205 lines
9.0 KiB
VB.net
205 lines
9.0 KiB
VB.net
|
#Region "Microsoft.VisualBasic::7832f705d2d954f961650e5493d73356, Microsoft.VisualBasic.Core\Scripting\MetaData\Cite.vb"
|
|||
|
|
|
|||
|
|
' Author:
|
|||
|
|
'
|
|||
|
|
' asuka (amethyst.asuka@gcmodeller.org)
|
|||
|
|
' xie (genetics@smrucc.org)
|
|||
|
|
' xieguigang (xie.guigang@live.com)
|
|||
|
|
'
|
|||
|
|
' Copyright (c) 2018 GPL3 Licensed
|
|||
|
|
'
|
|||
|
|
'
|
|||
|
|
' GNU GENERAL PUBLIC LICENSE (GPL3)
|
|||
|
|
'
|
|||
|
|
'
|
|||
|
|
' This program is free software: you can redistribute it and/or modify
|
|||
|
|
' it under the terms of the GNU General Public License as published by
|
|||
|
|
' the Free Software Foundation, either version 3 of the License, or
|
|||
|
|
' (at your option) any later version.
|
|||
|
|
'
|
|||
|
|
' This program is distributed in the hope that it will be useful,
|
|||
|
|
' but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|||
|
|
' MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|||
|
|
' GNU General Public License for more details.
|
|||
|
|
'
|
|||
|
|
' You should have received a copy of the GNU General Public License
|
|||
|
|
' along with this program. If not, see <http://www.gnu.org/licenses/>.
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
' /********************************************************************************/
|
|||
|
|
|
|||
|
|
' Summaries:
|
|||
|
|
|
|||
|
|
' Class Cite
|
|||
|
|
'
|
|||
|
|
' Properties: Abstract, AuthorAddress, Authors, DOI, ISSN
|
|||
|
|
' Issue, Journal, Keywords, Notes, Pages
|
|||
|
|
' PubMed, StartPage, Title, URL, Volume
|
|||
|
|
' Year
|
|||
|
|
'
|
|||
|
|
' Constructor: (+2 Overloads) Sub New
|
|||
|
|
' Function: __formatAbstractPreview, (+2 Overloads) GetCiteList, HTML, ToString
|
|||
|
|
'
|
|||
|
|
'
|
|||
|
|
' /********************************************************************************/
|
|||
|
|
|
|||
|
|
#End Region
|
|||
|
|
|
|||
|
|
Imports System.Reflection
|
|||
|
|
Imports System.Text
|
|||
|
|
Imports System.Text.RegularExpressions
|
|||
|
|
Imports Microsoft.VisualBasic.Linq.Extensions
|
|||
|
|
|
|||
|
|
Namespace Scripting.MetaData
|
|||
|
|
|
|||
|
|
''' <summary>
|
|||
|
|
''' EndNote tags
|
|||
|
|
''' </summary>
|
|||
|
|
<AttributeUsage(AttributeTargets.Module Or AttributeTargets.Method Or AttributeTargets.Class, AllowMultiple:=True, Inherited:=True)>
|
|||
|
|
Public Class Cite : Inherits Attribute
|
|||
|
|
|
|||
|
|
''' <summary>
|
|||
|
|
''' author(eMail);author(eMail)
|
|||
|
|
''' </summary>
|
|||
|
|
''' <returns></returns>
|
|||
|
|
Public Property Authors As String
|
|||
|
|
Public Property Year As Integer
|
|||
|
|
Public Property Title As String
|
|||
|
|
Public Property Journal As String
|
|||
|
|
Public Property Volume As Integer
|
|||
|
|
Public Property Issue As String
|
|||
|
|
Public Property Pages As String
|
|||
|
|
Public Property StartPage As Integer
|
|||
|
|
''' <summary>
|
|||
|
|
''' ISSN_1; ISSN_2; ISSN_3
|
|||
|
|
''' </summary>
|
|||
|
|
''' <returns></returns>
|
|||
|
|
Public Property ISSN As String
|
|||
|
|
Public Property DOI As String
|
|||
|
|
Public Property PubMed As Integer
|
|||
|
|
Public Property Keywords As String
|
|||
|
|
''' <summary>
|
|||
|
|
''' 文章的摘要，可以使用<p>或者<br/>来进行分段
|
|||
|
|
''' </summary>
|
|||
|
|
''' <returns></returns>
|
|||
|
|
Public Property Abstract As String
|
|||
|
|
Public Property Notes As String
|
|||
|
|
Public Property URL As String
|
|||
|
|
Public Property AuthorAddress As String
|
|||
|
|
|
|||
|
|
''' <summary>
|
|||
|
|
''' %x 是文章的摘要，可以使用<p>或者<br/>来进行分段
|
|||
|
|
''' </summary>
|
|||
|
|
''' <param name="EndNoteImports"></param>
|
|||
|
|
''' <remarks>
|
|||
|
|
''' %A Griffiths-Jones, Sam
|
|||
|
|
''' %A Bateman, Alex
|
|||
|
|
''' %A Marshall, Mhairi
|
|||
|
|
''' %A Khanna, Ajay
|
|||
|
|
''' %A Eddy, Sean R.
|
|||
|
|
''' %T Rfam: an RNA family database
|
|||
|
|
''' %0 Journal Article
|
|||
|
|
''' %D 2003
|
|||
|
|
''' %8 January 1, 2003
|
|||
|
|
''' %J Nucleic Acids Research
|
|||
|
|
''' %P 439-441
|
|||
|
|
''' %R 10.1093/nar/gkg006
|
|||
|
|
''' %V 31
|
|||
|
|
''' %N 1
|
|||
|
|
''' %U http://nar.oxfordjournals.org/content/31/1/439.abstract
|
|||
|
|
''' %X Rfam Is a collection of multiple sequence alignments And covariance models representing non-coding RNA families. Rfam Is available on the web in the UK at http://www.sanger.ac.uk/Software/Rfam/ And in the US at http://rfam.wustl.edu/. These websites allow the user to search a query sequence against a library of covariance models, And view multiple sequence alignments And family annotation. The database can also be downloaded in flatfile form And searched locally using the INFERNAL package (http://infernal.wustl.edu/). The first release of Rfam (1.0) contains 25 families, which annotate over 50 000 non-coding RNA genes in the taxonomic divisions of the EMBL nucleotide database.
|
|||
|
|
''' </remarks>
|
|||
|
|
Sub New(EndNoteImports As String)
|
|||
|
|
Dim lines As String() = EndNoteImports.LineTokens
|
|||
|
|
Dim dict As Dictionary(Of String, String()) = (From line As String In lines
|
|||
|
|
Where Not String.IsNullOrWhiteSpace(line)
|
|||
|
|
Let flag As String = line.Split.First
|
|||
|
|
Let value As String = Mid(line, Len(flag) + 1).Trim
|
|||
|
|
Select flag, value
|
|||
|
|
Group By flag Into Group) _
|
|||
|
|
.ToDictionary(Function(x) x.flag,
|
|||
|
|
Function(x) x.Group.Select(Function(xx) xx.value).ToArray)
|
|||
|
|
Authors = dict.TryGetValue("%A").JoinBy("; ")
|
|||
|
|
Title = dict.TryGetValue("%T", [default]:=New String() {}).FirstOrDefault
|
|||
|
|
DOI = dict.TryGetValue("%R", [default]:=New String() {}).FirstOrDefault
|
|||
|
|
Year = CInt(Val(dict.TryGetValue("%D", [default]:=New String() {}).FirstOrDefault))
|
|||
|
|
Pages = dict.TryGetValue("%P", [default]:=New String() {}).FirstOrDefault
|
|||
|
|
Journal = dict.TryGetValue("%J", [default]:=New String() {}).FirstOrDefault
|
|||
|
|
Volume = CInt(Val(dict.TryGetValue("%V", [default]:=New String() {}).FirstOrDefault))
|
|||
|
|
URL = dict.TryGetValue("%U", [default]:=New String() {}).FirstOrDefault
|
|||
|
|
Abstract = dict.TryGetValue("%X", [default]:=New String() {}).FirstOrDefault
|
|||
|
|
End Sub
|
|||
|
|
|
|||
|
|
Sub New()
|
|||
|
|
End Sub
|
|||
|
|
|
|||
|
|
Public Overrides Function ToString() As String
|
|||
|
|
Return $"{Authors}, {Title}, {Journal}. {Volume} ({Issue}) ({Year}) {Pages}."
|
|||
|
|
End Function
|
|||
|
|
|
|||
|
|
Public Shared Function GetCiteList(Of T)() As Cite()
|
|||
|
|
#If NET_40 = 0 Then
|
|||
|
|
Dim typeDef As Type = GetType(T)
|
|||
|
|
Dim attrs = typeDef.GetCustomAttributes(Of Cite)(inherit:=True)
|
|||
|
|
Return attrs
|
|||
|
|
#Else
|
|||
|
|
Throw New NotSupportedException
|
|||
|
|
#End If
|
|||
|
|
End Function
|
|||
|
|
|
|||
|
|
Public Shared Function GetCiteList(typeDef As Type) As Cite()
|
|||
|
|
#If NET_40 = 0 Then
|
|||
|
|
Dim attrs As Cite() = typeDef.GetCustomAttributes(Of Cite)(inherit:=True)
|
|||
|
|
Return attrs
|
|||
|
|
#Else
|
|||
|
|
Throw New NotSupportedException
|
|||
|
|
#End If
|
|||
|
|
End Function
|
|||
|
|
|
|||
|
|
Public Function HTML(absLen As Integer) As String
|
|||
|
|
Dim htmlBuilder As StringBuilder = New StringBuilder(1024)
|
|||
|
|
|
|||
|
|
Call htmlBuilder.Append($"<i>{Authors}</i>.({Year}). ""<strong>{Title}</strong>"", {Journal}. <strong>{Volume}</strong>({Issue}) {Pages}.")
|
|||
|
|
Call htmlBuilder.AppendLine($"<p><pre>{Me.__formatAbstractPreview(absLen)}</pre></p>")
|
|||
|
|
Call htmlBuilder.AppendLine("<font size=""2"">")
|
|||
|
|
Call htmlBuilder.AppendLine($"<p><font size=""2""><strong>Keywords: </strong> <i>{Keywords}</i><br /></font></p>")
|
|||
|
|
Call htmlBuilder.AppendLine($"<p><font size=""2""><strong>Author Contacts: </strong> {AuthorAddress}</font></p>")
|
|||
|
|
Call htmlBuilder.AppendLine("<i>")
|
|||
|
|
If Not String.IsNullOrEmpty(DOI) Then
|
|||
|
|
Call htmlBuilder.AppendLine($"<li>DOI: <a href=""http://doi.org/{DOI}"">{DOI}</a></li><br />")
|
|||
|
|
End If
|
|||
|
|
If Not PubMed = 0 Then
|
|||
|
|
Call htmlBuilder.AppendLine($"<li>PMC FullText: <a href=""http://www.ncbi.nlm.nih.gov/pubmed/{PubMed}"">{PubMed}</a></li>")
|
|||
|
|
End If
|
|||
|
|
Call htmlBuilder.AppendLine("
|
|||
|
|
</i>
|
|||
|
|
</font>")
|
|||
|
|
|
|||
|
|
Return htmlBuilder.ToString
|
|||
|
|
End Function
|
|||
|
|
|
|||
|
|
''' <summary>
|
|||
|
|
''' 摘要可能会有空值的
|
|||
|
|
''' </summary>
|
|||
|
|
''' <param name="absLen"></param>
|
|||
|
|
''' <returns></returns>
|
|||
|
|
Private Function __formatAbstractPreview(absLen As String) As String
|
|||
|
|
If String.IsNullOrEmpty(Abstract) Then
|
|||
|
|
Return ""
|
|||
|
|
End If
|
|||
|
|
|
|||
|
|
Dim Tokens As String() = Regex.Split(Abstract.Replace(vbCr, "").Replace(vbLf, " ").Replace(" ", " "), "<p>", RegexOptions.IgnoreCase Or RegexOptions.Singleline)
|
|||
|
|
Tokens = (From s As String In Tokens Select Regex.Split(s, "<br/>", RegexOptions.Singleline Or RegexOptions.IgnoreCase)).ToArray.ToVector
|
|||
|
|
Dim sbr As StringBuilder = New StringBuilder(1024)
|
|||
|
|
|
|||
|
|
For Each s As String In Tokens
|
|||
|
|
Call StringHelpers.Parts(s, absLen, sbr)
|
|||
|
|
Call sbr.AppendLine(" ")
|
|||
|
|
Next
|
|||
|
|
|
|||
|
|
Return sbr.ToString
|
|||
|
|
End Function
|
|||
|
|
End Class
|
|||
|
|
End Namespace
|