Feature/blast col search markfilter 231019

python/local/BlastLocalColumnSearch_subset.yaml

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+id: d35172ce-5e4b-945a-631d-14e47c9a1fc6
+name: Blast Local Column Search (subset)
+description: Performs a BLAST search of user selected databases using queries from a sequence column. Pre-configured BLAST databases can be downloaded from https://tinyurl.com/3d38p356
+category: Biopolymer
+version: 1.2.0
+serviceName: BlastLocalColumnSearch
+serviceUri: glysade.python
+executorId: Glysade.CPythonDataFxn
+inputFields:
+- control:
+    id: sequenceColumn
+    label: Select sequence column
+    type: columnselect
+    filters:
+    - dataType: string
+      contentType:
+      - chemical/x-sequence
+    - dataType: binary
+      contentType: chemical/x-genbank
+    validationRules:
+    - type: required
+      message: Must select column of sequences
+    limitByControlId: limitByField
+  request:
+    id: sequenceColumn
+    dataType: string
+    selectorType: column
+- control:
+    id: idColumn
+    label: ID Column (optional)
+    type: columnselect
+    multi: !!bool false
+    filters:
+    - dataType:
+      - string
+      - int
+      contentType: []
+    tooltip: ID column is not required for Genbank encoded sequences
+    limitByControlId: limitByField
+  request:
+    id: idColumn
+    dataType: string
+    selectorType: column
+- control:
+    id: method
+    label: Select method
+    type: select
+    options:
+    - text: 'BLASTP: protein(q)-protein(d)'
+      value: BLASTP
+    - text: 'BLASTN: nucleotide(q)-nucleotide(d)'
+      value: BLASTN
+    - text: 'BLASTX: nucleotide(q)+translation-protein(d)'
+      value: BLASTX
+    - text: 'TBLASTN: protein(q)-nucleotide(d)+translation'
+      value: TBLASTN
+    - text: 'TBLASTX: nucleotide(q)+translation-nucleotide(d)+translation'
+      value: TBLASTX
+    validationRules:
+    - type: required
+  request:
+    id: method
+    dataType: string
+    data: BLASTP
+- control:
+    id: databaseName
+    label: Select database
+    type: select
+    options:
+    - text: Human NCBI NR
+      value: human_nr
+    - text: Human Uniprot SwissProt
+      value: up_sp_human
+    - text: Human Uniprot Trembl
+      value: up_tbl_human
+    - text: Human PDB
+      value: human_pdbaa
+    - text: Human Patented Proteins
+      value: human_pataa
+    - text: Human IG Germline (Proteins)
+      value: human_IG_germline
+    - text: Human NCBI NT
+      value: human_nt
+    - text: Human EBI ENA
+      value: ena_cd_human
+    - text: Human Patented Nucleotides
+      value: human_patnt
+    - text: Mouse NCBI NR
+      value: mouse_nr
+    - text: Mouse PDB
+      value: mouse_pdbaa
+    - text: Mouse Patented Proteins
+      value: mouse_pataa
+    - text: Mouse NCBI NT
+      value: mouse_nt
+    - text: Mouse Patented Nucleotides
+      value: mouse_patnt
+    - text: Rat NCBI NR
+      value: rat_nr
+    - text: Rat PDB
+      value: rat_pdbaa
+    - text: Rat Patented Proteins
+      value: rat_pataa
+    - text: Rat NCBI NT
+      value: rat_nt
+    - text: Rat Patented Nucleotides
+      value: rat_patnt
+    validationRules:
+    - type: required
+  request:
+    id: databaseName
+    dataType: string
+- control:
+    id: maxHits
+    label: Max hits
+    type: text
+    validationRules:
+    - type: required
+      message: Must enter a value between 1 and 5000
+    - type: range
+      min: !!int 1
+      max: !!int 5000
+      message: Max hits must be a value between 1 and 5000
+  request:
+    id: maxHits
+    dataType: integer
+    data: !!int 100
+- control:
+    id: blastDbPath
+    label: Directory containing BLAST databases
+    type: file
+    mode: path
+    pathType: folder
+    validationRules:
+    - type: required
+      message: ''
+  request:
+    id: blastDbPath
+    dataType: string
+    data: C:\db\ncbi
+- control:
+    id: limitByField
+    label: Apply data function to
+    type: limitby
+  request:
+  - id: limitByField
+    dataType: string
+    field: limitBy
+    data: none
+  - id: limitByFieldMarking
+    dataType: string
+    field: marking
+tags:
+- color: '#337abc'
+  text: sequence
+- color: '#f7cb2d'
+  text: search
+ironPython: |
+  ####################################################
+  #  Copyright 2022 Glysade LLC, All Rights Reserved #
+  ####################################################
+
+  import sys,clr
+  from Spotfire.Dxp.Data import DataTable, DataManager
+  from Spotfire.Dxp.Application import PanelTypeIdentifiers
+  from Spotfire.Dxp.Application import Panel
+  import Spotfire.Dxp.Application.PanelCollection
+
+  from System import AppDomain
+  for asm in AppDomain.CurrentDomain.GetAssemblies():
+      if asm.GetName().Name == 'Charts':
+          clr.AddReference(asm.FullName)
+
+  from Charts import ChartsModel
+  model_type = ChartsModel
+
+  #tableId pass in args
+  dataTable = ResultTables[0]
+
+  if not dataTable:
+      raise Exception('target table not found')
+
+  page = Document.Pages.AddNew('Blast (local) column query Results')
+  panelsToHide = [PanelTypeIdentifiers.DataPanel, PanelTypeIdentifiers.DetailsOnDemandPanel]
+
+  for panel in page.Panels:
+      if panel.TypeId in panelsToHide:
+          if panel.Visible:
+              panel.Visible = False
+
+  filteringScheme = Document.FilteringSchemes[0]
+  page.FilterPanel.FilteringSchemeReference = filteringScheme
+
+  tableVis = page.Visuals.AddNew[model_type]()
+  tableVis.SetKeyValue('visualization','table-visualization')
+  tableVis.DataTable = dataTable
+  tableVis.ConfigureColumns()
+  tableVis.Marking = Document.Data.Markings.DefaultMarkingReference
+
+  tableVis.SetActiveVisual()
+  page.AutoConfigure()
+updateBehavior: manual
+maximumOutputColumns: !!int 0
+maximumOutputTables: !!int 1
+chemistryFunction: !!bool false
+allowedClients:
+- Analyst
+demoUrl: https://youtu.be/v7leIlBaiz4
+minimumChartsVersion: 4.4.0.0
+confirmSubmit: