975d6d..54a4b1d 100644 --- a/csharp/local/SequenceMotifSearch.yaml +++ b/csharp/local/SequenceMotifSearch.yaml @@ -71,11 +71,6 @@ updateBehavior: automatic maximumOutputColumns: !!int 2 maximumOutputTables: !!int 0 chemistryFunction: !!bool false -outputFields: -- id: ctrlColor - name: Color - source: inputField - type: color allowedClients: - Analyst - WebPlayer From 8fc4df4fe88a5c824dafe25048f6a8ae7902ca36 Mon Sep 17 00:00:00 2001 From: Kirk DeLisle Date: Tue, 24 Oct 2023 11:45:49 -0600 Subject: [PATCH 4/7] Bump version numbers; rename input field in Ab Seq Liab --- csharp/local/AntibodySequenceLiabilities.yaml | 4 ++-- csharp/local/SequenceMotifSearch.yaml | 2 +- csharp/local/SequenceRegionAnnotation.yaml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/csharp/local/AntibodySequenceLiabilities.yaml b/csharp/local/AntibodySequenceLiabilities.yaml index 93a6023..01bbfc2 100644 --- a/csharp/local/AntibodySequenceLiabilities.yaml +++ b/csharp/local/AntibodySequenceLiabilities.yaml @@ -2,7 +2,7 @@ id: 01010160-093b-55c7-746b-8a3c148111b7 name: Antibody Sequence Liabilities description: Create a set of boolean columns indicating the presence or absence of predefined antibody sequence liabilities. A column illustrating the sequence and the identified liability locations is also created. category: Biopolymer -version: 1.0.1 +version: 1.1.0 serviceName: AntibodySequenceLiabilities serviceUri: glysade.csharp executorId: Glysade.CSharpDataFxn @@ -36,7 +36,7 @@ inputFields: data: Annotated Liabilities - control: id: patterns - label: Match patterns + label: Sequence liabilities type: select multi: !!bool true options: diff --git a/csharp/local/SequenceMotifSearch.yaml b/csharp/local/SequenceMotifSearch.yaml index 54a4b1d..1ff6b6b 100644 --- a/csharp/local/SequenceMotifSearch.yaml +++ b/csharp/local/SequenceMotifSearch.yaml @@ -2,7 +2,7 @@ id: 70470634-68a8-4950-9d88-348bc19e3a1d name: Sequence Motif Search description: Creates boolean columns indicating the presence or absence of an input sequence motif in a sequence column - regular expressions are also supported. A column illustrating the sequence and the identified motif locations is also created. category: Biopolymer -version: 1.0.1 +version: 1.1.0 serviceName: SequenceMotifRegexSearch serviceUri: glysade.csharp executorId: Glysade.CSharpDataFxn diff --git a/csharp/local/SequenceRegionAnnotation.yaml b/csharp/local/SequenceRegionAnnotation.yaml index ec47d60..c3e6c8f 100644 --- a/csharp/local/SequenceRegionAnnotation.yaml +++ b/csharp/local/SequenceRegionAnnotation.yaml @@ -2,7 +2,7 @@ id: 1d863338-11e3-f287-a9c8-6d72792c320f name: Sequence Region Annotation description: Create GenBank region annotations for a sequence or GenBank column. category: Biopolymer -version: 1.0.0 +version: 1.1.0 serviceName: SequenceRegionAnnotationDataFunction serviceUri: glysade.csharp executorId: Glysade.CSharpDataFxn From 0f487a8af9994062d7aa8bbac58f7ec52fcc0ec7 Mon Sep 17 00:00:00 2001 From: Kirk DeLisle Date: Wed, 25 Oct 2023 10:34:43 -0600 Subject: [PATCH 5/7] Add output fields --- csharp/local/AntibodySequenceLiabilities.yaml | 19 ++++++++++++++++- csharp/local/SequenceMotifSearch.yaml | 21 +++++++++++++++++++ 2 files changed, 39 insertions(+), 1 deletion(-) diff --git a/csharp/local/AntibodySequenceLiabilities.yaml b/csharp/local/AntibodySequenceLiabilities.yaml index 01bbfc2..6b647d0 100644 --- a/csharp/local/AntibodySequenceLiabilities.yaml +++ b/csharp/local/AntibodySequenceLiabilities.yaml @@ -36,7 +36,7 @@ inputFields: data: Annotated Liabilities - control: id: patterns - label: Sequence liabilities + label: Sequence liabilities type: select multi: !!bool true options: @@ -90,6 +90,23 @@ updateBehavior: automatic maximumOutputColumns: !!int 10 maximumOutputTables: !!int 0 chemistryFunction: !!bool false +outputFields: +- id: sequenceColumn + name: Sequence column + source: inputField + type: default +- id: outputColumn + name: Annotated sequence output column + source: inputField + type: default +- id: patterns + name: Selected liabilities + source: inputField + type: default +- id: ctrlColor + name: Color + source: inputField + type: default allowedClients: - Analyst - WebPlayer diff --git a/csharp/local/SequenceMotifSearch.yaml b/csharp/local/SequenceMotifSearch.yaml index 1ff6b6b..7ee1c75 100644 --- a/csharp/local/SequenceMotifSearch.yaml +++ b/csharp/local/SequenceMotifSearch.yaml @@ -71,6 +71,27 @@ updateBehavior: automatic maximumOutputColumns: !!int 2 maximumOutputTables: !!int 0 chemistryFunction: !!bool false +outputFields: +- id: sequenceColumn + name: Sequence column + source: inputField + type: default +- id: columnName + name: Annotated sequence output column + source: inputField + type: default +- id: featureName + name: Motif name + source: inputField + type: default +- id: expression + name: Motif expression + source: inputField + type: default +- id: ctrlColor + name: Color + source: inputField + type: default allowedClients: - Analyst - WebPlayer From fe68ef34e3702b326b9ee4cf74d3b91f7865cf4a Mon Sep 17 00:00:00 2001 From: Kirk DeLisle Date: Wed, 25 Oct 2023 10:46:37 -0600 Subject: [PATCH 6/7] Adjust output field type --- csharp/local/AntibodySequenceLiabilities.yaml | 2 +- csharp/local/SequenceMotifSearch.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/csharp/local/AntibodySequenceLiabilities.yaml b/csharp/local/AntibodySequenceLiabilities.yaml index 6b647d0..f1c90c5 100644 --- a/csharp/local/AntibodySequenceLiabilities.yaml +++ b/csharp/local/AntibodySequenceLiabilities.yaml @@ -106,7 +106,7 @@ outputFields: - id: ctrlColor name: Color source: inputField - type: default + type: color allowedClients: - Analyst - WebPlayer diff --git a/csharp/local/SequenceMotifSearch.yaml b/csharp/local/SequenceMotifSearch.yaml index 7ee1c75..65d63d5 100644 --- a/csharp/local/SequenceMotifSearch.yaml +++ b/csharp/local/SequenceMotifSearch.yaml @@ -91,7 +91,7 @@ outputFields: - id: ctrlColor name: Color source: inputField - type: default + type: color allowedClients: - Analyst - WebPlayer From 2df85807a0ddf7254315069c848597e8c3b69a31 Mon Sep 17 00:00:00 2001 From: Kirk DeLisle Date: Wed, 13 Dec 2023 16:15:41 -0700 Subject: [PATCH 7/7] Add new definition to both required locations in .yaml --- csharp/local/AntibodySequenceLiabilities.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/csharp/local/AntibodySequenceLiabilities.yaml b/csharp/local/AntibodySequenceLiabilities.yaml index f1c90c5..3f5eeba 100644 --- a/csharp/local/AntibodySequenceLiabilities.yaml +++ b/csharp/local/AntibodySequenceLiabilities.yaml @@ -41,7 +41,7 @@ inputFields: multi: !!bool true options: - text: Asparagine Deamidation - value: Asparagine Deamidation,(?=(N[GSTN])) + value: Asparagine Deamidation,(?=(N[GSTNH])) - text: Aspartic Acid Fragmentation value: Aspartic Acid Fragmentation,DP - text: Aspartic Acid Isomerization @@ -62,7 +62,7 @@ inputFields: id: patterns dataType: list(string) data: - - Asparagine Deamidation,(?=(N[GSTN])) + - Asparagine Deamidation,(?=(N[GSTNH])) - Aspartic Acid Fragmentation,DP - Aspartic Acid Isomerization,(?=(D[GSTDH])) - Cysteine,C