Qbugbot source, updated October 14, 2019.
frmMain.vb
edit' frmMain.vb, by Robert Webster (CC BY-SA 3.0 US)
'
' simple form, with 5 buttons:
' - cmdList: Read a list of taxa from a text file and make pages for them.
' - cmdRandom: Make a set of pages for random taxa.
' - cmdUpdate: Update a set of pages for random taxa (qbugbot 3).
' - cmdRedir: Fix recursive redircets (qbugbot 4).
' - cmdEtc: page for various utility functions.
' mysql connection.net: nuget console> Install-Package MySql.Data -Version 8.0.13
' database is MariaDB.
Imports System.Net
Imports System.Net.Http
Imports System.Text
Imports System.Text.RegularExpressions
Imports System.Collections.Generic
Imports System.Math
Imports System.IO
Imports System.Data
Imports MySql.Data.MySqlClient
Imports Newtonsoft.Json
Imports Newtonsoft.Json.Linq
Public Class frmMain
Dim pagesMade As New List(Of String)
Dim nPagesSent, maxPagesSent As Integer
Dim clock As New Stopwatch
Dim madePage As New StringBuilder ' pages most recently created, same format as tmp file.
Sub qlogout(url As String)
' logout of a wiki
Dim parms As Dictionary(Of String, String)
Dim r1 As HttpResponseMessage
Dim qcontent As FormUrlEncodedContent
Dim s As String
parms = New Dictionary(Of String, String)
parms.Add("action", "logout")
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(url, qcontent).Result
s = r1.Content.ReadAsStringAsync().Result
End Sub
Function qlogin(url As String) As String
Dim parms As Dictionary(Of String, String)
Dim r1 As HttpResponseMessage
Dim qcontent As FormUrlEncodedContent
Dim json As JObject
Dim token As String
Dim s As String
Dim s1 As String
parms = New Dictionary(Of String, String)
parms.Add("action", "query")
parms.Add("meta", "tokens")
parms.Add("type", "login")
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(url, qcontent).Result
s = r1.Content.ReadAsStringAsync().Result
json = JObject.Parse(s)
token = json.SelectToken("query").SelectToken("tokens").SelectToken("logintoken")
parms = New Dictionary(Of String, String)
parms.Add("action", "login")
If url = urlWikiPedia Then
parms.Add("lgname", My.Settings.qlgname)
parms.Add("lgpassword", My.Settings.qlgpassword)
End If
parms.Add("lgtoken", token)
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(url, qcontent).Result
s = r1.Content.ReadAsStringAsync().Result
json = JObject.Parse(s)
s1 = json("login").SelectToken("result").ToString
If s1 = "Success" Then
Return s1
Else
Return s
End If
End Function
Private Sub frmMain_Shown(sender As Object, e As EventArgs) Handles Me.Shown
' necessary to handle cookies
cookies = New CookieContainer
handler = New HttpClientHandler
handler.CookieContainer = cookies
qClient = New HttpClient(handler) ' need this for cookies
End Sub
Function gettoken(url) As String
' get a token, required for upload or edit
' uses httpClient
Dim parms As Dictionary(Of String, String)
Dim r1 As HttpResponseMessage
Dim qcontent As FormUrlEncodedContent
Dim json As JObject
Dim s As String
parms = New Dictionary(Of String, String)
parms.Add("action", "query")
parms.Add("meta", "tokens")
parms.Add("type", "csrf")
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(url, qcontent).Result
s = r1.Content.ReadAsStringAsync().Result
json = JObject.Parse(s)
sToken = json.SelectToken("query.tokens.csrftoken")
Return sToken
End Function
Function fixHodges(descr As String) As String
' change "common name - Hodges #2453" to "common name (Hodges 2453)
' returns original if no "Hodges"
Dim s1 As String
Dim rMatch As RegularExpressions.Match
If Not LCase(descr).Contains("hodges") Then Return descr
If LCase(descr).StartsWith("hodges") Then
Return ""
Else
rMatch = Regex.Match(descr, "(.+) - Hodges (#\d+)")
If rMatch.Groups.Count = 3 Then
s1 = rMatch.Groups(1).ToString & " (Hodges " & rMatch.Groups(2).ToString & ")"
Return s1
Else
Return descr
End If
End If
End Function
Function wikiCaption(tMatch As taxrec, shortForm As Boolean) As String
' get a caption for a photo
Dim descr As String
Dim tax As String
tax = tMatch.taxon
descr = ""
If tMatch.commonNames.Count > 0 Then descr = tMatch.commonNames(0)
descr = fixHodges(descr)
If eqstr(tMatch.rank, "genus") Or eqstr(tMatch.rank, "species") Or
eqstr(tMatch.rank, "subspecies") Then tax = "''" & tax & "''"
If descr <> "" Then
descr = descr & ", " & tax
descr = UCase(descr.Substring(0, 1)) & descr.Substring(1)
End If
Return descr
End Function
Function sendWikiPage(pageTitle As String, content As String, url As String, editSummary As String,
sendingMode As Integer) As String
' transmit a page to a wiki.
' sendingmode 2 = update, 1 = create, 0 = don't send
Dim k As Integer
Dim s As String
Dim s1 As String = ""
Dim pageID As Integer
Dim sandBox As Boolean
Dim valid As Boolean
Dim r1 As HttpResponseMessage
Dim qcontent As FormUrlEncodedContent
Dim parms As Dictionary(Of String, String)
Dim minInterval As Integer = 10000 ' 10 seconds between edits
Dim jq As New JObject
Dim jt As JToken = Nothing
sandBox = True
If sendingMode = 0 Then Return "0"
For i As Integer = 1 To 10
k = clock.ElapsedMilliseconds
If k > 0 And k < minInterval Then Threading.Thread.Sleep(minInterval - k)
clock.Restart()
pageID = getPageID(pageTitle, url)
If pageID > 0 And (sendingMode = 1 And Not sandBox) Then
outLog(pageTitle & " exists. Not sent.")
Return ""
End If
parms = New Dictionary(Of String, String)
parms.Add("action", "edit")
If sandBox Then
parms.Add("title", "User:Edibobb/sandbox")
Else
parms.Add("title", pageTitle)
End If
parms.Add("text", content)
parms.Add("bot", "true")
parms.Add("maxlag", "5")
parms.Add("format", "json")
parms.Add("summary", editSummary)
parms.Add("token", sToken)
Try
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(url, qcontent).Result
s = ""
s = r1.Content.ReadAsStringAsync().Result
jq = JObject.Parse(s)
valid = jq.TryGetValue("edit", jt)
If valid Then Exit For
Catch ex As Exception
s1 = ex.Message
outLog("send error 1, " & pageTitle & ", " & s1 & ".")
Exit For
End Try
If jq.TryGetValue("error", jt) Then
s1 = jt("code").ToString
If Not eqstr(s1, "maxlag") Then
outLog("send error 2, " & pageTitle & ", " & s1 & ".")
End If
End If
Next i
If valid Then
If Not eqstr(jt("result").ToString, "success") Then Stop
s1 = jt("result").ToString
If jt("nochange") IsNot Nothing Then
outLog("Identical Page Exists, " & pageTitle & ".")
Return ""
Else
Try
s1 = jt("result").ToString & ", " & jt("pageid").ToString & ", " &
jt("newtimestamp").ToString & ", " & jt("title").ToString
Catch ex As Exception
s1 = "Send error 3, " & ex.Message & " " & s1
End Try
outLog("sent " & pageTitle & ", " & s1 & ".")
End If
Else
outLog("send failed, " & pageTitle & ", " & s1 & ".")
Return ""
End If
s = jt("pageid").ToString
Return s
End Function
Function extinctRange(tmatch As taxrec) As String
Dim prec As paleorec
Dim s1 As String = ""
' get paleo record
prec = getPaleo(tmatch)
If prec.earlyinterval <> "" Then s1 = "| oldest_fossil = " & prec.earlyinterval
If prec.lateinterval <> "" Then s1 &= "| youngest_fossil = " & prec.lateinterval
Return s1
End Function
Sub getDescr(tMatch As taxrec, ancestor As List(Of taxrec),
ByRef descr As String, ByRef upperRank As String, ByRef upperTax As String, ByRef commonWikiLink As String)
' returns descr, something like "beetles", and upperRank and upperTax, something like "Order", "Coleoptera".
' ancestors must have addons
Dim k As Integer
descr = ""
commonWikiLink = ""
upperRank = ""
upperTax = ""
If itisRankID(tMatch.rank) <= 180 Then k = 0 Else k = 2
For i1 As Integer = k To ancestor.Count - 1 ' skip current and next rank except for genus and above
If ancestor(i1).commonNames.Count > 0 Then
If itisRankID(tMatch.rank) < 220 OrElse (Not ancestor(i1).commonNames(0).Contains(" and ")) Then
descr = ancestor(i1).commonNames(0) ' common name for higher rank
commonWikiLink = ancestor(i1).commonWikiLink
Exit For
End If
End If
Next i1
' special cases
'If descr = "insects" AndAlso isAncestor(ancestor, "lepidoptera", 0) AndAlso
If itisRankID(tMatch.rank) <= 130 AndAlso isAncestor(ancestor, "lepidoptera", 0) AndAlso
descr.Contains(" and ") AndAlso
Not isAncestor(ancestor, "Papilionoidea", 0) Then descr = "moth" ' no superfamily or family name for some moths.
If isAncestor(ancestor, "Blattodea", 0) Then
If isAncestor(ancestor, "Termitoidae", 0) Then descr = "termites" Else descr = "cockroach"
End If
' select family, order, or class
For i1 As Integer = 1 To ancestor.Count - 1
Select Case LCase(ancestor(i1).rank)
Case "family"
upperRank = "family"
upperTax = ancestor(i1).taxon
Exit For
Case "order"
upperRank = "order"
upperTax = ancestor(i1).taxon
Exit For
Case "class"
upperRank = "class"
upperTax = ancestor(i1).taxon
Exit For
End Select
Next i1
End Sub
Function formatAncestors(tMatch As taxrec, ancestor As List(Of taxrec), dbAllowed As Integer) As String
' returns name and rank of a popular common ancestor, or generic "species" name.
' for example:
' "Psammodiini is a tribe of aphodiine dung beetles in the family Scarabaeidae.
' There are about 12 genera and at least 50 described species in Psammodiini."
Dim ss As List(Of String)
Dim sq As List(Of String)
Dim s As String
Dim s1, s2 As String
Dim descr As String = ""
Dim upperTax As String = ""
Dim upperRank As String = ""
Dim commonWikiLink As String = ""
Dim children As New List(Of taxrec)
Dim species As New List(Of taxrec)
Dim rmatch As RegularExpressions.Match
Dim sTaxon As String
Dim qualifier As String
Dim childCount, speciesCount As Integer
Dim sChildCount, sSpeciesCount As String
Dim verb As String
Dim firstChild As String
Dim genCommon As String
Dim m As taxrec
getDescr(tMatch, ancestor, descr, upperRank, upperTax, commonWikiLink)
If upperRank <> "" Then ' OK to use good english
' gencommon is a general common name: Argia is a genus of dancers in the DAMSELFLY family [[Coenagrionidae]]
s2 = ""
genCommon = ""
m = Nothing
If tMatch.commonNames IsNot Nothing AndAlso tMatch.commonNames.Count > 0 Then s2 = LCase(tMatch.commonNames(0))
If isAncestor(ancestor, "Zygoptera", 0) AndAlso
Not s2.Contains("damselfl") AndAlso Not descr.Contains("damselfl") Then
genCommon = "damselfly"
m = getAncestor(ancestor, "Zygoptera", 0)
ElseIf isAncestor(ancestor, "Anisoptera", 0) AndAlso
Not s2.Contains("dragonfl") AndAlso Not descr.Contains("dragonfl") Then
genCommon = "dragonfly"
m = getAncestor(ancestor, "Anisoptera", 0)
ElseIf isAncestor(ancestor, "Coleoptera", 0) AndAlso
Not s2.Contains("beetle") AndAlso Not descr.Contains("beetle") Then
genCommon = "beetle"
m = getAncestor(ancestor, "Coleoptera", 0)
ElseIf isAncestor(ancestor, "Papilionoidea", 0) AndAlso
Not s2.Contains("butterfl") AndAlso Not descr.Contains("butterfl") Then
genCommon = "butterfly"
m = getAncestor(ancestor, "Papilionoidea", 0)
ElseIf isAncestor(ancestor, "Lepidoptera", 0) AndAlso Not isAncestor(ancestor, "Papilionoidea", 0) AndAlso
Not s2.Contains("moth") AndAlso Not descr.Contains("moth") Then
genCommon = "moth"
m = getAncestor(ancestor, "Lepidoptera", 0)
ElseIf isAncestor(ancestor, "Araneae", 0) AndAlso
Not s2.Contains("spider") AndAlso Not descr.Contains("spider") Then
genCommon = "spider"
m = getAncestor(ancestor, "Araneae", 0)
End If
If m IsNot Nothing Then
If m.rank <> upperRank Then genCommon = "[[" & genCommon & "]]"
genCommon &= " "
End If
' If s1 <> "" Then genCommon = " of " & s1 & " known as"
' bold common names
ss = New List(Of String)
If tMatch.commonNames IsNot Nothing Then ss.AddRange(tMatch.commonNames)
For i As Integer = ss.Count - 1 To 0 Step -1
ss(i) = "'''" & ss(i) & "'''"
Next i
If "aeiou".Contains(LCase(tMatch.rank).Substring(0, 1)) Then verb = " is an " Else verb = " is a "
If tMatch.extinct Then verb = " is an extinct "
If eqstr(tMatch.rank, "species") Or eqstr(tMatch.rank, "subspecies") Then
' make description list singular, if necessary
' 2/3/18 - only change a list of two or a single item to be singular
If Not descr.Contains(",") Then
descr = descr.Replace(" and ", ",")
sq = descr.Split(",").ToList
For i1 As Integer = 0 To sq.Count - 1
sq(i1) = singular(sq(i1).Trim)
Next i1
descr = formatList(sq, "or")
descr = descr.Replace(" or the ", " or ")
End If
If commonWikiLink <> "" Then
If descr = commonWikiLink Then
descr = "[[" & descr & "]]"
Else
descr = "[[" & commonWikiLink & "|" & descr & "]]"
End If
End If
If ss.Count = 0 Then
If descr <> "" Then
s = verb & LCase(tMatch.rank) & " of " & descr & " in the " & genCommon & upperRank & " [[" & upperTax & "]]."
Else
s = verb & LCase(tMatch.rank) & " in the " & genCommon & upperRank & " [[" & upperTax & "]]."
End If
ElseIf ss.Count = 1 Then
rmatch = Regex.Match(ss(0), "[a-z]\'s")
If rmatch.Value = "" Then rmatch = Regex.Match(ss(0), "^[A-Za-z -]+?s\' ")
If rmatch.Value <> "" OrElse ss(0).StartsWith("'''the") Then
s1 = ", or "
Else
s1 = ", the " ' use "or" for possessive names, or if there's a "the" in descr
End If
s = s1 & ss(0) & "," & verb & LCase(tMatch.rank) & " of " & descr & " in the " & genCommon & upperRank & " [[" & upperTax & "]]."
ElseIf ss.Count = 2 Then
s1 = formatList(ss, "or")
If Not s1.StartsWith("'''the") Then s1 = "the " & s1
s = ", known generally as " & s1 & "," & verb & LCase(tMatch.rank) & " of " & descr & " in the " & genCommon & upperRank & " [[" & upperTax & "]]."
Else
s = ", known generally as " & ss(0) & "," & verb & LCase(tMatch.rank) & " of " & descr & " in the " & genCommon & upperRank & " [[" & upperTax & "]]."
ss.RemoveAt(0)
s1 = formatList(ss, "and")
If Not s1.StartsWith("'''the") Then s1 = "the " & s1
s &= " Other common names include " & s1 & "."
End If
Return s ' species and subspecies
Else ' genus or higher
descr = descr.Replace(" and the ", " and ")
If Not descr.Contains(",") And Not descr.Contains(" and ") And Not descr.Contains(" or ") Then
' check for wikilink
If commonWikiLink <> "" Then
If descr.StartsWith(commonWikiLink) AndAlso descr.Length - commonWikiLink.Length <= 3 Then
descr = "[[" & commonWikiLink & "]]" & descr.Substring(commonWikiLink.Length)
Else
descr = "[[" & commonWikiLink & "|" & descr & "]]"
End If
End If
End If
s = verb & LCase(tMatch.rank) & " of " & descr & " in the " & genCommon & upperRank & " [[" & upperTax & "]]."
' count and round descendants, 2 significant digits
sTaxon = tMatch.taxon
If itisRankID(tMatch.rank) < itisRankID("genus") Then
' rank is higher than genus
s1 = getLowerRank(tMatch.rank)
children = allDescendants(tMatch, s1, dbAllowed)
childCount = children.Count
If children.Count > 0 Then
s2 = getDisambig(children(0))
If s2 = "" Then
s2 = children(0).taxon
If (eqstr(children(0).rank, "species") Or eqstr(children(0).rank, "subspecies")) And children.Count = 1 Then s2 = abbreviate(s2)
Else
s2 = s2 & "|" & children(0).taxon ' should not happen for species or subspecies, so abbreviation won't matter
End If
firstChild = "[[" & s2 & "]]"
If itisRankID(s1) >= 180 Then firstChild = "''" & firstChild & "''"
Else
firstChild = ""
End If
species = allDescendants(tMatch, "species", dbAllowed)
speciesCount = species.Count
If speciesCount < 10 And childCount < 10 Then
sChildCount = numeral(childCount)
sSpeciesCount = numeral(speciesCount)
Else
sChildCount = Format(roundoff(childCount), "#,#")
sSpeciesCount = Format(roundoff(speciesCount), "#,#")
End If
qualifier = ""
If childCount >= 1 Then
If childCount = 1 Then
If speciesCount < 10 Or childCount = 1 Then
s &= " There is at least one " & s1 & ", " & firstChild & ","
Else
s &= " There is at least 1 " & s1 & ", " & firstChild & ","
End If
ElseIf childCount >= 20 Or childCount <= 4 Then
If roundoff(childCount) < childCount Then
s &= " There are more than " & sChildCount & " " & pluralRank(s1)
qualifier = "more than"
Else
s &= " There are at least " & sChildCount & " " & pluralRank(s1)
qualifier = "at least"
End If
Else
s &= " There are about " & sChildCount & " " & pluralRank(s1)
qualifier = "about"
End If
If speciesCount = 0 Or childCount = 1 Then
s &= " in " & sTaxon & "."
Else
If speciesCount = 1 Then
s2 = species(0).taxon
If s2 <> "" Then
s2 = s2.Replace(" ", " ")
s &= " and at least one described species, ''" & s2 & "'', in " & sTaxon & "." ' monotypic genus does not link to species?
End If
ElseIf speciesCount >= 20 Or speciesCount <= 4 Then
If roundoff(speciesCount) < speciesCount Then
If qualifier = "more than" Then s &= " and " Else s &= " and more than "
Else
If qualifier = "at least" Then s &= " and " Else s &= " and at least "
End If
s &= sSpeciesCount & " described species in " & sTaxon & "."
Else
If qualifier = "about" Then s &= " and " Else s &= " and about "
s &= sSpeciesCount & " described species in " & sTaxon & "."
End If
End If
End If
Else ' rank is genus or lower
If eqstr(tMatch.rank, "genus") Then sTaxon = "''" & sTaxon & "''"
s1 = getLowerRank(tMatch.rank)
children = allDescendants(tMatch, s1, dbAllowed)
childCount = children.Count
If childCount < 10 Then
sChildCount = numeral(childCount)
Else
sChildCount = Format(roundoff(childCount), "#,#")
End If
If childCount >= 1 Then
If childCount = 1 Then
s2 = children(0).taxon
If s2 <> "" Then s &= " There is one described species in " & sTaxon & ", ''" & abbreviate(s2) & "''" & "." ' monotypic genus doesn't link to species (used to be "at least one")
ElseIf childCount >= 20 Or childCount <= 4 Then
If roundoff(childCount) < childCount Then
s &= " There are more than " & sChildCount & " described species in " & sTaxon & "."
Else
s &= " There are at least " & sChildCount & " described species in " & sTaxon & "."
End If
Else
s &= " There are about " & sChildCount & " described species in " & sTaxon & "."
End If
End If
End If
Return s
End If
Else
Return "Oops!"
End If
End Function
Function roundoff(ByVal k2 As Integer) As Integer
' round to leave two significant digits on the left, used for "number of species is at least..."
Dim k1 As Integer
If k2 < 100 And k2 >= 20 Then
k2 = (k2 \ 10) * 10
Else
k1 = 10 ^ Floor(Log10(k2) - 1)
If k1 > 0 Then k2 = (k2 \ k1) * k1
End If
Return k2
End Function
Function WikiPedialist(tMatch As taxrec, children As List(Of taxrec), ancestor As List(Of taxrec),
showSource As Boolean, dbAllowed As Integer, sendingMode As Integer) As String
' makes a wikipedia list page, for a bunch of children of a taxon.
Dim s, s1, bugname As String
Dim childCount As Integer
Dim sChildcount As String
Dim species As New List(Of taxrec)
Dim sb As StringBuilder
Dim wikibug As String
Dim refs As New references
Dim wrefs As New List(Of refrec)
Dim source As String
Dim sourceUsed As Boolean = False
Dim uh As String
Dim spiderflag As Boolean
Dim rm As RegularExpressions.Match
Dim s2 As String
Dim descr As String = ""
Dim upperrank As String = ""
Dim uppertax As String = ""
Dim commonwikilink As String = ""
Dim ss As List(Of String)
Dim sq As List(Of String)
If children.Count <= 0 Then Return ""
sb = New StringBuilder
bugname = tMatch.taxon
s1 = getDisambig(tMatch)
If s1 = "" Then
wikibug = "[[" & tMatch.taxon & "]]"
Else
wikibug = "[[" & s1 & "|" & tMatch.taxon & "]]"
End If
If eqstr(tMatch.rank, "species") OrElse eqstr(tMatch.rank, "genus") OrElse eqstr(tMatch.rank, "subspecies") Then
bugname = "''" & bugname & "''"
wikibug = "''" & wikibug & "''"
End If
'ancestor = getancestors(tMatch, dbAllowed, True, "phylum", False)
defineRefs(tMatch, ancestor, bugname, refs, showSource)
wrefs = getWikiRefs(ancestor)
' if there's a taxlink species file and reference, use taxlink for a specific link in the reference
For Each wref As refrec In wrefs
If wref.url.ToLower.Contains("speciesfile.org") AndAlso tMatch.taxlink.ToLower.StartsWith(wref.url.ToLower) And
tMatch.taxlink.ToLower.Contains("taxonnameid") Then
' use it as a more specific species file link
rm = Regex.Match(tMatch.taxlink, ":\/\/(.+?)\.")
If rm.Groups.Count = 2 Then s1 = rm.Groups(1).Value Else s1 = ""
s1 = StrConv(s1, VbStrConv.ProperCase)
If s1 <> "" Then
s2 = tMatch.rank & " " & tMatch.taxon & " " & tMatch.authority
wref.url = tMatch.taxlink
wref.etc &= "|website = " & wref.title
wref.title = s2
End If
refs.addref("speciesfile", citation(wref))
Exit For
End If
Next wref
getDescr(tMatch, ancestor, descr, upperrank, uppertax, commonwikilink)
sb.AppendLine("{{DISPLAYTITLE:List of " & bugname & " " & pluralRank(children(0).rank) & "}}")
s = "These " & children.Count & " " & pluralRank(children(0).rank)
If tMatch.commonNames Is Nothing Then tMatch.commonNames = New List(Of String)
If tMatch.commonNames.Count > 0 OrElse (descr = "" Or upperrank = "" Or uppertax = "") Then
s &= " belong to the " & LCase(tMatch.rank) & " " & wikibug
If tMatch.commonNames.Count > 0 Then
s &= ", " & tMatch.commonNames(0) & "."
Else
s &= "."
End If
Else
If "aeiou".Contains(LCase(tMatch.rank).Substring(0, 1)) Then uh = ", an " Else uh = ", a "
s &= " belong to " & wikibug & uh & LCase(tMatch.rank) & " of " & descr & " in the " & upperrank & " [[" & uppertax & "]]."
End If
If s.EndsWith("..") Then s = s.Substring(0, s.Length - 1) ' etc..
If itisRankID(tMatch.rank) < 180 Then
species = allDescendants(tMatch, "species", dbAllowed)
childCount = species.Count
If childCount < 10 Then
sChildcount = numeral(childCount)
Else
sChildcount = Format(roundoff(childCount), "#,#")
End If
If childCount > 1 Then
If childCount >= 20 Or childCount <= 4 Then
s &= " There are at least " & sChildcount & " described species in " & bugname & "."
Else
s &= " There are about " & sChildcount & " described species in " & bugname & "."
End If
End If
End If
' these could be blank
If tMatch.itistsn <> 0 OrElse showSource Then s &= refs.Ref("itis")
If tMatch.gbifID <> "" OrElse showSource Then s &= refs.Ref("gbif")
If showSource Then s &= refs.Ref("catlife") ' catlife is only for showsource
s &= refs.Ref("spidercat")
If refs.refExists("bugguide", "") > 0 Then
s &= refs.Ref("bugguide") ' generic
Else
s &= refs.Ref("buglink") ' specific
End If
s &= refs.Ref("speciesfile") ' if it's there
s &= refs.Ref("paleo") ' if it's there
sb.AppendLine(s)
sb.AppendLine()
sb.AppendLine("==" & bugname & " " & LCase(pluralRank(children(0).rank)) & "==")
If children.Count >= maxColumn Then
If itisRankID(children(0).rank) >= 220 Then
sb.AppendLine("{{col div|colwidth=29em}}") ' species or subspecies
Else
sb.AppendLine("{{col div|colwidth=22em}}") ' single word taxon
End If
Else
sb.AppendLine()
End If
ss = New List(Of String)
spiderflag = False
For i1 As Integer = 0 To children.Count - 1
s1 = getDisambig(children(i1))
If s1 = "" Then
s1 = children(i1).taxon
If eqstr(tMatch.rank, "genus") AndAlso tMatch.extinct AndAlso (Not children(i1).taxon.StartsWith(tMatch.taxon)) Then
sq = s1.Split({ChrW(32)}, 2).ToList
If sq.Count = 2 AndAlso Not eqstr(sq(0), tMatch.taxon) Then
s1 = tMatch.taxon & " " & sq(1)
End If
End If
Else
s1 = s1 & "|" & children(i1).taxon
End If
If Not eqstr(children(i1).rank, "subspecies") Then s1 = "[[" & s1 & "]]" ' wikilink
If tMatch.spiderID > 0 And children(i1).spiderID <= 0 Then
s1 = "(" & s1 & ")"
spiderflag = True
End If
If eqstr(children(i1).rank, "species") OrElse eqstr(children(i1).rank, "genus") OrElse
eqstr(children(i1).rank, "subspecies") Then
s1 = "''" & s1 & "'' "
Else
s1 = s1 & " "
End If
If children(i1).extinct Then s1 = "† " & s1
s1 = "* " & s1
If children(i1).authority <> "" Then s1 &= "<small>" & children(i1).authority & "</small>"
source = ""
If showSource Then
If children(i1).itistsn > 0 Then source &= " i"
If children(i1).catLifeID IsNot Nothing AndAlso children(i1).catLifeID <> "" Then source &= " c"
If children(i1).gbifID <> "" Then source &= " g"
If LCase(children(i1).link).Contains("bugguide") Then source &= " b"
If children(i1).spiderID > 0 Then source &= " s"
If source <> "" Then
s1 &= "<span style=""color:gray""><sup>" & source & "</sup></span>"
sourceUsed = True
End If
End If
If children(i1).taxid <> "" Then
s = firstCommon(children(i1).taxid)
If s <> "" Then s1 &= " (" & s & ")"
End If
ss.Add(s1)
Next i1
ss.Sort()
For i As Integer = 0 To ss.Count - 1
sb.AppendLine(ss(i))
Next i
If children.Count >= maxColumn Then sb.AppendLine("{{Col div end}}") ' close column template
If sourceUsed Then
If isAncestor(ancestor, "Araneae", 0) Then
s1 = "<small>Data sources: i = ITIS," & refs.Ref("itis") & " c = Catalogue of Life," & refs.Ref("catlife") &
" g = GBIF," & refs.Ref("gbif") & " b = Bugguide.net," & refs.Ref("bugguide") &
" s = World Spider Catalog" & refs.Ref("spider") & "</small>"
sb.AppendLine(s1)
If spiderflag Then
s1 = vbCrLf & "<small>" & StrConv(tMatch.rank, VbStrConv.ProperCase) & "names in parentheses may no longer be valid.</small>"
sb.AppendLine(s1)
End If
Else
s1 = "<small>Data sources: i = ITIS," & refs.Ref("itis") & " c = Catalogue of Life," & refs.Ref("catlife") &
" g = GBIF," & refs.Ref("gbif") & " b = Bugguide.net" & refs.Ref("bugguide") & "</small>"
sb.AppendLine(s1)
End If
End If
sb.AppendLine()
sb.AppendLine("==References==")
sb.AppendLine("{{Reflist|refs=")
sb.AppendLine(refs.allRefs & "}}")
sb.AppendLine()
sb.AppendLine()
s = getCategoryRank(ancestor, 0)
If s <> "" Then sb.AppendLine("[[Category:" & s & "|*]]")
If isAncestor(ancestor, "insecta", 0) And eqstr(children(0).rank, "species") Then sb.AppendLine("[[Category:Lists of insect species]]")
If sendingMode = 1 Then sb.AppendLine(botCreateCategory)
sb.AppendLine()
sb.AppendLine()
Return sb.ToString
End Function
Function getListPageName(m As taxrec, children As List(Of taxrec)) As String
' for consistency
Return "List of " & m.taxon & " " & pluralRank(children(0).rank)
End Function
Function WikiPediaEntry(tMatch As taxrec, images As List(Of String), captions As List(Of String),
uprights As List(Of String), children As List(Of taxrec), ancestor As List(Of taxrec),
showSource As Boolean, dbAllowed As Integer, sendingMode As Integer) As String
' makes the text for a new wikipedia entry
Dim sb As New StringBuilder
Dim s, s1, s2 As String
Dim fName As String
Dim ss As List(Of String)
Dim nref As Integer = 0
Dim maxPics As Integer = 2
Dim reflist As New List(Of String)
Dim ix As New List(Of Integer)
Dim keys As New List(Of String)
Dim nextLetter = "a"
Dim refName, ref As String
Dim idup As Integer
Dim monoGenus As Boolean = False
Dim monoFamily As Boolean = False ' for anything above genus
Dim sq() As String
Dim kids As List(Of taxrec)
Dim m As New taxrec
Dim irec As New imagerec
Dim wrefs As New List(Of refrec)
Dim refs As New references
Dim bugName As String
Dim i2, k, pageid As Integer
Dim rm As RegularExpressions.Match
If tMatch.taxon = "" Then Return ""
If Not eqstr(ancestor(ancestor.Count - 1).rank, "phylum") Then
Stop
Return ""
End If
wrefs = getWikiRefs(ancestor)
' if there's a taxlink species file and reference, use taxlink for a specific link in the reference
For Each wref As refrec In wrefs
If wref.url.ToLower.Contains("speciesfile.org") AndAlso tMatch.taxlink.ToLower.StartsWith(wref.url.ToLower) And
tMatch.taxlink.ToLower.Contains("taxonnameid") Then
' use it as a more specific species file link
rm = Regex.Match(tMatch.taxlink, ":\/\/(.+?)\.")
If rm.Groups.Count = 2 Then s1 = rm.Groups(1).Value Else s1 = ""
s1 = StrConv(s1, VbStrConv.ProperCase)
If s1 <> "" Then
s2 = tMatch.rank & " " & tMatch.taxon & " " & tMatch.authority
wref.url = tMatch.taxlink
wref.etc &= "|website = " & wref.title
wref.title = s2
End If
End If
Next wref
If eqstr(tMatch.rank, "genus") OrElse eqstr(tMatch.rank, "species") OrElse
eqstr(tMatch.rank, "subspecies") Then
bugName = "''" & tMatch.taxon & "''"
Else
bugName = tMatch.taxon
End If
defineRefs(tMatch, ancestor, bugName, refs, showSource)
For i1 As Integer = 0 To images.Count - 1
images(i1) = images(i1).Replace("=", "%3D")
Next i1
If children.Count = 1 Then
If eqstr(children(0).rank, "species") AndAlso eqstr(tMatch.rank, "genus") Then monoGenus = True
If eqstr(children(0).rank, "genus") Then monoFamily = True
End If
If eqstr(tMatch.rank, "species") Or monoGenus Then
sb.AppendLine("{{Speciesbox")
Else
sb.AppendLine("{{Automatic taxobox")
End If
If images.Count >= 1 Then
ss = images(0).Split(" ").ToList
fName = ss(ss.Count - 1) ' last word is filename
irec = getImageRec(fName)
s1 = images(0)
If s1.StartsWith("File:") Then s1 = s1.Substring(5)
sb.AppendLine("| image = " & s1)
If captions.Count > 0 Then
sb.AppendLine("| image_caption = " & captions(0))
End If
If uprights(0) <> "" Then sb.AppendLine("| image_upright = " & uprights(0))
End If
' ----------- species box ----------------------
If monoGenus Then ' genus page, but show species also
sb.AppendLine("| genus = " & getTaxAmbig(tMatch.taxon))
sq = children(0).taxon.Split(" ")
sb.AppendLine("| species = " & sq(1))
If tMatch.authority <> "" Then sb.AppendLine("| parent_authority = " & tMatch.authority)
If children(0).authority <> "" Then sb.AppendLine("| authority = " & children(0).authority)
ElseIf monoFamily Then ' redirect to genus page, exit
s = "#REDIRECT [[" & children(0).taxon & "]]" & vbCrLf & "{{R from monotypic taxon}}" & vbCrLf
outLog("Redirect from " & tMatch.taxon & " to " & children(0).taxon)
Return s
Else ' normal, not monotypic from or to genus
If eqstr(tMatch.rank, "species") Then
sq = ancestor(0).taxon.Split(" ")
sb.AppendLine("| genus = " & getTaxAmbig(sq(0)))
sb.AppendLine("| species = " & sq(1))
Else ' not species, one word
sb.AppendLine("| taxon = " & getTaxAmbig(tMatch.taxon))
End If
If tMatch.authority <> "" Then sb.AppendLine("| authority = " & tMatch.authority)
End If
If tMatch.extinct Then
s1 = extinctRange(tMatch)
If s1 <> "" Then sb.AppendLine(s1)
End If
' display_parents = k
If tMatch.rank = "species" Then
s1 = getHigherRank("genus")
i2 = 2 ' skip genus when looking for higherrank.
k = 1 ' show an extra parent, for genus
Else
s1 = getHigherRank(tMatch.rank)
i2 = 1
k = 0
End If
For i As Integer = i2 To ancestor.Count - 1
If eqstr(ancestor(i).rank, s1) Then Exit For
k += 1
Next i
If k > 1 Then sb.AppendLine("| display_parents = " & k)
If tMatch.iucnStatus <> "" AndAlso Not eqstr(tMatch.iucnStatus, "dd") Then ' add endangered status
sb.AppendLine("| status = " & tMatch.iucnStatus)
sb.AppendLine("| status_system = iucn" & tMatch.iucnVersion)
If tMatch.iucnID <> "" Then sb.AppendLine("| status_ref = " & refs.Ref("iucn")) ' http://www.iucnredlist.org/details/42685/0
End If
If children.Count >= maxlist Then
sb.AppendLine("| diversity_link = " & getListPageName(tMatch, children))
sb.AppendLine("| diversity = at least " & roundoff(children.Count) & " " & pluralRank(children(0).rank))
End If
' show children?
kids = getChildren(tMatch, False, dbAllowed) ' get immediate children
For i As Integer = kids.Count - 1 To 0 Step -1
If Not itisRankID.ContainsKey(kids(i).rank) OrElse
itisRankID(kids(i).rank) >= 220 OrElse mainRank.IndexOf(kids(i).rank) >= 0 Then kids.RemoveAt(i)
Next i
If kids.Count > 1 Then ' minor ranks only
sb.AppendLine("| subdivision_ranks = " & StrConv(pluralRank(kids(0).rank), VbStrConv.ProperCase))
sb.AppendLine("| subdivision =")
ss = New List(Of String)
For Each kid As taxrec In kids
If kid.extinct Then s = "* † [[" & kid.taxon & "]]" Else s = "* [[" & kid.taxon & "]]"
If kid.authority <> "" Then s &= " <small>" & kid.authority & "</small>"
ss.Add(s)
Next kid
ss.Sort()
For Each s3 As String In ss
sb.AppendLine(s3)
Next s3
End If
If tMatch.synonyms IsNot Nothing AndAlso tMatch.synonyms.Count > 0 Then
sb.Append("| synonyms = ")
If eqstr(tMatch.rank, "species") Then
sb.AppendLine("{{Species list")
Else
sb.AppendLine("{{Taxon list")
End If
For j As Integer = 0 To tMatch.synonyms.Count - 1
If tMatch.synauth.Count > j Then
sb.AppendLine("| " & tMatch.synonyms(j) & " | " & tMatch.synauth(j))
Else
sb.AppendLine("| " & tMatch.synonyms(j) & " |")
End If
Next j
sb.AppendLine("}}") ' synonyms
If tMatch.itistsn > 0 Then sb.AppendLine("| synonyms_ref = " & refs.Ref("itis"))
End If
sb.AppendLine("}}")
sb.AppendLine()
'---------title-------------------
s = "'''" & bugName & "'''"
'---------introduction---------------
s &= formatAncestors(tMatch, ancestor, dbAllowed)
'---------common names------------------
If 1 = 0 Then
ss = New List(Of String)
ss.AddRange(tMatch.commonNames)
For i As Integer = 0 To ss.Count - 1
ss(i) = """" & ss(i) & """"
Next i
If tMatch.commonNames.Count > 0 Then
If eqstr(tMatch.rank, "species") Or eqstr(tMatch.rank, "subspecies") Then
s &= " The " & LCase(tMatch.rank) & " is known generally as " ' """ & tmatch.commonNames(0) & """."
s1 = formatList(ss, "or")
If Not s1.StartsWith("the") Then s1 = "the " & s1
s &= s1 & "."
Else
s &= "Members of the " & LCase(tMatch.rank) & " " & bugName & " include " ' & tmatch.commonNames(0) & "."
s1 = formatList(ss, "and")
If Not s1.StartsWith("the") Then s1 = "the " & s1
s &= s1 & "."
End If
End If
End If
'---------range----------------------
s1 = getRange(tMatch)
If s1 <> "" Then s &= " " & s1
'---------primary references----------------------
' some of these may be blank
' refs.ref sets the used flag (if not blank) -- required.
If tMatch.itistsn <> 0 OrElse showSource Then s &= refs.Ref("itis")
If tMatch.gbifID <> "" OrElse showSource Then s &= refs.Ref("gbif")
s &= refs.Ref("spidercat")
s &= refs.Ref("iucn")
s &= refs.Ref("buglink")
s &= refs.Ref("paleo") ' if it's there
sb.AppendLine(s)
'---------conservation status------------------
If tMatch.iucnStatus <> "" AndAlso Not eqstr(tMatch.iucnStatus, "dd") Then ' add endangered status
s = "The IUCN conservation status of " & bugName & " is " & iucnstatus(tMatch.iucnStatus, tMatch.iucnTrend, tMatch.iucnYear)
s &= refs.Ref("iucn")
sb.AppendLine()
sb.AppendLine(s)
End If
'-----------Hodges number-----------------
If tMatch.hodges <> "" Then
s = "The MONA or Hodges number for " & bugName & " is "
If isAncestor(ancestor, "Papilionoidea", 0) Then ' butterfly, don't link to moths
s &= tMatch.hodges & "." & refs.Ref("mpg")
Else
s &= "[[List of moths of North America|" & tMatch.hodges & "]]." & refs.Ref("mpg")
End If
sb.AppendLine()
sb.AppendLine(s)
End If
'---------additional references on page. These are at the end of the text, so use <ref>
s = "" : nextLetter = "a"
For i As Integer = 0 To wrefs.Count - 1
If LCase(wrefs(i).reftype).StartsWith("ref") Then ' reftype is refpub, refweb, refbook, etc. to go in the text.
refName = "ref" & Format(i, "00")
ref = citation(wrefs(i))
If wrefs(i).alast.Count > 0 Then ' use author name, year for ref name
refName = wrefs(i).alast
idup = refName.IndexOf("|")
If idup >= 0 Then refName = refName.Substring(0, idup)
refName &= wrefs(i).year
End If
idup = refs.refExists(refName, ref)
If idup = 1 Then ' name exists
refName &= nextLetter
nextLetter = ChrW(Asc(nextLetter) + 1)
End If
idup = refs.refExists(refName, ref)
If idup = 1 Then refs.Ref("ref" & i) ' duplicate name (should never happen)
If idup <= 1 Then ' 2 is duplicate reference content -- don't add it.
refs.addref(refName, ref)
s &= refs.Ref(refName)
End If
End If
Next i
If s <> "" Then sb.AppendLine(s)
'---------photos----------------------------
k = 1
For i As Integer = 1 To maxPics ' first one's been used.
Do While k <= images.Count - 1
pageid = getPageID(images(k), urlWikiMedia)
If pageid > 0 Then Exit Do
k += 1
Loop
If k >= images.Count Then Exit For
ss = images(k).Split(" ").ToList
fName = ss(ss.Count - 1)
s = "[[" & images(k) & "| thumb"
If uprights(k) <> "" Then s &= "| upright"
irec = getImageRec(fName)
If captions.Count > i AndAlso captions(k) <> "" Then
s &= "|" & captions(k) & "]]"
Else
s1 = wikiCaption(tMatch, True)
If s1 = "" Then
s &= "]]"
Else
If irec.taxonid = "" Then
s &= "|" & s1 & "]]"
Else
s &= "|" & s1 & "]]" 's &= "|" & s1 & xpref & "]]"
End If
End If
End If
sb.AppendLine(s)
k += 1
Next i
'---------children--------------------------------
If (children.Count > 1 And children.Count < maxlist) Then
s = formatchildren(tMatch, children, refs, ancestor, showSource)
If s <> "" Then
sb.AppendLine()
sb.AppendLine(s)
End If
End If
'---------see also (list page)---------------------
If children.Count >= maxlist Then
sb.AppendLine()
sb.AppendLine("==See also==")
sb.AppendLine("* [[" & getListPageName(tMatch, children) & "]]") ' function is for consistency
End If
sb.Replace("/>" & vbCrLf & "<ref", "/><ref") ' careful!
'---------inline references------------------------
sb.AppendLine()
sb.AppendLine("==References==")
sb.AppendLine("{{Reflist|refs=")
sb.AppendLine(refs.allRefs & "}}")
'---------further reading---------------------
reflist = New List(Of String)
For Each wref As refrec In wrefs
If Not LCase(wref.reftype).StartsWith("ref") Then ' no external links And Not LCase(wref.reftype).EndsWith("web") Then
reflist.Add(citation(wref)) ' paper reference
ix.Add(ix.Count) ' for sort
s1 = wref.alast
If s1 = "" Then s1 = wref.elast
'If s1 = "" Then s1 = wref.authors
If s1 = "" Then
s1 = wref.title
If s1.StartsWith("A ") Then s1 = s1.Substring(2)
If s1.StartsWith("An ") Then s1 = s1.Substring(3)
If s1.StartsWith("The ") Then s1 = s1.Substring(4)
End If
keys.Add(s1) ' for sort
End If
Next wref
If reflist.Count > 0 And Not tMatch.extinct Then ' no further reading for extinct bugs
sb.AppendLine()
sb.AppendLine("==Further reading==")
sb.AppendLine("{{refbegin}}")
MergeSort(keys, ix, 0, reflist.Count - 1)
For i1 As Integer = 0 To reflist.Count - 1
sb.AppendLine("* " & reflist(ix(i1)))
Next i1
sb.AppendLine("{{refend}}")
End If
sb.AppendLine()
If images.Count > 0 Then
sb.AppendLine("==External links==")
sb.AppendLine("{{refbegin}}")
'sb.AppendLine("* {{Commons category-inline|" & tMatch.taxon & "}}")
sb.AppendLine("* {{Commons-inline}}")
sb.AppendLine("{{refend}}")
sb.AppendLine()
End If
s1 = tMatch.wikidataid
If s1 = "" Then s1 = getQnumber(tMatch, ancestor)
If s1 <> "" Then
sb.AppendLine("{{Taxonbar|from=" & s1 & "}}")
Else
sb.AppendLine("{{Taxonbar}}")
End If
sb.AppendLine()
s = "[[Category:" & getCategoryRank(ancestor, 1) & "]]"
sb.AppendLine(s)
If isAncestor(ancestor, "diplopoda", 0) Then sb.AppendLine("[[Category:Millipedes of North America]]")
If sendingMode = 1 Then sb.AppendLine(botCreateCategory)
sb.AppendLine()
sb.AppendLine()
sb.AppendLine(getStubs(ancestor, images.Count))
Return sb.ToString
End Function
Function getStubs(ancestor As List(Of taxrec), nImages As Integer) As String
' return the appropriate stub tag
Dim tax As String
Dim stub As String = ""
If ancestor(0).extinct And (isAncestor(ancestor, "arthropoda", 0) Or isAncestor(ancestor, "euarthropoda", 0)) Then Return "{{Paleo-arthropod-stub}}"
For i1 As Integer = 0 To ancestor.Count - 1
tax = LCase(ancestor(i1).taxon)
If stubs.ContainsKey(tax) Then Return stubs(tax)
Next i1
If isAncestor(ancestor, "insecta", 0) Then Return "{{Insect-stub}}"
If isAncestor(ancestor, "arthropoda", 0) Then Return "{{Arthropod-stub}}"
If isAncestor(ancestor, "animalia", 0) Then Return "{{Animal-stub}}"
Return stub
End Function
Function getWikiUsers(titleParm As String, url As String, rvlimit As String) As List(Of String)
' loads pages from wiki, 1 or more (rvlimit) revisions
' 0 is the latest iteration, spages.count-1 is the original creator
Dim parms As New Dictionary(Of String, String)
Dim r1 As HttpResponseMessage
Dim qcontent As FormUrlEncodedContent
Dim s As String
Dim jq As JObject
Dim sPages As New List(Of String)
Dim pageID As String
parms = New Dictionary(Of String, String)
parms.Add("action", "query")
parms.Add("titles", titleParm)
parms.Add("prop", "revisions")
parms.Add("rvprop", "user")
If rvlimit <> "1" And rvlimit <> "" Then
parms.Add("rvlimit", rvlimit) ' number of revisions to return
End If
parms.Add("rvslots", "*") ' format?
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(url, qcontent).Result
s = r1.Content.ReadAsStringAsync().Result
jq = JObject.Parse(s)
Try
pageID = jq.SelectToken("query.pages.*").SelectToken("pageid")
If pageID IsNot Nothing Then
For i As Integer = 0 To jq.SelectToken("query.pages.*.revisions").Count - 1
sPages.Add(jq.SelectToken("query.pages.*.revisions(" & i & ").user").ToString)
Next i
End If
Catch ex As Exception
MsgBox("json error: " & ex.Message)
Return New List(Of String)
End Try
Return sPages
End Function
Function getWikiPages(titleParm As String, url As String, rvlimit As String) As List(Of String)
' loads pages from wiki, 1 or more (rvlimit) revisions
' 0 is the latest iteration
Dim parms As New Dictionary(Of String, String)
Dim r1 As HttpResponseMessage
Dim qcontent As FormUrlEncodedContent
Dim s As String
Dim ssk As List(Of JToken)
Dim jq As JObject
Dim sPages As New List(Of String)
Dim page As String
Dim pageID As String
If titleParm = "" Then Return New List(Of String)
parms = New Dictionary(Of String, String)
parms.Add("action", "query")
parms.Add("titles", titleParm)
parms.Add("prop", "revisions")
parms.Add("rvprop", "content")
If rvlimit <> "1" And rvlimit <> "" Then
parms.Add("rvlimit", rvlimit) ' number of revisions to return
End If
parms.Add("rvslots", "*") ' format?
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(url, qcontent).Result
s = r1.Content.ReadAsStringAsync().Result
jq = JObject.Parse(s)
Try
pageID = jq.SelectToken("query.pages.*").SelectToken("pageid")
If pageID IsNot Nothing Then
For i As Integer = 0 To jq.SelectToken("query.pages.*.revisions").Count - 1
Try
ssk = jq.SelectToken("query.pages.*.revisions(" & i & ").slots.main").ToList
If ssk.Count >= 3 Then
page = ssk(2)
sPages.Add(page)
End If
Catch ex As Exception
outLog("error reading " & titleParm & ", page " & i + 1 & ", " & ex.Message)
End Try
Next i
End If
Catch ex As Exception
MsgBox("json error: " & ex.Message)
Return New List(Of String)
End Try
Return sPages
End Function
Sub updatePageID(m As taxrec, pageID As String)
' save the wikipediapageid to the database. The ID is not used at the moment, just non-zero shows a wikipage exists
Dim k As Integer
If Not IsNumeric(pageID) OrElse m.taxid = "" Then Exit Sub
k = getScalar("select count(*) from oddinfo where taxid = @parm1", m.taxid)
If k = 0 Then
k = nonQuery("insert into oddinfo (taxid, name, wikipediapageid) values (@parm1, @parm2, @parm3);",
m.taxid, m.taxon, pageID)
If k <> 1 Then Stop
Else
k = nonQuery("update oddinfo set wikipediapageid = @parm1 where taxid = @parm2", pageID, m.taxid)
If k <> 1 Then Stop
End If
End Sub
Sub updatePagesMade(m As taxrec, pageTitle As String)
Dim s1 As String
Dim k As Integer
s1 = Format(Now, "yyyy-MM-dd HH:mm:ss")
k = getScalar("select count(*) from pagesmade where taxon = @parm1", m.taxon)
If k = 0 Then
k = nonQuery("insert into pagesmade (time, pagetitle, taxon, madeby) values (@parm1, @parm2, @parm3, 'qbugbot')",
s1, pageTitle, m.taxon)
Else
k = nonQuery("update pagesmade set time=@parm1, madeby='qbugbot' where taxon = @parm2", s1, m.taxon)
End If
If k <> 1 Then outLog("Database error, inserting into pagesmade")
End Sub
Sub getwikipics(m As taxrec, ByRef images As List(Of String), ByRef captions As List(Of String),
ByRef uprights As List(Of String), dbAllowed As Integer)
' returns a list of images for a single taxon
Dim ds As New DataSet
ds = getDS("select * from wikipics where wikipics.taxon = @parm1", m.taxon)
For Each dr As DataRow In ds.Tables(0).Rows
If (dr("taxon") <> m.taxon) AndAlso dr("taxon") <> "" AndAlso m.taxon <> "" Then ' Stop
End If
images.Add(dr("wikititle"))
If eqstr(m.rank, "species") OrElse eqstr(m.rank, "genus") OrElse eqstr(m.rank, "subspecies") Then
captions.Add("''" & m.taxon & "''")
Else
captions.Add(m.taxon)
End If
uprights.Add(dr("upright")) ' upright parameter for aspect ratio
Next dr
End Sub
Function checktaxtemplate(ancestor As List(Of taxrec), pagesmade As List(Of String), pageTitle As String) As List(Of String)
' generate taxonomy templates for the ancestors that are missing.
' returns a string of all generated templates
Dim pageID As Integer
Dim template As String
Dim s As String
Dim k As Integer
Dim topEmpty As Integer
Dim lastTaxon As String
Dim pages As List(Of String)
Dim s1 As String
Dim m As taxrec
Dim upperRank As String = ""
Dim upperTax As String = ""
pages = New List(Of String)
topEmpty = ancestor.Count - 2
lastTaxon = ancestor(topEmpty + 1).taxon
' start at the bottom and find the last missing rank
For i1 As Integer = 0 To ancestor.Count - 2 ' skip topmost rank
lastTaxon = ancestor(i1).taxon
If itisRankID(ancestor(i1).rank) > 60 AndAlso itisRankID(ancestor(i1).rank) < 220 Then
' rank is lower than class and >= genus.
If ancestor(i1).taxid <> "" Then
s = getScalar("select taxtemplateid from oddinfo where taxid = @parm1;", ancestor(i1).taxid)
Else
s = ""
End If
If IsNumeric(s) Then pageID = s Else pageID = 0
s1 = getTaxAmbig(ancestor(i1).taxon)
If pageID = 0 Then pageID = getPageID("Template:Taxonomy/" & s1, urlWikiPedia)
'If itisRankID(ancestor(i1).rank) >= 100 Then pageID = 0 ' for debugging!
If pageID > 0 Then
topEmpty = i1 - 1
lastTaxon = ancestor(i1).taxon
Exit For
End If
End If
Next i1
k = getTaxFam(ancestor, topEmpty + 1, upperRank, upperTax)
If k = 0 Then outLog("Ancestor not in tax template for " & lastTaxon & ", " & upperRank & " " & upperTax)
For i1 As Integer = topEmpty To 0 Step -1
If itisRankID(ancestor(i1).rank) > 60 AndAlso itisRankID(ancestor(i1).rank) < 220 Then
' rank is lower than class and >= genus.
If ancestor(i1).taxid <> "" Then
s = getScalar("select taxtemplateid from oddinfo where taxid = @parm1;", ancestor(i1).taxid)
Else
s = ""
End If
If IsNumeric(s) Then pageID = s Else pageID = 0
'If itisRankID(ancestor(i1).rank) >= 100 Then pageID = 0 ' for debugging!
If pageID <= 0 Then
s1 = getTaxAmbig(ancestor(i1).taxon)
template = "template:Taxonomy/" & s1
If pagesmade.IndexOf(template) < 0 Then
pageID = getPageID(template, urlWikiPedia)
'If itisRankID(ancestor(i1).rank) >= 100 Then pageID = 0 ' for debugging!
If pageID = 0 Then
m = ancestor(i1)
taxrecAddon(m)
If i1 = 0 AndAlso m.ambigLink = "" And pageTitle.Contains("(") Then m.ambigLink = pageTitle ' read from taxlist.txt
If ancestor(i1).itistsn > 0 OrElse ancestor(i1).catLifeID <> "" OrElse (ancestor(i1).gbifID <> "" And ancestor(i1).gbifID <> "0") OrElse
ancestor(i1).spiderlink <> "" OrElse (ancestor(i1).taxid <> "") Then
s = createTaxTemplate(m, lastTaxon)
If s <> "" Then
pages.Add(template)
pages.Add(s)
End If
outLog("created " & template)
pagesmade.Add(template)
End If
Else ' save an internet call next time
If ancestor(i1).taxid <> "" Then
k = getScalar("select count(*) from oddinfo where taxid = @parm1", ancestor(i1).taxid)
If k > 0 Then ' update oddinfo record
k = nonQuery("update oddinfo set taxtemplateid = @parm1 where taxid = @parm2;",
pageID, ancestor(i1).taxid)
If k <> 1 Then Stop
Else ' insert record into oddinfo
k = nonQuery("insert into oddinfo (taxid, name, taxtemplateid) values (@parm1, @parm2, @parm3)",
ancestor(i1).taxid, ancestor(i1).taxon, pageID)
If k <> 1 Then Stop
End If
End If
End If
End If
End If
End If
lastTaxon = ancestor(i1).taxon
Next i1
Return pages
End Function
Function getTaxFam(anc As List(Of taxrec), taxStart As Integer, ByRef taxRank As String, ByRef taxTaxon As String) As Boolean
' determines whether the taxobox will conflict with article text in " in the family 'taxTaxon' " (formatancestor)
Dim ancTax As String
Dim taxPage As String = ""
Dim taxTitle As String = ""
Dim rank As String = ""
Dim parent As String = ""
Dim rm As RegularExpressions.Match
Dim iCount As Integer
' get family, order, or class of the taxonomy templates in ancestor
ancTax = ""
taxTaxon = ""
taxRank = ""
parent = anc(taxStart).taxon
' select family, order, or class
For i1 As Integer = 1 To anc.Count - 1
Select Case LCase(anc(i1).rank)
Case "family"
taxRank = "family"
ancTax = anc(i1).taxon
Exit For
Case "order"
taxRank = "order"
ancTax = anc(i1).taxon
Exit For
Case "class"
taxRank = "class"
ancTax = anc(i1).taxon
Exit For
End Select
Next i1
If ancTax = "" Then Return False
iCount = 0
Do While iCount = 0 Or
(parent <> "" AndAlso (Not itisRankID.ContainsKey(rank) OrElse itisRankID(taxRank) < itisRankID(rank)) And iCount < 50)
taxTitle = parent
taxPage = getWikiPage("Template:taxonomy/" & taxTitle, urlWikiPedia)
rm = Regex.Match(taxPage, "\| *?rank *?= *?([a-zA-Z]+?)[^a-zA-Z]")
If rm.Groups.Count = 2 Then rank = rm.Groups(1).Value
rm = Regex.Match(taxPage, "\| *?parent *?= *?([a-zA-Z]+?)[^a-zA-Z]")
If rm.Groups.Count = 2 Then parent = rm.Groups(1).Value
iCount += 1
Loop
If itisRankID.ContainsKey(rank) AndAlso itisRankID(taxRank) > itisRankID(rank) Then
Return True ' skipped taxRank, let it go
End If
If eqstr(rank, latinRank(taxRank)) Then
taxTaxon = taxTitle
Return eqstr(taxTaxon, ancTax)
Else
taxTaxon = ""
Return False
End If
End Function
Sub makePage(m As taxrec, dbRequired As Integer, dbAllowed As Integer, pageTitle As String,
templateOnly As Boolean, sendingMode As Integer, alteration As String)
' makes a wikipedia page, and ancestor pages as needed.
' handles overhead and calls wikipiaentry and wikipedialist.
' sendingmode 2 = update, 1 = create, 0 = don't send
Dim s, s1, s2 As String
Dim k As Integer
Dim ancestor As List(Of taxrec) = Nothing
Dim taxAncestor As List(Of taxrec) = Nothing
Dim images As New List(Of String)
Dim captions As New List(Of String)
Dim uprights As New List(Of String)
Dim children As New List(Of taxrec)
Dim sp As New List(Of String)
Dim sTalk As String
Dim inPages As List(Of String)
Dim bugname As String
Dim monoType As Boolean
Dim mp As taxrec
Dim showSource As Boolean = False
getwikipics(m, images, captions, uprights, dbAllowed)
s = validTaxon(m, dbRequired)
If s <> "" Then
If LCase(s).Contains("itis") AndAlso images.Count > 0 Then
outLog("No itis, but imagecount = " & images.Count & ". " & m.taxon)
Exit Sub ' remove to relax itis restriction for pages with images
Else
outLog("invalid taxon: " & m.taxon & ", " & s)
Exit Sub
End If
End If
ancestor = getancestors(m, dbAllowed, True, "phylum")
children = allDescendants(m, getLowerRank(m.rank), dbAllowed) ' get children
bugname = m.taxon ' for edit summary
If eqstr(m.rank, "species") OrElse eqstr(m.rank, "genus") OrElse eqstr(m.rank, "subspecies") Then
bugname = "''" & bugname & "''"
End If
If itisRankID(m.rank) >= 100 Then ' get pics if rank is order through but not including species
' get descendant images for upper taxons
For Each m3 As taxrec In children
getwikipics(m3, images, captions, uprights, dbAllowed)
Next m3
If images.Count > 2 Then
images = {images(0), images(images.Count - 1)}.ToList ' get first and last image if there are several
captions = {captions(0), captions(captions.Count - 1)}.ToList ' get first and last image if there are several
uprights = {uprights(0), uprights(uprights.Count - 1)}.ToList ' get first and last image if there are several
End If
End If
' sTalk is the project name for the stub notice on the talk page.
If isAncestor(ancestor, "lepidoptera", 0) Then
sTalk = "Lepidoptera"
ElseIf isAncestor(ancestor, "coleoptera", 0) Then
sTalk = "Beetles"
ElseIf isAncestor(ancestor, "formicidae", 0) Then
sTalk = "Insects|ants=yes"
ElseIf isAncestor(ancestor, "hymenoptera", 0) Then
sTalk = "Insects|Hymenoptera=yes|Hymenoptera-importance=low"
ElseIf isAncestor(ancestor, "insecta", 0) Then
sTalk = "Insects"
ElseIf isAncestor(ancestor, "Araneae", 0) Then
sTalk = "Spiders"
ElseIf isAncestor(ancestor, "Arthropoda", 0) Then
sTalk = "Arthropods"
ElseIf isAncestor(ancestor, "Amphibia", 0) Then
sTalk = "Amphibians and Reptiles"
ElseIf isAncestor(ancestor, "Reptilia", 0) Then
sTalk = "Amphibians and Reptiles"
ElseIf isAncestor(ancestor, "Animalia", 0) Then
sTalk = "Animals"
ElseIf isAncestor(ancestor, "Aves", 0) Then
sTalk = "Birds"
ElseIf isAncestor(ancestor, "Bivalvia", 0) Then
sTalk = "Bivalves"
ElseIf isAncestor(ancestor, "Felidae", 0) Then
sTalk = "Cats"
ElseIf isAncestor(ancestor, "Cephalopoda", 0) Then
sTalk = "Cephalopods"
ElseIf isAncestor(ancestor, "Cetacea", 0) Then
sTalk = "Cetaceans"
ElseIf isAncestor(ancestor, "Dinosauria", 0) Then
sTalk = "Dinosaurs"
ElseIf isAncestor(ancestor, "Canis", 0) Then
sTalk = "Dogs"
ElseIf isAncestor(ancestor, "Agnatha", 0) Then
sTalk = "Fishes"
ElseIf isAncestor(ancestor, "Chondrichthyes", 0) Then
sTalk = "Fishes"
ElseIf isAncestor(ancestor, "Osteichthyes", 0) Then
sTalk = "Fishes"
ElseIf isAncestor(ancestor, "Gastropoda", 0) Then
sTalk = "Gastropods"
ElseIf isAncestor(ancestor, "Mammalia", 0) Then
sTalk = "Mammals"
ElseIf isAncestor(ancestor, "Plantae", 0) Then
sTalk = "Plants"
ElseIf isAncestor(ancestor, "Primates", 0) Then
sTalk = "Primates"
ElseIf isAncestor(ancestor, "Rodentia", 0) Then
sTalk = "Rodents"
ElseIf isAncestor(ancestor, "Selachimorpha", 0) Then
sTalk = "Sharks"
ElseIf isAncestor(ancestor, "Testudines", 0) Then
sTalk = "Turtles"
Else
sTalk = "Animals"
End If
sTalk = "{{WikiProject " & sTalk & "|class=stub|importance=low}}" & vbCrLf
If m.extinct Then sTalk &= "{{WikiProject Palaeontology|class=stub|importance=low}}" & vbCrLf
If sendingMode = 1 Then
sTalk &= vbCrLf & botCreateMessage & vbCrLf ' create page
k = getPageID(pageTitle, urlWikiPedia)
If k > 0 Then outLog("page exists: " & m.taxon) Else Stop
End If
If k <= 0 Or sendingMode <> 1 Then ' make the pages sendingmode 2 = update, 1 = create, 0 = don't send
taxAncestor = getancestors(ancestor(0), 27, True, "phylum") ' allow itis, catlife, etc. for the templates
sp = checktaxtemplate(taxAncestor, pagesMade, pageTitle)
For i1 As Integer = 0 To sp.Count - 1 Step 2
madePage.Append("=================" & sp(i1) & "======================" & vbCrLf) ' title
madePage.Append(sp(i1 + 1) & vbCrLf & vbCrLf & vbCrLf) ' content
If sendingMode <> 0 And nPagesSent < maxPagesSent Then ' update or create
s2 = "Created " & sp(i1)
sendWikiPage(sp(i1), sp(i1 + 1), urlWikiPedia, s2, 1) ' sendingmode: create only for templates
End If
Next i1
If Not templateOnly Then
madePage.Append("=================" & pageTitle & "======================" & vbCrLf)
s = WikiPediaEntry(m, images, captions, uprights, children, ancestor, showSource, dbAllowed, sendingMode)
madePage.Append(s)
'If images.Count = 0 Then sTalk = sTalk.Replace("}}", "|needs-photo=yes}}")
If s <> "" Then
If sendingMode <> 0 And nPagesSent < maxPagesSent Then
If sendingMode = 2 Then s2 = alteration Else s2 = "Created page for the " & LCase(m.rank) & " " & bugname
s = sendWikiPage(pageTitle, s, urlWikiPedia, s2, sendingMode)
If IsNumeric(s) Then
updatePageID(m, s) ' mark as "page exists" in database
updatePagesMade(m, pageTitle) ' update pagesmade database
End If
addTalkPage(sendingMode, pageTitle, sTalk, "Created talk page: stub class, low importance")
nPagesSent += 1
appendPageTitle(pageTitle)
If nPagesSent >= maxPagesSent Then outLog("Pages sent: " & nPagesSent & ", max: " & maxPagesSent)
End If
End If
madePage.Append(vbCrLf & vbCrLf & sTalk)
outLog("saved page: " & m.taxon)
If children.Count >= maxlist And sendingMode <> 2 Then ' create a list page
s = WikiPedialist(m, children, ancestor, showSource, dbAllowed, sendingMode) ' make a list page for the children
sTalk = sTalk.Replace("|class=stub", "|class=list")
'sTalk = sTalk.Replace("|needs-photo=yes}}", "}}")
madePage.Append("=======================================" & vbCrLf)
madePage.Append(s)
madePage.Append(vbCrLf & vbCrLf & sTalk)
outLog("saved page: " & m.taxon & " list page")
s2 = getListPageName(m, children) ' to be consistent with link in main page
If sendingMode <> 0 And nPagesSent < maxPagesSent Then
s1 = sendWikiPage(s2, s, urlWikiPedia, "Created list page for the " & LCase(m.rank) & " " & bugname, sendingMode)
If IsNumeric(s1) Then
updatePagesMade(m, s2)
addTalkPage(sendingMode, s2, sTalk, "Created talk page: list class, low importance")
End If
nPagesSent += 1
appendPageTitle(s2)
If nPagesSent >= maxPagesSent Then outLog("Pages sent: " & nPagesSent & ", max: " & maxPagesSent)
End If
End If
pagesMade.Add(m.taxon)
End If
End If
'End If
If Not templateOnly Then
' crawl up the ancestors and make missing pages, (creation only)
If sendingMode = 1 Then
For i1 As Integer = 1 To ancestor.Count - 1
mp = ancestor(i1)
If mp.unimportant = 0 AndAlso pagesMade.IndexOf(mp.taxon) < 0 Then
If mp.taxid <> "" Then
k = getScalar("select count(*) from oddinfo where wikipediapageid > 0 and taxid = @parm1", mp.taxid)
Else
k = 0
End If
If k <= 0 Then ' no wikipedia id in database
s1 = getDisambig(mp)
If s1 = "" Then s1 = mp.taxon
k = getPageID(s1, urlWikiPedia) ' not on wikipedia
If k = 0 Then
makePage(mp, dbRequired, dbAllowed, s1, templateOnly, sendingMode, "") ' make an ancestor page
End If
End If
End If
Next i1
End If
If Not monoType Then
'If sendingMode Then ' check for orphans
inPages = orphanCheck(pageTitle)
If inPages.Count = 0 Then
outLog("orphan: " & pageTitle)
If sendingMode <> 0 Then appendPageTitle("orphan" & vbTab & ancestor(1).taxon)
Else
' see if it's an orphan except for child's link
k = 0
For i1 As Integer = 0 To children.Count - 1
If inPages.IndexOf(children(i1).taxon) >= 0 Then k += 1
Next i1
If k >= inPages.Count Then
outLog("orphan almost: " & pageTitle)
If sendingMode <> 0 Then appendPageTitle("orphan" & vbTab & ancestor(1).taxon & vbTab & ancestor(2).taxon)
End If
End If
End If
End If
End Sub
Sub addTalkPage(sendingMode As Integer, pageTitle As String, sTalk As String, logMessage As String)
Dim s As String
If sendingMode = 1 Then ' create
s = sendWikiPage("Talk:" & pageTitle, sTalk, urlWikiPedia, logMessage, sendingMode)
ElseIf sendingMode = 2 Then ' update
s = getWikiPage("Talk:" & pageTitle, urlWikiPedia)
If Not s.ToLower.Contains("{{wikiproject") Then
If s = "" Then
s = sTalk
Else
s = s.Trim & vbCrLf & vbCrLf & sTalk
End If
s = sendWikiPage("Talk:" & pageTitle, s, urlWikiPedia, logMessage, sendingMode)
End If
End If
End Sub
Sub loadTaxList()
' reads a list of titles from taxlist file and makes pages for all the items, even if they've been done before.
Dim i1 As Integer
Dim s1 As String
Dim ds As DataSet
Dim m, m2 As New taxrec
Dim ss As List(Of String)
Dim pageTitle As String
Dim dbRequired, dbAllowed As Integer
Dim templateOnly As Boolean
Dim result As MsgBoxResult
Dim sendingMode As Integer
File.WriteAllText(outFile, "")
madePage = New StringBuilder
ss = New List(Of String)
ss = File.ReadAllLines(My.Settings.taxlist).ToList
dbRequired = 0 ' 1 = taxa, 2 = itis, 4 = catlife, 8 = gbif, 16 = spidercat(andable)
'dbAllowed = 31 ' allowed: all (taxa=1, itis=2, catlife = 4, gbif = 8, 16 = spidercat) for ancestors and children
'dbAllowed = 29 ' allowed: not itis (taxa=1, itis=2, catlife = 4, gbif = 8, 16 = spidercat) for ancestors and children
'dbAllowed = 27 ' allowed: not catlife (taxa=1, itis=2, catlife = 4, gbif = 8, 16 = spidercat) for ancestors and children
dbAllowed = 27 ' allowed: (taxa=1, itis=2, catlife = 4, gbif = 8, 16 = spidercat) for ancestors and children
templateOnly = False
sendingMode = 0
nPagesSent = 0
maxPagesSent = 20
If sendingMode <> 0 Then
result = MsgBox("Send Pages?", MsgBoxStyle.YesNoCancel)
If result <> MsgBoxResult.Yes Then
Me.Cursor = Cursors.Default
Exit Sub
End If
s1 = qlogin(urlWikiPedia)
sToken = gettoken(urlWikiPedia)
End If
pagesMade = New List(Of String)
'pagesToMake = New List(Of String)
For Each rec As String In ss
rec = rec.Trim
rec = rec.Replace(Chr(&HE2) & Chr(&H80) & Chr(&H8E), "")
rec = rec.Replace(Chr(&HE2), "")
rec = rec.Replace(Chr(&H80), "")
rec = rec.Replace(Chr(&H8E), "")
' get disambig pagetitle if it's in the file.
i1 = rec.IndexOf("(")
If i1 >= 0 Then
pageTitle = rec
rec = rec.Substring(0, i1)
Else
pageTitle = ""
End If
If rec.Trim <> "" Then
If rec.StartsWith("---") Then Exit For
m = loadMatch(rec, True)
If eqstr(m.taxon, rec) Then ' leaves out species single words
If pageTitle = "" Then pageTitle = getDisambig(m)
If pageTitle = "" Then pageTitle = m.taxon
makePage(m, dbRequired, dbAllowed, pageTitle, templateOnly, sendingMode, "") ' change to true to make a page that has a wikipediapageid, true to require itis
Else
outLog("not in taxa database: " & rec)
ds = getDS("select * from itis.taxonomic_units where complete_name = @parm1 and name_usage = 'valid';", rec)
If ds.Tables(0).Rows.Count > 0 Then
For Each dr As DataRow In ds.Tables(0).Rows
m = getItisTaxrec(dr, True)
If pageTitle = "" Then pageTitle = getDisambig(m)
If pageTitle = "" Then pageTitle = m.taxon
makePage(m, dbRequired, dbAllowed, pageTitle, templateOnly, sendingMode, "") ' change to true to make a page that has a wikipediapageid, true to require itis
Next dr
Else
ds = getDS("select * from gbif.tax where name = @parm1 and usable <> ''", rec)
If ds.Tables(0).Rows.Count > 0 Then
For Each dr As DataRow In ds.Tables(0).Rows
m = getTaxrecg(dr, True)
If pageTitle = "" Then pageTitle = getDisambig(m)
If pageTitle = "" Then pageTitle = m.taxon
makePage(m, dbRequired, dbAllowed, pageTitle, templateOnly, sendingMode, "") ' change to true to make a page that has a wikipediapageid, true to require itis
Next dr
Else
ds = getDS("select * from catlife.tax where name = @parm1 and namestatus = 'accepted name';", rec)
If ds.Tables(0).Rows.Count > 0 Then
For Each dr As DataRow In ds.Tables(0).Rows
m = getCatLifeTaxrec(dr, True)
If pageTitle = "" Then pageTitle = getDisambig(m)
If pageTitle = "" Then pageTitle = m.taxon
makePage(m, dbRequired, dbAllowed, pageTitle, templateOnly, sendingMode, "") ' change to true to make a page that has a wikipediapageid, true to require itis
Next dr
Else
ds = getDS("select * from spidercat where name = @parm1;", rec)
If ds.Tables(0).Rows.Count > 0 Then
For Each dr As DataRow In ds.Tables(0).Rows
m = getspiderTaxrec(dr, True)
If pageTitle = "" Then pageTitle = getDisambig(m)
If pageTitle = "" Then pageTitle = m.taxon
makePage(m, dbRequired, dbAllowed, pageTitle, templateOnly, sendingMode, "") ' change to true to make a page that has a wikipediapageid, true to require itis
Next dr
End If
End If
End If
End If
End If
End If
File.AppendAllText(outFile, madePage.ToString)
madePage = New StringBuilder
Next rec
madePage.Append("=======================================" & vbCrLf)
File.AppendAllText(outFile, madePage.ToString)
madePage = New StringBuilder
End Sub
Private Sub cmdList_Click(sender As Object, e As EventArgs) Handles cmdList.Click
' make wikipedia pages from a list of taxa.
Me.Cursor = Cursors.WaitCursor
loadTaxList()
Me.Cursor = Cursors.Default
End Sub
Private Sub cmdRandom_Click(sender As Object, e As EventArgs) Handles cmdRandom.Click
' generate a set of pages selected over the database randomly.
' it doesn't seem very random, but that's not important.
Dim ds As DataSet
Dim dr As DataRow
Dim m, m2 As New taxrec
Dim s As String
Dim i As Integer
Dim nPages As Integer
Dim dbRequired, dbAllowed As Integer
Dim templateOnly As Boolean
Dim result As MsgBoxResult
Dim sendingMode As Integer
Me.Cursor = Cursors.WaitCursor
File.WriteAllText(outFile, "")
madePage = New StringBuilder
pagesMade = New List(Of String)
dbRequired = 3 ' requires itis and taxa for initial page
dbAllowed = 27 ' allows taxa, itis, and catlife (taxa=1, itis=2, catlife = 4, gbif = 8, spidercat = 16) for ancestors and children
templateOnly = False
sendingMode = 0
Rnd(-1) : Randomize(1) ' repeatable sequence of randoms. Increment randomize parameter for new set
nPagesSent = 0
maxPagesSent = 3
nPages = maxPagesSent * 1.5 ' number from database (some will be excluded)
If sendingMode <> 0 Then
result = MsgBox("Send Pages?", MsgBoxStyle.YesNoCancel)
If result <> MsgBoxResult.Yes Then
Me.Cursor = Cursors.Default
Exit Sub
End If
qlogout(urlWikiPedia)
s = qlogin(urlWikiPedia)
If s <> "Success" Then
MsgBox("login failure")
Me.Cursor = Cursors.Default
Exit Sub
End If
sToken = gettoken(urlWikiPedia)
appendPageTitle("")
End If
ds = getDS("select * from taxatable where rank = 'species';")
For i1 As Integer = 0 To ds.Tables(0).Rows.Count - 1
' i = i1 for finish
i = Rnd() * ds.Tables(0).Rows.Count
dr = ds.Tables(0).Rows(i)
m = getTaxrec(dr, True)
makePage(m, dbRequired, dbAllowed, m.taxon, templateOnly, sendingMode, "") ' m, make existing pages, itis required
File.AppendAllText(outFile, madePage.ToString)
madePage = New StringBuilder
If nPagesSent >= maxPagesSent Then Exit For
Next i1
madePage.Append("=======================================" & vbCrLf)
File.AppendAllText(outFile, madePage.ToString)
madePage = New StringBuilder
Me.Cursor = Cursors.Default
End Sub
Function readrefs(rec As String) As List(Of refrec)
' gets the {{cite...}} references from the string rec and returns a list of refrecs
Dim rm As RegularExpressions.MatchCollection
Dim s As String
Dim sq() As String
Dim sv() As String
Dim ref As New refrec
Dim refs As New List(Of refrec)
rm = Regex.Matches(rec, "\{\{(.+?)\}\}", RegexOptions.Singleline Or RegexOptions.IgnoreCase)
For Each r As RegularExpressions.Match In rm
If r.Groups.Count > 1 Then
s = r.Groups(1).ToString
s = Regex.Replace(s, "(\[\[[^\]]+?)\|(.+?\]\])", "$1~~$2") ' change | inside wikilinks to ~~ temporarily
sq = s.Split("|")
If sq.Count >= 2 AndAlso s.Contains("=") Then
ref = New refrec
ref.pubtype = sq(0).Trim.Split(" ")(1)
For i As Integer = 1 To sq.Count - 1 ' skip first
sq(i) = sq(i).Replace("~~", "|")
sv = sq(i).Split("=")
sv(0) = LCase(sv(0).Trim)
sv(1) = sv(1).Trim
Select Case sv(0)
Case "title"
ref.title = sv(1)
Case "year"
ref.year = sv(1)
Case "date"
ref.year = sv(1)
Case "url"
ref.url = sv(1)
Case "series"
ref.series = sv(1)
Case "journal"
ref.journal = sv(1)
Case "volume"
ref.volume = sv(1)
Case "issue"
ref.issue = sv(1)
Case "chapter"
ref.chapter = sv(1)
Case "publisher"
ref.publisher = sv(1)
Case "pages", "page"
ref.pages = sv(1)
Case "isbn"
ref.isbn = sv(1)
Case "issn"
ref.issn = sv(1)
Case "doi"
ref.doi = sv(1)
Case "doi-access"
ref.doiaccess = sv(1)
Case "etc"
ref.etc = sv(1)
Case "comment"
ref.comment = sv(1)
Case "accessdate"
Case "displayauthors"
End Select
If sv(0).StartsWith("first") Then
If ref.afirst = "" Then ref.afirst = sv(1) Else ref.afirst &= "|" & sv(1)
End If
If sv(0).StartsWith("last") Then
If ref.alast = "" Then ref.alast = sv(1) Else ref.alast &= "|" & sv(1)
End If
If sv(0).StartsWith("editor") AndAlso sv(0).EndsWith("first") Then
If ref.efirst = "" Then ref.efirst = sv(1) Else ref.efirst &= "|" & sv(1)
End If
If sv(0).StartsWith("editor") AndAlso sv(0).EndsWith("last") Then
If ref.elast = "" Then ref.elast = sv(1) Else ref.elast &= "|" & sv(1)
End If
Next i
refs.Add(ref)
End If
End If
Next r
Return refs
End Function
Function crlf(source) As String
' convert lf to crlf
Dim page As String
page = source
page = page.Replace(vbCrLf, "~^~")
page = page.Replace(vbLf, "~^~")
page = page.Replace(vbCr, vbCrLf)
page = page.Replace("~^~", vbCrLf)
Return page
End Function
Function updatePage(tax As String, title As String, ByRef alteration As String) As String
' updates a page previously made by this bot
' alteration tells what changes were made for the wikipedia watchlist
Dim sPages As List(Of String)
Dim sUsers As List(Of String)
Dim original, current, page As String
Dim s, pageTitle As String
If title <> "" Then pageTitle = title Else pageTitle = tax
madePage = New StringBuilder
sPages = getWikiPages(title, urlWikiPedia, "max")
If sPages.Count > 0 Then
sUsers = getWikiUsers(title, urlWikiPedia, "max")
If sUsers.Count > 0 AndAlso eqstr(sUsers(sUsers.Count - 1), "qbugbot") Then ' only update pages created by qbugbot
original = crlf(sPages(sPages.Count - 1))
current = crlf(sPages(0))
page = current
s = botban(page, "qbugbot")
If s <> "" Then
outLog(tax & " - bot ban: " & s)
Return ""
End If
alteration = ""
s = current
page = checkTaxobox(tax, original, s)
If s <> page Then
If s.Contains("Speciesbox") Then alteration &= "speciesbox, " Else alteration &= "taxobox, "
s = page
End If
page = checkText(tax, original, s)
If s <> page Then
alteration &= "introduction/references, "
s = page
End If
page = refReplace(tax, original, s, "Further reading", "External links")
If s <> page Then
alteration &= "further reading, "
s = page
End If
page = addPhotos(tax, original, s)
If s <> page Then
alteration &= "photos, "
s = page
End If
page = removeTags(tax, s)
If s <> page Then
alteration &= "removed tags, "
s = page
End If
page = addcommons(tax, s)
If s <> page Then alteration &= "external links, "
If alteration.EndsWith(", ") Then alteration = alteration.Substring(0, alteration.Length - 2)
' fix faulty line spacing
page = Regex.Replace(page, "(\r\n)*\{\{Taxonbar", vbCrLf & vbCrLf & "{{Taxonbar")
page = Regex.Replace(page, "(\r\n)+==", vbCrLf & vbCrLf & "==")
page = page.Trim
If page = current.Trim Then
outLog(tax & " - no change: " & pageTitle)
alteration = ""
Return ""
Else
If alteration = "" Then Return ""
Return page
End If
End If
Else
outLog(tax & " - missing page or creator: " & pageTitle)
Return ""
End If
Return ""
End Function
Function addcommons(tax As String, page As String) As String
' add a commons-inline in external links
Dim i As Integer
If Regex.Match(page, "\{\{ *commons", RegexOptions.IgnoreCase).ToString = "" Then ' commons not already there
If Regex.Match(page, "\| *image *=", RegexOptions.IgnoreCase).ToString <> "" Or
Regex.Match(page, "\[\[ *file:", RegexOptions.IgnoreCase).ToString <> "" Then
i = LCase(page).IndexOf(vbCrLf & "{{taxonbar")
If i < 0 Then i = LCase(page).IndexOf(vbLf & "{{taxonbar")
If i >= 0 Then page = page.Substring(0, i) & vbCrLf & vbCrLf &
"==External links==" & vbCrLf &
"{{refbegin}}" & vbCrLf &
"* {{Commons category-inline|" & tax & "}}" & vbCrLf &
"{{refend}}" & vbCrLf &
page.Substring(i)
End If
End If
Return page
End Function
Function botban(page As String, botname As String) As String
' check and see if the bot is banned, return "" if it's OK.
'{{nobots}} Ban all compliant bots (shortcut)
'{{bots}} Allow all bots (shortcut)
'{{bots|allow=<botlist>}} Ban all compliant bots not in the list
'{{bots|deny=<botlist>}} Ban all compliant bots in the list
'{{bots|allow=SineBot,Legobot}}
'{{bots|allow=all}} Allow all bots
'{{bots|allow=none}} Ban all compliant bots
'{{bots|deny=all}} Ban all compliant bots
'{{bots|deny=none}}
Dim rbot As RegularExpressions.Match
Dim sq As New List(Of String)
Dim s As String
If Regex.Match(page, "\{\{ *nobots *\}\}", RegexOptions.IgnoreCase).Value <> "" Then Return "nobots"
rbot = Regex.Match(page, "(\{\{bots[ " & vbCrLf & "]*\|[ " & vbCrLf & "]*([a-z]+?)[ " &
vbCrLf & "]*=(([ " & vbCrLf & "]*,?[ " & vbCrLf & "]*[a-z]+?)*)[ " & vbCrLf & "]*\}\})",
RegexOptions.Singleline Or RegexOptions.IgnoreCase)
If rbot.Groups.Count >= 4 Then
s = rbot.Groups(3).Value ' comma separated botlist
sq = s.Split(",".ToCharArray, StringSplitOptions.RemoveEmptyEntries).ToList
For i1 As Integer = 0 To sq.Count - 1 : sq(i1) = LCase(sq(i1)).Trim : Next i1
If eqstr(rbot.Groups(2).Value.Trim, "deny") AndAlso
(sq.IndexOf(botname) >= 0 Or sq.IndexOf("all") >= 0) Then Return "denied"
If eqstr(rbot.Groups(2).Value.Trim, "allow") AndAlso
(sq.IndexOf(botname) < 0 Or sq.IndexOf("none") >= 0) Then Return "not allowed"
End If
Return ""
End Function
Function checkTaxobox(tax As String, original As String, current As String) As String
' update taxobox if it hasn't changed, but leave the original image
Dim s, s1 As String
Dim rMatch As RegularExpressions.Match
Dim m As taxrec
Dim page As String
Dim tx, oldtx, newtx As String
Dim search As String
Dim pageTitle As String
Dim dbAllowed, dbRequired As Integer
Dim newimage, tximage, imgsearch As String
page = current
search = "^(.+?\}\})[" & vbLf & vbCr & "]+?('{3,5}" & tax & ")" ' page start to end of taxobox
'search = "(\}\}[" & vbLf & vbCr & "]+?('{3,5}" & tax & ".+?)==Further)"
rMatch = Regex.Match(original, search, RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' get intro text through references in a string
If rMatch.Groups.Count = 3 Then
oldtx = rMatch.Groups(1).ToString
Else
Return current
End If
rMatch = Regex.Match(current, search, RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' get intro text through references in a string
If rMatch.Groups.Count = 3 Then
tx = rMatch.Groups(1).ToString
Else
Return current
End If
If tx.Replace(vbLf, "").Replace(" ", "") = oldtx.Replace(vbLf, "").Replace(" ", "") Then ' it has not been modified -- go ahead and update the text.
dbRequired = 0 ' 1 = taxa, 2 = itis, 4 = catlife, 8 = gbif, 16 = spidercat(andable)
dbAllowed = 27 ' allowed: itis and catlife (taxa=1, itis=2, catlife = 4, gbif = 8, 16 = spidercat) for ancestors and children
m = loadMatch(tax, True)
pageTitle = getDisambig(m)
If pageTitle = "" Then pageTitle = tax
If madePage.ToString = "" Then makePage(m, dbRequired, dbAllowed, pageTitle, False, 0, "")
s = madePage.ToString
rMatch = Regex.Match(s, "^===[=]+?" & tax & "[=]+?[" & vbCr & vbLf & "]{1}(.*)$", RegexOptions.Singleline Or RegexOptions.IgnoreCase)
s1 = rMatch.Groups(1).ToString
rMatch = Regex.Match(s1, search, RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' get citations in a string
If rMatch.Groups.Count = 3 Then
newtx = rMatch.Groups(1).ToString
newtx = newtx.Replace("reflist", "Reflist")
' keep the old image in the taxobox if it's there.
imgsearch = "^.+?((\| *image *=.+?)(\| *image.+?=.+?)?(\| *image.+?=.+?)?)\|"
rMatch = Regex.Match(newtx, imgsearch, RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' get image in taxobox (if any)
newimage = rMatch.Groups(1).Value
rMatch = Regex.Match(tx, imgsearch, RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' get image in taxobox (if any)
tximage = rMatch.Groups(1).Value
If tximage <> "" And newimage <> "" Then newtx = newtx.Replace(newimage, tximage)
If tx <> newtx Then page = current.Replace(tx, newtx)
End If
End If
Return page.Trim
End Function
Function checkText(tax As String, original As String, current As String) As String
Dim s, s1 As String
Dim rMatch As RegularExpressions.Match
Dim m As taxrec
Dim page As String
Dim tx, oldtx, newtx As String
Dim search As String
Dim pageTitle As String
Dim dbAllowed, dbRequired As Integer
page = current
search = "(\}\}[" & vbLf & vbCr & "]+?('{3,5}" & tax & ".+?)(==Further|==External|\{\{Taxonbar))"
'search = "(\}\}[" & vbLf & vbCr & "]+?('{3,5}" & tax & ".+?)==Further)"
rMatch = Regex.Match(original, search, RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' get intro text through references in a string
If rMatch.Groups.Count = 4 Then
oldtx = rMatch.Groups(2).ToString
oldtx = oldtx.Replace("reflist", "Reflist")
Else
Return current
End If
rMatch = Regex.Match(current, search, RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' get intro text through references in a string
If rMatch.Groups.Count = 4 Then
tx = rMatch.Groups(2).ToString
tx = tx.Replace("reflist", "Reflist")
Else
Return current
End If
If tx.Replace(vbLf, "").Replace(" ", "") = oldtx.Replace(vbLf, "").Replace(" ", "") Then ' it has not been modified -- go ahead and update the text.
dbRequired = 0 ' 1 = taxa, 2 = itis, 4 = catlife, 8 = gbif, 16 = spidercat(andable)
dbAllowed = 27 ' allowed: itis and catlife (taxa=1, itis=2, catlife = 4, gbif = 8, 16 = spidercat) for ancestors and children
m = loadMatch(tax, True)
pageTitle = getDisambig(m)
If pageTitle = "" Then pageTitle = tax
If madePage.ToString = "" Then makePage(m, dbRequired, dbAllowed, pageTitle, False, 0, "")
s = madePage.ToString
rMatch = Regex.Match(s, "^===[=]+?" & tax & "[=]+?[" & vbCr & vbLf & "]{1}(.*)$",
RegexOptions.Singleline Or RegexOptions.IgnoreCase)
s1 = rMatch.Groups(1).ToString
rMatch = Regex.Match(s1, search, RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' get citations in a string
If rMatch.Groups.Count = 4 Then
newtx = rMatch.Groups(2).ToString
If tx <> newtx Then page = current.Replace("reflist", "Reflist").Replace(tx, newtx)
End If
End If
Return page
End Function
Function addPhotos(tax As String, original As String, current As String) As String
Dim page As String
Dim ds As DataSet
Dim pic, pictax, picUpright As String
Dim dr As DataRow
page = current
If Regex.Match(page, "\| *image *=", RegexOptions.IgnoreCase).ToString <> "" Or
Regex.Match(page, "\[\[ *file:", RegexOptions.IgnoreCase).ToString <> "" Then Return current
'({{Automatic taxobox|{{Speciesbox|{{Taxobox.+?)
'\1\r\n| Image = asdf.jpg
' first one in taxobox
ds = getDS("select * from wikipics where taxon = @parm1", tax)
If ds.Tables(0).Rows.Count = 0 Then Return current
pic = ds.Tables(0).Rows(0)("wikititle")
pictax = ds.Tables(0).Rows(0)("taxon")
pic = pic.Replace("File:", "")
pic = "| image = " & pic
picUpright = ds.Tables(0).Rows(0)("upright")
If Not eqstr(tax, pictax) Then pic &= vbCrLf & "| caption = ''" & pictax & "''"
If picUpright <> "" Then pic &= vbCrLf & "| upright = " & picUpright
page = Regex.Replace(page, "({{Automatic taxobox|{{Speciesbox|{{Taxobox.+?)", "$1" & vbCrLf & pic,
RegexOptions.Singleline Or RegexOptions.IgnoreCase)
' the rest underneath taxobox
For i1 As Integer = 1 To ds.Tables(0).Rows.Count - 1
dr = ds.Tables(0).Rows(i1)
pic = dr("wikititle")
If Not pic.StartsWith("File:") Then pic = "File:" & pic
pictax = dr("taxon")
If picUpright <> "" Then picUpright = "upright |"
page = Regex.Replace(page, "((\{\{Automatic taxobox|\{\{Speciesbox|\{\{Taxobox.+?).+?(\{\{.+?\}\})+?.*\}\}" & vbCrLf & ")",
"$1" & "[[" & pic & "| thumb |''" & picUpright & pictax & "'']]" & vbCrLf,
RegexOptions.Singleline Or RegexOptions.IgnoreCase)
Next i1
Return page
End Function
Function removeTags(tax As String, current As String) As String
' remove orphan and underlink tags from current page
Dim page As String
Dim rm As RegularExpressions.Match
Dim k As Integer
Dim multi As String
page = current
page = Regex.Replace(page, "(\{\{Underlink.+?\}\})[\r\n]{0,2}", "", RegexOptions.Singleline Or RegexOptions.IgnoreCase)
page = Regex.Replace(page, "(\{\{Orphan.+?\}\})[\r\n]{0,2}", "", RegexOptions.Singleline Or RegexOptions.IgnoreCase)
multi = "(\{\{multiple issues.+?(\{\{.+?\}\})?[^\{\}]+?\}\})[\r\n]{0,2}"
rm = Regex.Match(page, multi, RegexOptions.Singleline Or RegexOptions.IgnoreCase)
k = Regex.Matches(rm.Value, "(\{\{)", RegexOptions.Singleline Or RegexOptions.IgnoreCase).Count
If k = 1 Then
page = Regex.Replace(page, multi, "", RegexOptions.Singleline Or RegexOptions.IgnoreCase)
ElseIf k = 2 Then
page = Regex.Replace(page, multi, rm.Groups(2).Value, RegexOptions.Singleline Or RegexOptions.IgnoreCase)
End If
Return page
End Function
Function refReplace(taxon As String, original As String, current As String, pubtype As String, pubtype2 As String) As String
' replace old references with new in a web page
' original is the original page as made by the bot at first
' current is the currently edited version of the page
' pubtype is "further reading", pubtype2 is "external links"
' external links gets merged with further reading and the external links section is deleted
Dim s As String
Dim refs As New List(Of refrec)
Dim oldrefs As New List(Of refrec)
Dim newrefs As New List(Of refrec)
Dim rMatch As RegularExpressions.Match
Dim ancestor As New List(Of taxrec)
Dim m As taxrec
Dim found As Integer
Dim page As String
Dim search, search2 As String
search = "(==[ ]?" & pubtype & "[ ]?==.+?refbegin\}\}(.+?)\{\{refend\}\})"
rMatch = Regex.Match(original, search, RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' get citations in a string
If rMatch.Groups.Count = 3 Then
oldrefs = readrefs(rMatch.Groups(2).ToString)
End If
' get original references in oldrefs
If pubtype2 <> "" Then ' count external links as further reading, add to oldrefs
search2 = search.Replace(pubtype, pubtype2)
rMatch = Regex.Match(original, search2, RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' get old citations in a string
If rMatch.Groups.Count = 3 Then
oldrefs.AddRange(readrefs(rMatch.Groups(2).ToString))
End If
End If
' get current references in refs
rMatch = Regex.Match(current, search, RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' get current citations in a string
If rMatch.Groups.Count = 3 Then
refs = readrefs(rMatch.Groups(2).ToString)
End If
' add any current external links to refs
If pubtype2 <> "" Then ' count external links as further reading, add to current refs
search2 = search.Replace(pubtype, pubtype2)
rMatch = Regex.Match(current, search2, RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' get citations in a string
If rMatch IsNot Nothing AndAlso rMatch.Groups.Count = 3 Then
refs.AddRange(readrefs(rMatch.Groups(2).ToString))
End If
End If
m = loadMatch(taxon, True)
ancestor = getancestors(m, 27, True, "phylum")
newrefs = getWikiRefs(ancestor)
' remove all the inline citations "refpub", etc., this is for "further reading". Otherwise they're duplicated both places.
For i As Integer = newrefs.Count - 1 To 0 Step -1
If LCase(newrefs(i).reftype).StartsWith("ref") Then
found = -1
' these are in the inline citations, so remove them from current further reading
For i1 As Integer = refs.Count - 1 To 0 Step -1
If newrefs(i).title = refs(i1).title OrElse
(newrefs(i).alast <> "" And newrefs(i).alast = refs(i1).alast And newrefs(i).year = refs(i1).year) Then
found = i ' newrefs(i) is found in refs. Remove it from refs
Exit For
End If
Next i1
If found >= 0 Then refs.RemoveAt(found) ' it was in the new inline citations.
newrefs.RemoveAt(i) ' remove inline citation from new list of further reading
End If
Next i
' remove any current references (refs) that are in the original version (oldrefs), to be replaced by those in newrefs
For i As Integer = refs.Count - 1 To 0 Step -1
found = -1
For Each ref As refrec In oldrefs
If refs(i).title = ref.title OrElse
(refs(i).alast <> "" And refs(i).alast = ref.alast And refs(i).year = ref.year) Then
found = i ' refs(i) is found in oldrefs. Remove it from refs
Exit For
End If
Next ref
If found >= 0 Then refs.RemoveAt(found) ' it was in the original version.
Next i
' add any existing references not in the original revision
For i As Integer = 0 To refs.Count - 1
found = -1
For Each ref As refrec In newrefs
If refs(i).title = ref.title OrElse
(refs(i).alast <> "" And refs(i).alast = ref.alast And refs(i).year = ref.year) Then
found = i
Exit For
End If
Next ref
If found < 0 Then ' ref added by someone else, not already in newrefs
newrefs.Add(refs(i))
End If
Next i
If newrefs.Count = 0 Then
s = vbCrLf
Else
s = vbCrLf & "==" & pubtype & "==" & vbCrLf & "{{refbegin}}" & vbCrLf
For i As Integer = 0 To newrefs.Count - 1
s &= "* " & citation(newrefs(i)) & vbCrLf
Next i
s &= "{{refend}}" & vbCrLf
End If
page = current
page = Regex.Replace(page, "\r\n(==" & pubtype2 & "==.+?refbegin\}\}(.+?)\{\{refend\}\})\r\n", vbCrLf,
RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' remove external links
page = Regex.Replace(page, "\r\n(==" & pubtype & "==.+? *\{\{refbegin.*?\}\}(.+?)\{\{refend\}\})\r\n", s,
RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' replace further reading
page = Regex.Replace(page, "\r\n\{\{(clear|-)\}\}", "",
RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' remove clear template
page = Regex.Replace(page, "\r\n\<ref name=eol>.+?</ref>", "",
RegexOptions.Singleline Or RegexOptions.IgnoreCase) ' remove eol references
page = Regex.Replace(page, "<ref name=eol/>", "",
RegexOptions.Singleline Or RegexOptions.IgnoreCase)
Return page
End Function
Function taxFamily(mm As List(Of taxrec), toprank As String) As String
' returns "" if genus, family, and order taxonomy templates match mm.
Dim mrank As New List(Of String) ' list of tax templates ranks up to toprank
Dim mtax As New List(Of String) ' list of tax templates names to toprank
Dim parent, rank, tax As String
Dim pages As List(Of String)
Dim rmatch As RegularExpressions.Match
Dim i, k As Integer
Dim msg As String = ""
Dim s1 As String
If eqstr(mm(0).rank, "species") Then k = 1 Else k = 0
parent = mm(k).taxon
rank = ""
Do While rank = "" OrElse (Not itisRankID.ContainsKey(rank)) OrElse itisRankID(rank) >= itisRankID(toprank)
tax = parent
pages = getWikiPages("Template:Taxonomy/" & getTaxAmbig(tax), urlWikiPedia, 1)
If pages.Count > 0 Then
s1 = Regex.Match(pages(0), "(#REDIRECT .+?\]\])").ToString
If s1 <> "" Then Return mm(0).taxon & vbTab & s1
rmatch = Regex.Match(pages(0), "parent[ ]*=[ ]*(.+?)[\n\|\}]")
If rmatch.Groups.Count = 2 Then parent = rmatch.Groups(1).ToString.Trim
rmatch = Regex.Match(pages(0), "rank[ ]*=[ ]*(.+?)[\n|]")
If rmatch.Groups.Count = 2 Then rank = rmatch.Groups(1).ToString.Trim
If rank = "" Then Return mm(0).taxon & vbTab & "error - no rank" & vbTab & tax
Else
Return mm(0).taxon & vbTab & "missing template" & vbTab & tax
End If
rank = rank.Replace("familia", "family")
rank = rank.Replace("ordo", "order")
If mainRank.IndexOf(rank) >= 0 Then ' save the template name, rank
mrank.Add(LCase(rank))
mtax.Add(LCase(tax))
End If
Loop
For i1 As Integer = mainRank.Count - 1 To 0 Step -1
k = itisRankID(mainRank(i1))
If k < itisRankID(toprank) Then Exit For
If k <= 180 Then
i = mrank.IndexOf(mainRank(i1))
For i2 As Integer = 0 To mm.Count - 1
If eqstr(mm(i2).rank, mainRank(i1)) Then
If i < 0 Then
Return mm(i2).taxon & vbTab & "no template" & vbTab & mainRank(i1)
Else
If Not eqstr(mm(i2).taxon, mtax(i)) Then ' different taxa
Return mm(i2).taxon & vbTab & "different taxa" & vbTab & mtax(i) & vbTab & mainRank(i1)
End If
End If
End If
Next i2
End If
Next i1
Return ""
End Function
Private Sub cmdUpdate_Click(sender As Object, e As EventArgs) Handles cmdUpdate.Click
' update a page's references, etc.
' qbugbot 3
Dim tax As String
Dim pageTitle As String
Dim m As New taxrec
Dim s, s1 As String
Dim page As String
Dim k As Integer
Dim nPages As Integer
Dim nSent As Integer
Dim result As MsgBoxResult
Dim sendingMode As Integer
Dim alteration As String = ""
Dim dr As DataRow
Me.Cursor = Cursors.WaitCursor
File.WriteAllText(outFile, "")
sendingMode = 2 ' 2 = update only (1 = create only, 0 = no sending)
Rnd(-1) : Randomize(2) ' repeatable sequence of randoms. Increment randomize parameter for new set
nSent = 0
maxPagesSent = 20000
'nPages = maxPagesSent * 1.5 ' number from database (some will be excluded)
If sendingMode <> 0 Then
result = MsgBox("Send Pages?", MsgBoxStyle.YesNoCancel)
If result <> MsgBoxResult.Yes Then
Me.Cursor = Cursors.Default
Exit Sub
End If
qlogout(urlWikiPedia)
s = qlogin(urlWikiPedia)
If s <> "Success" Then
MsgBox("login failure")
Me.Cursor = Cursors.Default
Exit Sub
End If
sToken = gettoken(urlWikiPedia)
appendPageTitle("")
End If
Using ds As DataSet = getDS("select * from pagesmade where updated = '' and madeby = 'qbugbot';")
nPages = 20000
If nPages > ds.Tables(0).Rows.Count Then nPages = ds.Tables(0).Rows.Count
For i1 As Integer = 0 To nPages - 1
dr = ds.Tables(0).Rows(i1)
m = loadMatch(dr("taxon"), True)
'ss = File.ReadAllLines("c:\taxlist.txt")
'For i1 As Integer = 0 To ss.Count - 1
'If ss(i1).StartsWith("---") Then Exit For
'm = loadMatch(ss(i1), False)
If m.taxon <> "" Then
tax = m.taxon
pageTitle = getDisambig(m)
If pageTitle = "" Then pageTitle = tax
page = updatePage(tax, pageTitle, alteration)
If page <> "" Then
File.AppendAllText(outFile, vbCrLf & "=============" & tax & "================" &
vbCrLf & page & vbCrLf & vbCrLf)
If sendingMode <> 0 And nSent < maxPagesSent Then
If alteration <> "" Then alteration = "Page update: " & alteration
s1 = sendWikiPage(pageTitle, page, urlWikiPedia, alteration, sendingMode)
If s1 <> "" Then
nSent += 1
k = nonQuery("update pagesmade set updated = @parm1 where pagetitle = @parm2", Format(Now, "yyyy-MM-dd HH:mm:ss"), pageTitle)
If k > 1 Then Stop
If k = 0 Then outLog("database pagesmade not updated. pagetitle: " & pageTitle)
outLog("update: " & pageTitle & ", " & alteration)
Else
outLog("not sent: " & pageTitle)
End If
End If
If nSent >= maxPagesSent Then Exit For
Else
outLog("no update necessary: " & pageTitle)
k = nonQuery("update pagesmade set updated = @parm1 where pagetitle = @parm2", "Checked " & Format(Now, "yyyy-MM-dd HH:mm:ss"), pageTitle)
If k <> 1 Then outLog("cannot update pagesmade database: " & pageTitle & ", " & alteration)
End If
End If
Next i1
End Using
File.AppendAllText(outFile, "=========================================" & vbCrLf)
Me.Cursor = Cursors.Default
End Sub
Private Sub cmdEtc_Click(sender As Object, e As EventArgs) Handles cmdEtc.Click
' utility command button
Me.Cursor = Cursors.WaitCursor
formatChildList(False, 27)
Me.Cursor = Cursors.Default
End Sub
Sub selfredirect()
' reads a list of titles from the self-redir file and makes pages for redirect pages or delinks the recursive links.
' qbugbot 4
Dim m, m2 As New taxrec
Dim tax, lasttax As String
Dim mm As New List(Of taxrec)
Dim ss As List(Of String)
Dim sr As List(Of String)
Dim dbRequired, dbAllowed As Integer
Dim sendingMode As Integer
Dim n, n1, n2, n3 As Integer
Dim s As String
Dim replacePage As Boolean
Dim page, pagetitle, editsummary As String
Dim result As MsgBoxResult
maxPagesSent = 3
nPagesSent = 0
sendingMode = 0 ' 0 = no sending, 1 = create only, 2 = update possible
dbRequired = 0
dbAllowed = 27
If sendingMode <> 0 Then
result = MsgBox("Send Pages?", MsgBoxStyle.YesNoCancel)
If result <> MsgBoxResult.Yes Then
Me.Cursor = Cursors.Default
Exit Sub
End If
qlogout(urlWikiPedia)
s = qlogin(urlWikiPedia)
If s <> "Success" Then
MsgBox("login failure")
Me.Cursor = Cursors.Default
Exit Sub
End If
sToken = gettoken(urlWikiPedia)
End If
File.WriteAllText(outFile, "")
n = 0 : n1 = 0 : n2 = 0 : n3 = 0
tax = ""
ss = New List(Of String)
ss = File.ReadAllLines(My.Settings.redirlist).ToList
lasttax = ""
page = "" : pagetitle = "" : editsummary = ""
For i1 As Integer = 0 To ss.Count - 1
If nPagesSent >= maxPagesSent Then Exit For
If ss(i1).Trim.StartsWith("----") Then Exit For
sr = ss(i1).Split(vbTab.ToCharArray).ToList
If sr.Count >= 4 AndAlso eqstr(sr(0), "arthropoda") Then ' process a record
tax = sr(1).Split("(")(0)
If tax.StartsWith("List of") Then tax = tax.Split(" ")(2)
If tax <> lasttax And page <> "" Then
s = botban(page, "qbugbot")
If s <> "" Then
outLog(tax & " - bot ban: " & s)
File.AppendAllText(outFile, " - bot ban: " & s & vbCrLf & "=========================" & vbCrLf)
Else
If getDisambig(m2) <> "" Then Stop
nPagesSent += 1
s = sendWikiPage(pagetitle, page, urlWikiPedia, editsummary, sendingMode)
File.AppendAllText(outFile, "=========mod===" & pagetitle & "=============" & vbCrLf & page & vbCrLf & "=========================" & vbCrLf)
End If
page = "" : pagetitle = "" : editsummary = ""
End If
m = loadMatch(tax, True)
If m.taxon = "" Then Stop ' parent not found.
m2 = loadMatch(sr(3), True)
If m2.taxon = "" OrElse Not eqstr(m2.rank, sr(4)) Then ' child not found or different ranks. Remove the link
File.AppendAllText(outFile, "=======================" & vbCrLf & "Redirect page not in database (or different rank): " & sr(3) & vbCrLf)
replacePage = False
ElseIf m.rank = m2.rank Then ' probably synonyms
replacePage = False
ElseIf eqstr(m2.rank, "species") Then ' make page if not monotypic, else remove link
If Not eqstr(tax, lasttax) Then
mm = getChildren(m, False, 27)
End If
If mm.Count = 1 Then ' single child in database. remove link
replacePage = False
Else ' not monotypic - replace page
replacePage = True
End If
Else ' not species
If eqstr(m2.rank, "genus") Or eqstr(m2.rank, "family") Then ' make page
replacePage = True
End If
End If
If replacePage Then ' replace the redirect page, m2
If getDisambig(m2) <> "" Then Stop
' make sure it's a redirect
s = getWikiPage(m2.taxon, urlWikiPedia).ToLower
If Not s.Contains("#redirect") Then
outLog(m2.taxon & " - not a redirect page")
File.AppendAllText(outFile, "========= Not a redirect page: " & m2.taxon & vbCrLf &
"=========================" & vbCrLf)
Else
s = botban(page, "qbugbot")
If s <> "" Then
outLog(tax & " - bot ban: " & s)
File.AppendAllText(outFile, " - bot ban: " & s & vbCrLf & "=========================" & vbCrLf)
Else
makePage(m2, dbRequired, dbAllowed, sr(3), False, sendingMode, "qBugbot replaced self-redirect with article.")
File.AppendAllText(outFile, madePage.ToString)
madePage = New StringBuilder
End If
End If
Else ' remove link to self-redirect
If page = "" Then
page = getWikiPage(sr(1), urlWikiPedia)
If page = "" Then Stop
pagetitle = sr(1)
End If
s = page
page = page.Replace("[[" & sr(3) & "]]", sr(3))
page = Regex.Replace(page, "\[\[" & sr(3) & "\|(.+?)\]\]", "$1")
If s <> page Then
If editsummary = "" Then
editsummary = "Removed link to a self-redirect page."
Else
editsummary = "Removed links to self-redirect pages."
End If
Else
If editsummary = "" Then page = "" ' no change so far
End If
End If
lasttax = tax
End If
Next i1
If page <> "" Then ' last page
s = botban(page, "qbugbot")
If s <> "" Then
outLog(tax & " - bot ban: " & s)
File.AppendAllText(outFile, " - bot ban: " & s & vbCrLf & "=========================" & vbCrLf)
Else
If getDisambig(m2) <> "" Then Stop
nPagesSent += 1 : If nPagesSent <= maxPagesSent Or sendingMode = 0 Then
s = sendWikiPage(pagetitle, page, urlWikiPedia, editsummary, sendingMode)
File.AppendAllText(outFile, "=========mod===" & pagetitle & "=============" & vbCrLf & page & vbCrLf & "=========================" & vbCrLf)
End If
End If
End If
End Sub
Private Sub cmdRedir_Click(sender As Object, e As EventArgs) Handles cmdRedir.Click
Me.Cursor = Cursors.WaitCursor
selfredirect()
Me.Cursor = Cursors.Default
End Sub
End Classmain.vb
edit' main.vb, by Robert Webster (CC BY-SA 3.0 US)
' various functions, global variables, main sub (startup)
Imports System.Net
Imports System.Net.Http
Imports System.Text
Imports System.Text.RegularExpressions
Imports System.Collections.Generic
Imports System.IO
Imports System.Data
Imports MySql.Data.MySqlClient
Imports Newtonsoft.Json
Imports Newtonsoft.Json.Linq
Public Module main
Structure refstruc
Dim used As Boolean
Dim shortref As String
Dim longref As String
End Structure
Public Class taxrec
Public rank As String
Public taxon As String
Public descr As String
Public taxid As String
Public parentid As String
Public imageCounter As Integer
Public childimageCounter As Integer
Public link As String
Public taxlink As String
Public authority As String
Public extinct As Boolean ' string in database
Public parentTsn As Integer ' not in database, used for list pages
Public catLifeID As String ' not in database, used for list pages
Public catLifeParentID As String ' not in database, used for list pages
Public gbifID As String ' not in database, used for list pages
Public gbifParent As String ' not in database, used for list pages
Public gbifUsable As String ' not in taxatable, in gbif
Public spiderID As Integer ' not in database, used for list pages
Public spiderParent As Integer ' not in database, used for list pages
Public spiderlink As String ' not in database, used for list pages
Public spiderdist As String ' not in database, used for list pages
Public iucnStatus As String ' not in taxatable, in iucn
Public iucnTrend As String ' not in taxatable, in iucn
Public iucnYear As String ' not in taxatable, in iucn
Public iucnID As String ' not in taxatable, in iucn
Public iucnVersion As String ' not in taxatable, in iucn
Public itistsn As Integer
' old wikirec stuff, now in oddinfo
Public synonyms As List(Of String)
Public synauth As List(Of String)
Public syresource As List(Of String)
Public wikipediaPageID As String
Public commonNames As List(Of String)
Public commonWikiLink As String
Public hodges As String
Public wikidataid As String
Public ambigLink As String
Public unimportant As Integer ' tells whether it's an autogenerated ancestor
Sub New()
rank = ""
taxon = ""
descr = ""
taxid = ""
parentid = ""
link = ""
taxlink = ""
authority = ""
catLifeID = ""
catLifeParentID = ""
gbifID = ""
gbifParent = ""
gbifUsable = ""
spiderlink = ""
spiderdist = ""
commonNames = New List(Of String)
ambigLink = ""
unimportant = 0
itistsn = 0
' old wikirec stuff, now in oddinfo
synonyms = New List(Of String)
synauth = New List(Of String)
syresource = New List(Of String)
wikipediaPageID = 0
commonWikiLink = ""
hodges = ""
wikidataid = ""
extinct = False
iucnStatus = ""
iucnTrend = ""
iucnYear = ""
iucnID = ""
iucnVersion = ""
End Sub
End Class
Class refrec
Public refid As Integer
Public reftype As String
Public pubtype As String
Public afirst As String
Public alast As String
Public efirst As String
Public elast As String
Public year As String
Public title As String
Public journal As String
Public publisher As String
Public series As String
Public volume As String
Public issue As String
Public chapter As String
Public pages As String
Public url As String
Public isbn As String
Public issn As String
Public doi As String
Public doiaccess As String
Public taxon As String
Public taxonExcept As String
Public bottomRank As Integer
Public updated As String
Public etc As String ' a set of "| a = b| c = d..."
Public urlAccessed As String ' last access date for cite web
Public comment As String ' a set of "| a = b| c = d..."
Sub New()
refid = 0
reftype = ""
pubtype = ""
afirst = ""
alast = ""
efirst = ""
elast = ""
year = ""
title = ""
journal = ""
publisher = ""
series = ""
volume = ""
issue = ""
chapter = ""
pages = ""
url = ""
isbn = ""
issn = ""
doi = ""
doiaccess = ""
taxon = ""
taxonExcept = ""
bottomRank = 0
etc = ""
updated = ""
urlAccessed = ""
End Sub
End Class
Structure imagerec
Dim imageid As Integer
Dim filename As String
Dim photodate As String
Dim dateadded As String
Dim modified As String
Dim taxonid As String
Dim gps As String
Dim elevation As String
Dim rating As Integer
Dim confidence As Integer
Dim remarks As String
Dim originalpath As String
Dim bugguide As String
Dim size As String
Dim location As String
Dim county As String
Dim state As String
Dim country As String
End Structure
Public maxlist As Integer = 100 ' how many in a list before you make a list page
Public maxColumn As Integer = 12 ' how many in a list before you use multiple columns
Public taxaConn As String ' mysql connection string
Public stubs As New Dictionary(Of String, String)(System.StringComparer.OrdinalIgnoreCase)
Public taxAmbig As New Dictionary(Of String, String)(System.StringComparer.OrdinalIgnoreCase)
Public itisRankID As New Dictionary(Of String, Integer)(System.StringComparer.OrdinalIgnoreCase)
Public itisRanks As New Dictionary(Of Integer, String)
Public pluralRank As New Dictionary(Of String, String)(System.StringComparer.OrdinalIgnoreCase)
Public mainRank As New List(Of String)
Public latinRank As New Dictionary(Of String, String)(System.StringComparer.OrdinalIgnoreCase)
Public locationID As New Dictionary(Of String, String)(System.StringComparer.OrdinalIgnoreCase)
Public numeral As New Dictionary(Of Integer, String)
Public urlWikiMedia As String = "https://commons.wikimedia.org/w/api.php"
Public urlWikiPedia As String = "https://en.wikipedia.org/w/api.php"
Public urlWikiData As String = "https://www.wikidata.org/w/api.php"
Public urlwikiSpecies As String = "https://species.wikimedia.org/w/api.php"
Public cookies As CookieContainer
Public handler As HttpClientHandler
Public qClient As HttpClient ' need these for cookies
Public outFile As String
Public botCreateMessage As String = "This article was created by the bot Qbugbot. " &
"For more information, see [[User:Qbugbot/info]]. " &
"For questions and comments, leave a message at [[User:Qbugbot/talk]]."
Public botCreateCategory As String = "[[Category:Articles created by Qbugbot]]"
Public sToken As String ' editing token
Sub main()
Dim ds As DataSet
taxaConn = My.Settings.taxaconn
outFile = My.Settings.outFile ' output file for pages
ds = getDS("select * from stubs order by taxon")
For Each dr As DataRow In ds.Tables(0).Rows
stubs.Add(dr("taxon"), "{{" & dr("stubname") & "-stub}}")
Next dr
numeral.Add(0, "zero")
numeral.Add(1, "one")
numeral.Add(2, "two")
numeral.Add(3, "three")
numeral.Add(4, "four")
numeral.Add(5, "five")
numeral.Add(6, "six")
numeral.Add(7, "seven")
numeral.Add(8, "eight")
numeral.Add(9, "nine")
locationID.Add("1", "Europe")
locationID.Add("2", "Africa")
locationID.Add("3", "temperate Asia")
locationID.Add("4", "tropical Asia")
locationID.Add("5", "Australasia")
locationID.Add("6", "the Pacific Ocean")
locationID.Add("7", "North America")
locationID.Add("8", "South America")
locationID.Add("9", "the Antarctic")
locationID.Add("10", "northern Europe")
locationID.Add("11", "Middle Europe")
locationID.Add("12", "southwestern Europe")
locationID.Add("13", "southeastern Europe")
locationID.Add("14", "eastern Europe")
locationID.Add("20", "northern Africa")
locationID.Add("21", "Macaronesia")
locationID.Add("22", "west tropical Africa")
locationID.Add("23", "west-central tropical Africa")
locationID.Add("24", "northeast Tropical Africa")
locationID.Add("25", "east tropical Africa")
locationID.Add("26", "south tropical Africa")
locationID.Add("27", "southern Africa")
locationID.Add("28", "the mid Atlantic Ocean")
locationID.Add("29", "the western Indian Ocean")
locationID.Add("30", "Siberia")
locationID.Add("31", "the Russian Far East")
locationID.Add("32", "Middle Asia")
locationID.Add("33", "Caucasus")
locationID.Add("34", "western Asia")
locationID.Add("35", "the Arabian Peninsula")
locationID.Add("36", "China")
locationID.Add("37", "Mongolia")
locationID.Add("38", "eastern Asia")
locationID.Add("40", "the Indian subcontinent")
locationID.Add("41", "Indo-China")
locationID.Add("42", "Malesia")
locationID.Add("43", "Papuasia")
locationID.Add("50", "Australia")
locationID.Add("51", "New Zealand")
locationID.Add("60", "the southwestern Pacific")
locationID.Add("61", "the south-central Pacific")
locationID.Add("62", "the northwestern Pacific")
locationID.Add("63", "the north-central Pacific")
locationID.Add("70", "subarctic America")
locationID.Add("71", "western Canada")
locationID.Add("72", "eastern Canada")
locationID.Add("73", "the northwestern United States")
locationID.Add("74", "the north-central United States")
locationID.Add("75", "the northeastern United States")
locationID.Add("76", "the southwestern United States")
locationID.Add("77", "the south-central United States")
locationID.Add("78", "the southeastern United States")
locationID.Add("79", "Mexico")
locationID.Add("80", "Central America")
locationID.Add("81", "Caribbean")
locationID.Add("82", "northern South America")
locationID.Add("83", "western South America")
locationID.Add("84", "Brazil")
locationID.Add("85", "southern South America")
locationID.Add("90", "the Subantarctic Islands")
locationID.Add("91", "the Antarctic continent")
' for template:taxonomy/ disambiguation
taxAmbig.Add("Abroma", "Abroma (cicada)")
taxAmbig.Add("Acanthocephala", "Acanthocephala (bug)")
taxAmbig.Add("Agathis", "Agathis (wasp)")
taxAmbig.Add("Apoda", "Apoda (moth)")
taxAmbig.Add("Anisotoma", "Anisotoma (beetle)")
taxAmbig.Add("Baloghia", "Baloghia (arachnid)")
taxAmbig.Add("Bremia", "Bremia (gall midge)")
taxAmbig.Add("Chrysopogon", "Chrysopogon (fly)")
taxAmbig.Add("Clusia", "Clusia (fly)")
taxAmbig.Add("Colocasia", "Colocasia (moth)")
taxAmbig.Add("Collinsia", "Collinsia(spider)")
taxAmbig.Add("Crossosoma", "Crossosoma (millipede)")
taxAmbig.Add("Ctenophora", "Ctenophora (fly)")
taxAmbig.Add("Danae", "Danae (beetle)")
taxAmbig.Add("Dasypogon", "Dasypogon (fly)")
taxAmbig.Add("Dictyoptera", "Dictyoptera (genus)")
taxAmbig.Add("Eremothera", "Eremothera (arachnid)")
taxAmbig.Add("Euclea", "Euclea (moth)")
taxAmbig.Add("Euthyneura", "Euthyneura (insect)")
taxAmbig.Add("Gesneria", "Gesneria (moth)")
taxAmbig.Add("Hubbardia", "Hubbardia (arachnid)")
taxAmbig.Add("Iris", "Iris (insect)")
taxAmbig.Add("Isotoma", "Isotoma (springtail)")
taxAmbig.Add("Lobopoda", "Lobopoda (beetle)")
taxAmbig.Add("Luperini", "Luperini (beetle)")
taxAmbig.Add("Malagasia", "Malagasia (cicada)")
taxAmbig.Add("Osbornia", "Osbornia (bug)")
taxAmbig.Add("Pellaea", "pellaea (bug)")
taxAmbig.Add("Pelophila", "Pelophila (beetle)")
taxAmbig.Add("Pentagramma", "Pentagramma (bug)")
taxAmbig.Add("Phaleria", "Phaleria (beetle)")
taxAmbig.Add("Platynota", "Platynota (moth)")
taxAmbig.Add("Podolasia", "Podolasia (beetle)")
taxAmbig.Add("Raphia", "Raphia (moth)")
taxAmbig.Add("Reichenbachia", "Reichenbachia (beetle)")
taxAmbig.Add("Rustia", "Rustia (cicada)")
taxAmbig.Add("Sagenista", "Sagenista (wasp)")
taxAmbig.Add("Scaphium", "Scaphium (beetle)")
taxAmbig.Add("Sida", "Sida (arthropod)")
taxAmbig.Add("Stelis", "Stelis (insect)")
taxAmbig.Add("Thesium", "Thesium (beetle)")
taxAmbig.Add("Thryallis", "Thryallis (beetle)")
taxAmbig.Add("Trichodesma", "Trichodesma (beetle)")
taxAmbig.Add("Trichopetalum", "Trichopetalum (millipede)")
itisRankID.Add("kingdom", 10)
itisRankID.Add("subkingdom", 20)
itisRankID.Add("infrakingdom", 25)
itisRankID.Add("superphylum", 27)
itisRankID.Add("phylum", 30)
itisRankID.Add("subphylum", 40)
itisRankID.Add("infraphylum", 45)
itisRankID.Add("superclass", 50)
itisRankID.Add("class", 60)
itisRankID.Add("subclass", 70)
itisRankID.Add("infraclass", 80)
itisRankID.Add("superorder", 90)
itisRankID.Add("order", 100)
itisRankID.Add("suborder", 110)
itisRankID.Add("infraorder", 120)
itisRankID.Add("parvorder", 122)
itisRankID.Add("nanorder", 123)
itisRankID.Add("section", 124)
itisRankID.Add("subsection", 126)
itisRankID.Add("superfamily", 130)
itisRankID.Add("epifamily", 135)
itisRankID.Add("family", 140)
itisRankID.Add("subfamily", 150)
itisRankID.Add("supertribe", 155)
itisRankID.Add("tribe", 160)
itisRankID.Add("subtribe", 170)
itisRankID.Add("genus", 180)
itisRankID.Add("subgenus", 190)
itisRankID.Add("species", 220)
itisRankID.Add("subspecies", 230)
' add latin ranks (where different)
itisRankID.Add("regnum", 10)
itisRankID.Add("subregnum", 20)
itisRankID.Add("infraregnum", 25)
itisRankID.Add("superclassis", 50)
itisRankID.Add("classis", 60)
itisRankID.Add("subclassis", 70)
itisRankID.Add("infraclassis", 80)
itisRankID.Add("superordo", 90)
itisRankID.Add("ordo", 100)
itisRankID.Add("subordo", 110)
itisRankID.Add("infraordo", 120)
itisRankID.Add("parvordo", 122)
itisRankID.Add("nanordo", 123)
itisRankID.Add("sectio", 124)
itisRankID.Add("subsectio", 126)
itisRankID.Add("superfamilia", 130)
itisRankID.Add("epifamilia", 135)
itisRankID.Add("familia", 140)
itisRankID.Add("subfamilia", 150)
itisRankID.Add("supertribus", 155)
itisRankID.Add("tribus", 160)
itisRankID.Add("subtribus", 170)
itisRanks.Add(10, "kingdom")
itisRanks.Add(20, "subkingdom")
itisRanks.Add(25, "infrakingdom")
itisRanks.Add(27, "superphylum")
itisRanks.Add(30, "phylum")
itisRanks.Add(40, "subphylum")
itisRanks.Add(45, "infraphylum")
itisRanks.Add(50, "superclass")
itisRanks.Add(60, "class")
itisRanks.Add(70, "subclass")
itisRanks.Add(80, "infraclass")
itisRanks.Add(90, "superorder")
itisRanks.Add(100, "order")
itisRanks.Add(110, "suborder")
itisRanks.Add(120, "infraorder")
itisRanks.Add(124, "section")
itisRanks.Add(126, "subsection")
itisRanks.Add(130, "superfamily")
itisRanks.Add(135, "epifamily")
itisRanks.Add(140, "family")
itisRanks.Add(150, "subfamily")
itisRanks.Add(155, "supertribe")
itisRanks.Add(160, "tribe")
itisRanks.Add(170, "subtribe")
itisRanks.Add(180, "genus")
itisRanks.Add(190, "subgenus")
itisRanks.Add(220, "species")
itisRanks.Add(230, "subspecies")
pluralRank.Add("class", "classes")
pluralRank.Add("family", "families")
pluralRank.Add("epifamily", "epifamilies")
pluralRank.Add("genus", "genera")
pluralRank.Add("infraclass", "infraclasses")
pluralRank.Add("infrakingdom", "infrakingdoms")
pluralRank.Add("infraorder", "infraorders")
pluralRank.Add("infraphylum", "infraphylums")
pluralRank.Add("order", "orders")
pluralRank.Add("phylum", "phylums")
pluralRank.Add("section", "sections")
pluralRank.Add("species", "species")
pluralRank.Add("subclass", "subclasses")
pluralRank.Add("subfamily", "subfamilies")
pluralRank.Add("subgenus", "subgenera")
pluralRank.Add("subkingdom", "subkingdoms")
pluralRank.Add("suborder", "suborders")
pluralRank.Add("subphylum", "subphylums")
pluralRank.Add("subsection", "subsections")
pluralRank.Add("subspecies", "subspecies")
pluralRank.Add("subtribe", "subtribes")
pluralRank.Add("superclass", "superclasses")
pluralRank.Add("superfamily", "superfamilies")
pluralRank.Add("superorder", "superorders")
pluralRank.Add("superphylum", "superphylums")
pluralRank.Add("supertribe", "supertribes")
pluralRank.Add("tribe", "tribes")
pluralRank.Add("kingdom", "kingdoms")
mainRank.Add("phylum")
mainRank.Add("class")
mainRank.Add("order")
mainRank.Add("order")
mainRank.Add("family")
mainRank.Add("genus")
mainRank.Add("species")
mainRank.Add("subspecies")
latinRank.Add("class", "classis")
latinRank.Add("cohort", "cohort")
latinRank.Add("division", "divisio")
latinRank.Add("domain", "domain")
latinRank.Add("epifamily", "epifamilia")
latinRank.Add("family", "familia")
latinRank.Add("form", "forma")
latinRank.Add("genus", "genus")
latinRank.Add("grandorder", "grandordo")
latinRank.Add("infraclass", "infraclassis")
latinRank.Add("infrakingdom", "infraregnum")
latinRank.Add("infralegion", "infralegio")
latinRank.Add("infraorder", "infraordo")
latinRank.Add("infraphylum", "infraphylum")
latinRank.Add("infratribe", "infratribus")
latinRank.Add("kingdom", "regnum")
latinRank.Add("legion", "legio")
latinRank.Add("magnorder", "magnordo")
latinRank.Add("microphylum", "microphylum")
latinRank.Add("microrder", "micrordo")
latinRank.Add("mirorder", "mirordo")
latinRank.Add("nanophylum", "nanophylum")
latinRank.Add("nanorder", "nanordo")
latinRank.Add("order", "ordo")
latinRank.Add("parafamily", "parafamilia")
latinRank.Add("parvorder", "parvordo")
latinRank.Add("phylum", "phylum")
latinRank.Add("section", "sectio")
latinRank.Add("species", "species")
latinRank.Add("subclass", "subclassis")
latinRank.Add("subcohort", "subcohort")
latinRank.Add("subdivision", "subdivisio")
latinRank.Add("subfamily", "subfamilia")
latinRank.Add("subgenus", "subgenus")
latinRank.Add("subkingdom", "subregnum")
latinRank.Add("sublegion", "sublegio")
latinRank.Add("suborder", "subordo")
latinRank.Add("subphylum", "subphylum")
latinRank.Add("subsection", "subsectio")
latinRank.Add("subspecies", "subspecies")
latinRank.Add("subtribe", "subtribus")
latinRank.Add("superclass", "superclassis")
latinRank.Add("supercohort", "supercohort")
latinRank.Add("superdivision", "superdivisio")
latinRank.Add("superdomain", "superdomain")
latinRank.Add("superfamily", "superfamilia")
latinRank.Add("superkingdom", "superregnum")
latinRank.Add("superlegion", "superlegio")
latinRank.Add("superorder", "superordo")
latinRank.Add("superphylum", "superphylum")
latinRank.Add("supertribe", "supertribus")
latinRank.Add("tribe", "tribus")
latinRank.Add("variety", "varietas")
Application.Run(frmMain)
End Sub
Function singular(s As String) As String
' converts most (not all) plural nouns to singular
Dim s1 As String
s1 = s
' this line makes "singular" a nongeneral function
If s1.Contains(" and ") Or s1.Contains(", ") Or s1.Contains(" & ") Then Return s1
If s1.EndsWith("is") Or s1.EndsWith("us") Then Return s1 ' not general, but works for common names.
If s1 = "barracks" Or
s1 = "cantus" Or
s1 = "chassis" Or
s1 = "corps" Or
s1 = "debris" Or
s1 = "diabetes" Or
s1 = "gallows" Or
s1 = "headquarters" Or
s1 = "herpes" Or
s1 = "mumps" Or
s1 = "news" Or
s1 = "nexus" Or
s1 = "rabies" Or
s1 = "rhinoceros" Or
s1 = "series" Or
s1 = "species" Or
s1 = "testes" Or
s1 = "thrips" Then Return s1
If s = s1 Then s1 = s1.Replace("atlases", "atlas") Else Return s1
If s = s1 Then s1 = s1.Replace("cookies", "cookie") Else Return s1
If s = s1 Then s1 = s1.Replace("corpuses", "corpus") Else Return s1
If s = s1 Then s1 = s1.Replace("curves", "curve") Else Return s1
If s = s1 Then s1 = s1.Replace("foes", "foe") Else Return s1
If s = s1 Then s1 = s1.Replace("genera", "genus") Else Return s1
If s = s1 Then s1 = s1.Replace("genies", "genie") Else Return s1
If s = s1 Then s1 = s1.Replace("hooves", "hoof") Else Return s1
If s = s1 Then s1 = s1.Replace("leaves", "leaf") Else Return s1
If s = s1 Then s1 = s1.Replace("loaves", "loaf") Else Return s1
If s = s1 Then s1 = s1.Replace("niches", "niche") Else Return s1
If s = s1 Then s1 = s1.Replace("octopuses", "octopus") Else Return s1
If s = s1 Then s1 = s1.Replace("opuses", "opus") Else Return s1
If s = s1 Then s1 = s1.Replace("penises", "penis") Else Return s1
If s = s1 Then s1 = s1.Replace("testes", "testis") Else Return s1
If s = s1 Then s1 = s1.Replace("waves", "wave") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "([nrlm]ese|deer|fish|sheep|measles|ois|pox|media|ss)$", "$1") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "^(sea[- ]bass)$", "$1") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(s)tatuses$", "$1tatus") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(f)eet$", "$1oot") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(t)eeth$", "$1ooth") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "^(.*)(menu)s$", "$1\2") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(quiz)zes$", "$\1") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(matr)ices$", "$1ix") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(vert|ind)ices$", "$1ex") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "^(ox)en", "$1") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(alias)(es)*$", "$1") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(alumn|bacill|cact|foc|fung|nucle|radi|stimul|syllab|termin|viri?)i$", "$1us") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "([ftw]ax)es", "$1") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(cris|ax|test)es$", "$1is") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(shoe|slave)s$", "$1") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(o)es$", "$1") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "ouses$", "ouse") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "([^a])uses$", "\1us") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "([m|l])ice$", "$1ouse") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(x|ch|ss|sh)es$", "$1") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(m)ovies$", "$1\2ovie") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(s)eries$", "$1\2eries") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "([^aeiouy]|qu)ies$", "$1y") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "([lr])ves$", "$1f") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(tive)s$", "$1") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(hive)s$", "$1") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(drive)s$", "$1") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "([^fo])ves$", "$1fe") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(^analy)ses$", "$1sis") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(analy|diagno|^ba|(p)arenthe|(p)rogno|(s)ynop|(t)he)ses$", "$1\2sis") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "([ti])a$", "$1um") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(p)eople$", "$1\2erson") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(m)en$", "$1an") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(c)hildren$", "$1\2hild") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "(n)etherlands$", "$1\2etherlands") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "eaus$", "eau") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "^(.*us)$", "$1") Else Return s1
If s = s1 Then s1 = Regex.Replace(s1, "s$", "")
Return s1
End Function
Function getLowerRank(rank As String) As String
' returns the next lower main rank
If rank = "" Then Return ""
For i1 As Integer = 0 To mainRank.Count - 1
If itisRankID(mainRank(i1)) > itisRankID(rank) Then Return mainRank(i1)
Next i1
Return ""
End Function
Function getHigherRank(rank As String) As String
' returns the next higher main rank
If rank = "" Then Return ""
For i1 As Integer = mainRank.Count - 1 To 0 Step -1
If itisRankID(mainRank(i1)) < itisRankID(rank) Then Return mainRank(i1)
Next i1
Return ""
End Function
Function getDS(ByVal scmd As String,
Optional ByRef parm1 As Object = "",
Optional ByRef parm2 As Object = "",
Optional ByRef parm3 As Object = "",
Optional ByRef parm4 As Object = "",
Optional ByRef parm5 As Object = "") As DataSet
' returns ds, uses @parm1, @parm2, etc. in query
Dim cmd As MySqlCommand = Nothing
Dim da As New MySqlDataAdapter
Dim ds As New DataSet
ds.Clear()
Try
Using conn As New MySqlConnection(taxaConn)
conn.Open()
cmd = New MySqlCommand(scmd, conn)
cmd.Parameters.AddWithValue("@parm1", parm1)
cmd.Parameters.AddWithValue("@parm2", parm2)
cmd.Parameters.AddWithValue("@parm3", parm3)
cmd.Parameters.AddWithValue("@parm4", parm4)
cmd.Parameters.AddWithValue("@parm5", parm5)
da.SelectCommand = cmd
da.Fill(ds)
cmd.Dispose()
End Using
Catch ex As Exception
MsgBox("Error, getDS: " & ex.Message)
If cmd IsNot Nothing Then cmd.Dispose()
Return Nothing
End Try
Return ds
End Function
Function nonQuery(ByVal scmd As String,
Optional ByRef parm1 As Object = "", Optional ByRef parm2 As Object = "",
Optional ByRef parm3 As Object = "", Optional ByRef parm4 As Object = "",
Optional ByRef parm5 As Object = "", Optional ByRef parm6 As Object = "",
Optional ByRef parm7 As Object = "", Optional ByRef parm8 As Object = "",
Optional ByRef parm9 As Object = "") As Object
' does a nonquery database call. uses @parm1 and @parm2 in query
Dim cmd As MySqlCommand = Nothing
Dim i As Integer
Try
Using conn As New MySqlConnection(taxaConn)
conn.Open()
cmd = New MySqlCommand(scmd, conn)
cmd.Parameters.AddWithValue("@parm1", parm1)
cmd.Parameters.AddWithValue("@parm2", parm2)
cmd.Parameters.AddWithValue("@parm3", parm3)
cmd.Parameters.AddWithValue("@parm4", parm4)
cmd.Parameters.AddWithValue("@parm5", parm5)
cmd.Parameters.AddWithValue("@parm6", parm6)
cmd.Parameters.AddWithValue("@parm7", parm7)
cmd.Parameters.AddWithValue("@parm8", parm8)
cmd.Parameters.AddWithValue("@parm9", parm9)
i = cmd.ExecuteNonQuery
cmd.Dispose()
Return i
End Using
Catch ex As Exception
MsgBox("Error, nonQuery: " & ex.Message)
If cmd IsNot Nothing Then cmd.Dispose()
Return 0
End Try
End Function
Function getScalar(ByVal scmd As String,
Optional ByRef parm1 As Object = "", Optional ByRef parm2 As Object = "",
Optional ByRef parm3 As Object = "") As Object
' returns scalar query result, uses @parm1 and @parm2 in query
Dim cmd As MySqlCommand = Nothing
Dim q As Object
Try
Using conn As New MySqlConnection(taxaConn)
conn.Open()
cmd = New MySqlCommand(scmd, conn)
cmd.Parameters.AddWithValue("@parm1", parm1)
cmd.Parameters.AddWithValue("@parm2", parm2)
cmd.Parameters.AddWithValue("@parm3", parm3)
q = cmd.ExecuteScalar
If IsDBNull(q) OrElse q Is Nothing Then
Return ""
Else
Return q
End If
End Using
Catch ex As Exception
MsgBox("Error, getScalar: " & ex.Message)
If cmd IsNot Nothing Then cmd.Dispose()
Return Nothing
End Try
End Function
Function getTaxrecByID(ByVal taxid As String, addon As Boolean) As List(Of taxrec)
' gbif ids start with g: g1234, for example.
Dim ds As New DataSet
Dim m As New taxrec
Dim matches As New List(Of taxrec)
If taxid = "" Then Return matches
If eqstr(taxid.Substring(0, 1), "g") Then ' gbif database
ds = getDS("select * from gbif.tax where taxid = @parm1 and usable <> '';",
taxid.Substring(1).Trim)
'ds = getDS("select * from gbif.tax join taxa.gbifplus using (taxid) where taxid = @parm1 and usable <> '';",
' taxid.Substring(1).Trim)
If ds IsNot Nothing Then
For Each dr As DataRow In ds.Tables(0).Rows
m = getTaxrecg(dr, addon)
matches.Add(m)
Next dr
End If
Else ' taxatable database
ds = getDS("select * from taxatable where taxid = @parm1", taxid)
If ds IsNot Nothing Then
For Each dr As DataRow In ds.Tables(0).Rows
m = getTaxrec(dr, addon)
matches.Add(m)
Next dr
End If
End If
Return matches
End Function
Function getTaxrec(ByRef dr As DataRow, addon As Boolean) As taxrec
Dim match As New taxrec
' load drow into match
If IsDBNull(dr("rank")) Then match.rank = "" Else match.rank = dr("rank")
If IsDBNull(dr("taxon")) Then match.taxon = "" Else match.taxon = dr("taxon")
If IsDBNull(dr("descr")) Then match.descr = "" Else match.descr = dr("descr")
If IsDBNull(dr("taxid")) Then match.taxid = "" Else match.taxid = dr("taxid")
If IsDBNull(dr("parentid")) Then match.parentid = "" Else match.parentid = dr("parentid")
If IsDBNull(dr("imagecounter")) Then match.imageCounter = 0 Else match.imageCounter = dr("imagecounter")
If IsDBNull(dr("childimagecounter")) Then match.childimageCounter = 0 Else match.childimageCounter = dr("childimagecounter")
If IsDBNull(dr("link")) Then match.link = "" Else match.link = dr("link")
If IsDBNull(dr("taxlink")) Then match.taxlink = "" Else match.taxlink = dr("taxlink")
If IsDBNull(dr("authority")) Then match.authority = "" Else match.authority = dr("authority")
match.authority = match.authority.Replace(" and ", " & ")
If IsDBNull(dr("extinct")) OrElse dr("extinct") = "" Then match.extinct = False Else match.extinct = True ' yes or extinct (or anything else) = true
If addon Then taxrecAddon(match)
Return match
End Function
Function getTaxrecg(ByRef dr As DataRow, addon As Boolean) As taxrec
' get a taxref from gbif database
Dim match As New taxrec
Dim matches As New List(Of taxrec)
Dim vnames As New List(Of String)
Dim taxid As String
Dim ds As DataSet
Dim s As String
Dim ss() As String
If IsDBNull(dr("taxid")) Then taxid = "" Else taxid = dr("taxid")
If taxid <> "" Then match.taxid = "g" & taxid ' gbif id prefix
' load dr into match
If IsDBNull(dr("rank")) Then match.rank = "" Else match.rank = dr("rank")
If IsDBNull(dr("name")) Then match.taxon = "" Else match.taxon = dr("name")
If IsDBNull(dr("parent")) Then match.parentid = "" Else match.parentid = "g" & dr("parent")
If IsDBNull(dr("authority")) Then match.authority = "" Else match.authority = dr("authority")
match.authority = match.authority.Replace(" and ", " & ")
If IsDBNull(dr("usable")) Then match.gbifUsable = "" Else match.gbifUsable = dr("usable")
' get image counters and links, if possible
ds = getDS("select * from gbifplus where taxid = @parm1", taxid)
For Each dr2 As DataRow In ds.Tables(0).Rows
If IsDBNull(dr2("imagecounter")) Then match.imageCounter = 0 Else match.imageCounter = dr2("imagecounter")
If IsDBNull(dr2("childimagecounter")) Then match.childimageCounter = 0 Else match.childimageCounter = dr2("childimagecounter")
If IsDBNull(dr2("link")) Then match.link = "" Else match.link = dr2("link")
Next dr2
' get common names from oddinfo
ds = getDS("select * from oddinfo where name = @parm1", match.taxon)
For Each dr2 As DataRow In ds.Tables(0).Rows
If dr2("commonnames") <> "" Then
s = dr2("commonnames")
ss = s.Split("|")
If ss.Count >= 1 AndAlso ss(0) <> "" Then
match.commonNames = ss.ToList
End If
Exit For
End If
Next dr2
' get descr from taxatable, if possible
ds = getDS("select * from taxatable where taxon = @parm1", match.taxon)
For Each dr2 As DataRow In ds.Tables(0).Rows
If dr2("descr") <> "" Then
match.descr = dr2("descr")
Exit For
End If
Next dr2
If addon Then taxrecAddon(match)
If match.taxlink = "" Then match.taxlink = "https://www.gbif.org/species/" & match.taxid.Substring(1) ' no "g"
Return match
End Function
Sub getCatLifeTaxByID(ByVal taxid As String, ByRef match As taxrec)
Dim dset As New DataSet
dset = getDS("select * from catlife.tax where taxid = @parm1 limit 1;", taxid)
If dset IsNot Nothing AndAlso dset.Tables(0).Rows.Count >= 1 Then
match = getCatLifeTaxrec(dset.Tables(0).Rows(0), True)
Else
match = New taxrec
End If
End Sub
Function getGbifVernacular(taxid As String, toprank As String) As List(Of String)
' returns a list of gbif vernacular names
' upCount tells how far up the ancestry to go, "" for no ancestors
Dim tax As String
Dim ds As DataSet
Dim s As String
Dim k As Integer
Dim rank, parent As String
Dim vNames As New List(Of String)
If Not taxid.StartsWith("g") Then Return vNames ' empty list - not gbif
tax = taxid.Substring(1) ' no "g"
Do While vNames.Count = 0 And k <= 10
ds = getDS("select * from gbif.tax where taxid = @parm1", tax)
parent = ds.Tables(0).Rows(0)("parent")
rank = ds.Tables(0).Rows(0)("rank")
ds = getDS("select * from gbif.vernacularname where taxid = @parm1 and language = 'en'", tax)
If ds IsNot Nothing Then
For Each dr As DataRow In ds.Tables(0).Rows
s = dr("vernacularname")
If vNames.IndexOf(s) < 0 Then vNames.Add(LCase(s))
Next dr
End If
If Not itisRankID.ContainsKey(toprank) OrElse Not itisRankID.ContainsKey(rank) OrElse
itisRankID(rank) < itisRankID(toprank) Then Exit Do ' stop at toprank
tax = parent
k += 1
Loop
Return vNames
End Function
Sub taxrecAddon(ByRef m As taxrec)
' load up the non-database things into m
Dim s As String
Dim k As Integer
Dim ss() As String
Dim ds As DataSet
Dim dr As DataRow
Dim catRank As String
Dim vNames As List(Of String)
s = getScalar("select is_extant from paleo.tax where taxon_name = @parm1", m.taxon)
If eqstr(s, "extinct") Then m.extinct = True
If m.itistsn = 0 Then
ds = getDS("select * from itis.taxonomic_units where name_usage = 'valid' and kingdom_id = 5 and complete_name = @parm1", m.taxon)
If ds.Tables(0).Rows.Count = 1 Then
m.itistsn = ds.Tables(0).Rows(0)("tsn")
m.parentTsn = ds.Tables(0).Rows(0)("parent_tsn")
End If
Else
If m.parentTsn = 0 Then
k = getScalar("select parent_tsn from itis.taxonomic_units where tsn = @parm1", m.itistsn)
'If IsNumeric(v) Then m.parentTsn = v
m.parentTsn = k
End If
End If
If m.catLifeID = "" Then
m.catLifeParentID = ""
catRank = m.rank
If eqstr(catRank, "Subspecies") Then catRank = "Infraspecies"
ds = getDS("select * from catlife.tax where name = @parm1 and rank = @parm2", m.taxon, catRank)
If ds.Tables(0).Rows.Count = 1 Then
dr = ds.Tables(0).Rows(0)
If Not IsDBNull(dr("author")) AndAlso m.authority = "" Then m.authority = dr("author")
m.authority = m.authority.Replace(" and ", " & ")
If Not IsDBNull(dr("taxid")) Then m.catLifeID = dr("taxid")
If Not IsDBNull(dr("parent")) Then m.catLifeParentID = dr("parent")
End If
End If
If m.gbifID = "" Or m.gbifID = "0" Then
m.gbifParent = ""
ds = getDS("select * from gbif.tax where name = @parm1 and rank = @parm2 and usable <> ''",
m.taxon, m.rank)
'ds = getDS("select * from gbif.tax join taxa.gbifplus using (taxid) where name = @parm1 and rank = @parm2 and usable <> ''",
' m.taxon, m.rank) ' and status = 'accepted'
If ds.Tables(0).Rows.Count = 1 Then
dr = ds.Tables(0).Rows(0)
If Not IsDBNull(dr("authority")) AndAlso m.authority = "" Then m.authority = dr("authority")
m.authority = m.authority.Replace(" and ", " & ")
If Not IsDBNull(dr("taxid")) Then m.gbifID = dr("taxid")
If Not IsDBNull(dr("parent")) Then m.gbifParent = dr("parent")
If Not IsDBNull(dr("usable")) Then m.gbifUsable = dr("usable")
'If m.gbifUsable = "extinct" Then ' ignore extinct in gbif -- it's unreliable.
End If
End If
If m.spiderID = 0 Then
m.spiderParent = 0
ds = getDS("select * from spidercat where name = @parm1 and rank = @parm2", m.taxon, m.rank)
If ds.Tables(0).Rows.Count = 1 Then
dr = ds.Tables(0).Rows(0)
If Not IsDBNull(dr("authority")) AndAlso m.authority = "" Then m.authority = dr("authority")
m.authority = m.authority.Replace(" and ", " & ")
If Not IsDBNull(dr("idq")) Then m.spiderID = dr("idq")
If Not IsDBNull(dr("parentid")) Then m.spiderParent = dr("parentid")
If Not IsDBNull(dr("url")) Then m.spiderlink = dr("url")
If Not IsDBNull(dr("distribution")) Then m.spiderdist = dr("distribution")
End If
End If
m.iucnStatus = ""
m.iucnTrend = ""
m.iucnYear = ""
m.iucnID = ""
m.iucnVersion = ""
ds = getDS("select * from iucn where name = @parm1;", m.taxon)
If ds.Tables(0).Rows.Count = 1 Then
dr = ds.Tables(0).Rows(0)
m.iucnStatus = dr("status")
m.iucnTrend = dr("populationtrend")
m.iucnYear = dr("yearassessed")
m.iucnID = dr("speciesid")
m.iucnVersion = dr("criteriaversion")
End If
m.commonNames = New List(Of String)
If m.taxid.StartsWith("g") Then ' gbif
vNames = getGbifVernacular(m.taxid, "")
If vNames.Count > 0 Then m.commonNames = vNames
End If
' get the old wikirec (now part of taxrec) from oddinfo
If m.taxid <> "" Then ds = getDS("select * from oddinfo where taxid = @parm1", m.taxid) Else ds = Nothing
If ds IsNot Nothing AndAlso ds.Tables(0).Rows.Count = 1 Then
dr = ds.Tables(0).Rows(0)
s = ""
If m.taxid <> "" Then
s = dr("commonnames")
ss = s.Split("|")
If ss.Count >= 1 AndAlso ss(0) <> "" Then m.commonNames = ss.ToList ' replaces anything already here (like gbif)
End If
If Not IsDBNull(dr("ambiglink")) Then m.ambigLink = dr("ambiglink") Else m.ambigLink = ""
If Not IsDBNull(dr("unimportant")) Then m.unimportant = dr("unimportant") Else m.unimportant = ""
m.synonyms = New List(Of String)
m.synauth = New List(Of String)
ds = getDS("select * from syns where taxonid = @parm1", m.taxid)
For Each dr1 As DataRow In ds.Tables(0).Rows
m.synonyms.Add(dr1("syname"))
m.synauth.Add(dr1("synauth"))
Next dr1
If m.synonyms IsNot Nothing Then
m.synonyms.Sort()
For i As Integer = m.synonyms.Count - 1 To 0 Step -1
m.synonyms(i) = m.synonyms(i).Trim
If m.synonyms(i) = "" Then
m.synonyms.RemoveAt(i) ' remove blank
ElseIf i < m.synonyms.Count - 1 AndAlso m.synonyms(i) = m.synonyms(i + 1) Then
m.synonyms.RemoveAt(i) ' remove dup
End If
Next i
End If
If Not IsDBNull(dr("wikipediaPageID")) Then m.wikipediaPageID = dr("wikipediaPageID")
If Not IsDBNull(dr("commonwikilink")) Then m.commonWikiLink = dr("commonwikilink")
If Not IsDBNull(dr("hodges")) Then m.hodges = dr("hodges")
If Not IsDBNull(dr("wikidataid")) Then m.wikidataid = dr("wikidataid")
If Not IsDBNull(dr("ambiglink")) Then m.ambigLink = dr("ambiglink")
If Not IsDBNull(dr("unimportant")) Then m.unimportant = dr("unimportant")
End If
If m.commonNames.Count = 0 AndAlso m.descr <> "" AndAlso Not m.descr.Contains(" and ") AndAlso
Not m.descr.ToLower.Contains("hodges") Then m.commonNames.Add(m.descr.ToLower)
End Sub
Function getImageRec(fname As String) As imagerec
' gets an imagerec from the taxa database, based on the file name.
Dim dset As New DataSet
Dim drow As DataRow
Dim irec As New imagerec
dset = getDS("SELECT * FROM images WHERE filename = @parm1 limit 1", fname)
If dset IsNot Nothing AndAlso dset.Tables(0).Rows.Count > 0 Then
drow = dset.Tables(0).Rows(0)
If IsDBNull(drow("taxonid")) Then Return irec
Else
Return irec
End If
irec = getimagerecDr(drow) ' load drow into irec
Return irec
End Function
Function getimagerecDr(drow As DataRow) As imagerec
Dim irec As New imagerec
' load drow into irec
If IsDBNull(drow.Item("imageid")) Then irec.imageid = 0 Else irec.imageid = drow.Item("imageid")
If IsDBNull(drow.Item("filename")) Then irec.filename = "" Else irec.filename = drow.Item("filename")
If IsDBNull(drow.Item("photodate")) Then irec.photodate = "" Else irec.photodate = drow.Item("photodate")
If IsDBNull(drow.Item("dateadded")) Then irec.dateadded = "" Else irec.dateadded = drow.Item("dateadded")
If IsDBNull(drow.Item("modified")) Then irec.modified = "" Else irec.modified = drow.Item("modified")
If IsDBNull(drow.Item("taxonid")) Then irec.taxonid = "" Else irec.taxonid = drow.Item("taxonid")
If IsDBNull(drow.Item("gps")) Then irec.gps = "" Else irec.gps = drow.Item("gps")
If IsDBNull(drow.Item("elevation")) Then irec.elevation = "" Else irec.elevation = drow.Item("elevation")
If IsDBNull(drow.Item("rating")) Then irec.rating = 0 Else irec.rating = drow.Item("rating")
If IsDBNull(drow.Item("confidence")) Then irec.confidence = 0 Else irec.confidence = drow.Item("confidence")
If IsDBNull(drow.Item("remarks")) Then irec.remarks = "" Else irec.remarks = drow.Item("remarks")
If IsDBNull(drow.Item("originalpath")) Then irec.originalpath = "" Else irec.originalpath = drow.Item("originalpath")
If IsDBNull(drow.Item("bugguide")) Then irec.bugguide = "" Else irec.bugguide = drow.Item("bugguide")
If IsDBNull(drow.Item("size")) Then irec.size = "" Else irec.size = drow.Item("size")
If IsDBNull(drow.Item("location")) Then irec.location = "" Else irec.location = drow.Item("location")
If IsDBNull(drow.Item("county")) Then irec.county = "" Else irec.county = drow.Item("county")
If IsDBNull(drow.Item("state")) Then irec.state = "" Else irec.state = drow.Item("state")
If IsDBNull(drow.Item("country")) Then irec.country = "" Else irec.country = drow.Item("country")
Return irec
End Function
Function getDescr(ByRef inMatch As taxrec, ByVal shortForm As Boolean) As String
' start at taxon, then ascend through the parents until a description is found.
' shortform is true to omit "Family: Brushfoot etc."
Dim match As New taxrec
Dim mm As List(Of taxrec)
Dim parent As Integer
Dim iter As Integer = 0
If inMatch.parentid = "" Then ' inmatch might only have the taxonid
' load everything else into inmatch
'getTaxonByID(i, inMatch) Then
mm = getTaxrecByID(inMatch.taxid, False)
If mm.Count > 1 Then Stop
inMatch = mm(0)
End If
If inMatch.descr <> "" Or shortForm Then Return inMatch.descr
parent = inMatch.parentid
Do While parent >= 0 And iter < 25
iter = iter + 1
'getTaxonByID(parent, match)
mm = getTaxrecByID(parent, False)
If mm.Count = 0 Then Return "" Else If mm.Count > 1 Then Stop
match = mm(0)
If match.descr <> "" AndAlso match.rank <> "No Taxon" And
(match.rank <> "Species" Or inMatch.rank = "Subspecies") And match.rank <> "Subspecies" Then
Return match.rank & ": " & match.descr.Trim
End If
parent = match.parentid
Loop
Return ""
End Function
Function TaxonkeySearch(ByVal findme As String) As DataSet
' get dataset taxatable record for taxon or common name findme
Dim ds As New DataSet
If findme Is Nothing OrElse findme.Trim = "" Then Return Nothing
findme = findme.Trim
ds = getDS("select * from taxatable where taxon = @parm1 order by taxon;", findme)
Return ds
End Function
Function validTaxon(m As taxrec, dbRequired As Integer) As String
Dim ds As DataSet = Nothing
Dim ds2 As DataSet = Nothing
Dim ds3 As DataSet = Nothing
Dim dr As DataRow = Nothing
Dim dr2 As DataRow = Nothing
'Dim n, iRow As Integer
Dim s, s1 As String
s = LCase(m.taxon)
If s.Split(" ").Length > 3 OrElse
(s.Contains(" ") AndAlso (itisRankID.ContainsKey(m.rank) AndAlso itisRankID(m.rank) < 220)) OrElse
s.Contains("""") OrElse
s.Contains("(") OrElse
s.Contains("--") OrElse
s.Contains("-cf-") OrElse
s.Contains("-new-") OrElse
s.Contains("-non-") OrElse
s.Contains("-nr-") OrElse
s.Contains("-or-") OrElse
s.Contains("-sp-") OrElse
s.Contains("-idae") OrElse
s.Contains(".") OrElse
s.Contains("/") OrElse
s.Contains("assigned") OrElse
s.Contains("adventive") OrElse
s.Contains("established") OrElse
s.Contains("incertae") OrElse
s.Contains("introduction") OrElse
s.Contains("maybe") OrElse
s.Contains("near-") OrElse
s.Contains("possible") OrElse
s.Contains("possibly") OrElse
s.Contains("likely") OrElse
s.Contains("probably") OrElse
s.Contains("sensu lato") OrElse
s.Contains("suspected") OrElse
s.Contains("undescribed") OrElse
s.Contains("undetermined") OrElse
s.Contains("known") OrElse
s.Contains("unnamed") OrElse
s.Contains("placed") OrElse
s.EndsWith("-cf") OrElse
s.EndsWith("-like") OrElse
s.EndsWith("-sp") OrElse
s.EndsWith("complex") OrElse
s.EndsWith("group") OrElse
s.EndsWith("pseudo") OrElse
s.StartsWith("cf-") OrElse
s.StartsWith("n-") OrElse
s.StartsWith("new-") OrElse
s.StartsWith("non-") OrElse
s.StartsWith("nr-") OrElse
s.StartsWith("on-") OrElse
s.StartsWith("-xxxx") OrElse
s.StartsWith("sp-") Then Return "non-taxonomic text in name."
s1 = ""
If (dbRequired And 1) And m.taxid = "" Then s1 &= " taxa"
If (dbRequired And 2) And m.itistsn <= 0 Then s1 &= " itis"
If (dbRequired And 4) And m.catLifeID = "" Then s1 &= " catlife"
If (dbRequired And 8) And m.gbifID = "" Then s1 &= " gbif"
If (dbRequired And 16) And m.spiderID = 0 Then s1 &= " spidercat"
If s1 <> "" Then Return m.taxon & " was not found in" & s1 & ", dbRequired = " & dbRequired & "."
If Not itisRankID.ContainsKey(m.rank) Then Return "Invalid rank in taxa."
Return ""
End Function
Function getParent(ByVal m As taxrec, dbAllowed As Integer)
' returns parent based on dbAllowed: priority high to low for 1=bugguide/gbif, 16=spider 8=gbif, 2=itis, 4=catlife (anded)
Dim mp, mp1 As New taxrec
Dim mm As List(Of taxrec)
Dim mi As New taxrec
Dim ds As DataSet
If m.parentid IsNot Nothing AndAlso
(((dbAllowed And 1) And Not m.parentid.StartsWith("g")) Or
((dbAllowed And 8) And m.parentid.StartsWith("g"))) Then
mm = getTaxrecByID(m.parentid, True)
If mm.Count > 0 Then mp = mm(0)
End If
If mp.taxon = "" AndAlso (dbAllowed And 16) AndAlso m.spiderParent <> 0 Then
ds = getDS("select * from spidercat where idq = @parm1", m.spiderParent)
If ds.Tables(0).Rows.Count = 1 Then mp = getspiderTaxrec(ds.Tables(0).Rows(0), True)
End If
If mp.taxon = "" AndAlso (dbAllowed And 8) AndAlso m.gbifParent <> "" Then
ds = getDS("select name from gbif.tax where taxid = @parm1", m.gbifParent)
If ds.Tables(0).Rows.Count = 1 Then mp = loadMatch(ds.Tables(0).Rows(0)("name"), True)
End If
If (dbAllowed And 2) AndAlso m.parentTsn > 0 Then ' check even if there is one already
ds = getDS("select * from itis.taxonomic_units where tsn = @parm1", m.parentTsn)
If ds.Tables(0).Rows.Count = 1 Then
mp1 = getItisTaxrec(ds.Tables(0).Rows(0), True)
If mp.taxon = "" Then ' OrElse
'(mp.rank IsNot Nothing AndAlso mp1.rank IsNot Nothing AndAlso
'itisRankID.ContainsKey(mp1.rank) AndAlso itisRankID.ContainsKey(mp.rank) AndAlso
'itisRankID(mp1.rank) > itisRankID(mp.rank)) Then
mp = mp1 ' Itis has a lower rank (like subfamily vs. family)
End If
End If
End If
If mp.taxon = "" AndAlso (dbAllowed And 4) AndAlso m.catLifeParentID <> "" Then
ds = getDS("select name from catlife.tax where taxid = @parm1", m.catLifeParentID)
If ds.Tables(0).Rows.Count = 1 Then mp = loadMatch(ds.Tables(0).Rows(0)("name"), True)
End If
Return mp
End Function
Function getancestors(ByVal m1 As taxrec, dbAllowed As Integer,
ByVal excludeNoTaxon As Boolean, ByVal StopAt As String) As List(Of taxrec)
' returns a list of ancestors for ancestor(0). call with a single taxrec in the list "ancestor".
' StopAt the topmost rank, phylum if "".
Dim match As New taxrec
Dim m As New taxrec
Dim iter As Integer = 0
Dim catLifeID As String = ""
Dim ancestor As New List(Of taxrec)
ancestor.Add(m1)
match = getParent(m1, dbAllowed)
Do While (match.taxon <> "") And iter < 50
If (Not excludeNoTaxon OrElse Not eqstr(match.rank, "no taxon")) AndAlso
validTaxon(match, 0) = "" Then
ancestor.Add(match)
End If
If eqstr(match.rank, StopAt) Or (match.taxon = "") Then Exit Do
match = getParent(match, dbAllowed)
iter = iter + 1
Loop
Return ancestor
End Function
Function isAncestor(ancestor As List(Of taxrec), tax As String, start As Integer) As Boolean
' is taxon an ancestor? start tells where in ancestor to start looking.
For i1 As Integer = start To ancestor.Count - 1
If eqstr(ancestor(i1).taxon, tax) Then Return True
Next i1
Return False
End Function
Function getAncestor(ancestor As List(Of taxrec), tax As String, start As Integer) As taxrec
' is taxon an ancestor? start tells where in ancestor to start looking.
For i1 As Integer = start To ancestor.Count - 1
If eqstr(ancestor(i1).taxon, tax) Then Return ancestor(i1)
Next i1
Return Nothing
End Function
Function getCategoryRank(ancestor As List(Of taxrec), istart As Integer) As String
' returns the lowest existing category
' istart is 0 to include current taxon as a potential category, 1 for next higher, etc.
Dim tax, commoncat As String
Dim ds As DataSet
' istart is zero to include current taxon as a potential category.
For i As Integer = istart To ancestor.Count - 1
ds = getDS("select * from wikicats where taxon = @parm1", ancestor(i).taxon)
If ds.Tables(0).Rows.Count = 1 Then
tax = ds.Tables(0).Rows(0)("taxon")
commoncat = ds.Tables(0).Rows(0)("commoncat")
If commoncat <> "" Then Return commoncat Else Return tax
End If
Next i
If isAncestor(ancestor, "Arthropoda", 0) Then
Return "Arthropods"
Else
Return "Animals"
End If
End Function
Function getWikiPage(titleParm As String, url As String) As String
Dim parms As New Dictionary(Of String, String)
Dim r1 As HttpResponseMessage
Dim qcontent As FormUrlEncodedContent
Dim s As String
Dim jq As JObject
Dim pageID As String
Dim pageText As String
parms = New Dictionary(Of String, String)
parms.Add("action", "query")
parms.Add("titles", titleParm) ' "File:Aeoloplides turnbulli P1490124a.jpg"
parms.Add("prop", "revisions")
parms.Add("rvprop", "content")
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
Try
r1 = qClient.PostAsync(url, qcontent).Result
s = r1.Content.ReadAsStringAsync().Result
jq = JObject.Parse(s)
pageID = jq.SelectToken("query.pages.*").SelectToken("pageid")
If pageID IsNot Nothing Then
pageText = jq.SelectToken("query.pages.*.revisions").ToList(0).ToList(2)
Else
pageText = ""
End If
Catch ex As Exception
pageText = ""
End Try
Return pageText
End Function
Public Function getPageID(title As String, wikiurl As String) As Integer
' get the pageID for any wiki page based on title, url.
Dim s, s1 As String
Dim jq As JObject = Nothing
Dim jt As JToken = Nothing
Dim r1 As HttpResponseMessage
Dim qcontent As FormUrlEncodedContent
Dim parms As Dictionary(Of String, String)
If title.Trim = "" Then Return ""
parms = New Dictionary(Of String, String)()
parms.Add("action", "query")
parms.Add("titles", title)
parms.Add("prop", "revisions")
parms.Add("rvprop", "content")
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(wikiurl, qcontent).Result
s = r1.Content.ReadAsStringAsync().Result
If s.Contains("Wiki Error") Then
outLog("GetPageID error: " & title)
Return ""
End If
Try
jq = JObject.Parse(s)
jt = jq.SelectToken("$.query.pages.*")
If jt IsNot Nothing Then s1 = jt.SelectToken("pageid") Else s1 = ""
Catch ex As Exception
s1 = ""
Stop
End Try
If IsNumeric(s1) Then Return Int(s1) Else Return 0
End Function
Sub sortTaxrec(ByRef children As List(Of taxrec))
' sort a list of taxrecs
' this is ugly. I am lazy.
Dim ix As New List(Of Integer)
Dim keys As New List(Of String)
Dim sorted As New List(Of taxrec)
For i1 As Integer = 0 To children.Count - 1
ix.Add(i1)
keys.Add(children(i1).taxon)
sorted.Add(New taxrec)
Next i1
MergeSort(keys, ix, 0, ix.Count - 1)
For i1 As Integer = 0 To ix.Count - 1
sorted(i1) = children(ix(i1))
Next i1
children = New List(Of taxrec)
children.AddRange(sorted)
End Sub
Function getAncestorRank(ancestor As List(Of taxrec), rank As String) As taxrec
' return the ancestor at a given rank
For i As Integer = 0 To ancestor.Count - 1
If eqstr(ancestor(i).rank, rank) Then Return ancestor(i)
Next i
Return Nothing
End Function
Function getdescrMatch(ancestor As List(Of taxrec), sMinrank As String, sMaxrank As String,
sUsedRank As String, checkCurrent As Boolean) As taxrec
' return the lowest ancestor with a common name, upto and including maxrank
Dim checkNow As Boolean = False
Dim minRank, maxRank, usedRank, itisRank As Integer
If itisRankID.ContainsKey(sMinrank) Then minRank = itisRankID(sMinrank) Else minRank = 0
If itisRankID.ContainsKey(sMaxrank) Then maxRank = itisRankID(sMaxrank) Else maxRank = 0
If itisRankID.ContainsKey(sUsedRank) Then usedRank = itisRankID(sUsedRank) Else usedRank = 0
For i As Integer = 0 To ancestor.Count - 1
If itisRankID.ContainsKey(ancestor(i).rank) Then
itisRank = itisRankID(ancestor(i).rank)
Else
itisRank = 0
End If
If itisRank = minRank And checkCurrent Then checkNow = True
If checkNow Then
If ancestor(i).descr <> "" AndAlso itisRank <> usedRank AndAlso
itisRank <> 0 Then Return ancestor(i)
If itisRank = maxRank AndAlso itisRank <> usedRank Then
Return ancestor(i)
End If
Else
If itisRank <= minRank Then checkNow = True ' higher ranks have lower numbers
End If
Next i
Return Nothing
End Function
Function getChildren(tMatch As taxrec, addon As Boolean, dballowed As Integer) As List(Of taxrec)
' get all the immediate children of tmatch, in all database tables
Dim ds As DataSet
Dim desc As New List(Of taxrec)
Dim childNames As New List(Of String)
Dim m As New taxrec
If (dballowed And 1) Then
If tMatch.taxid <> "" Then
ds = getDS("select * from taxatable where parentid = @parm1", tMatch.taxid)
For Each dr As DataRow In ds.Tables(0).Rows
m = getTaxrec(dr, addon)
desc.Add(m)
childNames.Add(m.taxon)
Next dr
End If
End If
If tMatch.taxlink.ToLower.Contains("speciesfile.org") Then Return desc ' speciesfile implies correct, complete children.
If (dballowed And 2) AndAlso tMatch.itistsn > 0 Then
ds = getDS("select * from itis.taxonomic_units " &
"where parent_tsn = @parm1 and name_usage = 'valid';", tMatch.itistsn)
For Each dr As DataRow In ds.Tables(0).Rows
m = getItisTaxrec(dr, addon)
If childNames.IndexOf(m.taxon) < 0 Then ' new match
desc.Add(m)
childNames.Add(m.taxon)
End If
Next dr
End If
If (dballowed And 8) AndAlso tMatch.gbifID <> "" Then
ds = getDS("select * from gbif.tax where parent = @parm1 and usable <> '';", tMatch.gbifID)
'ds = getDS("select * from gbif.tax join taxa.gbifplus using (taxid) where parent = @parm1 and usable <> '';",
' tMatch.gbifID)
For Each dr As DataRow In ds.Tables(0).Rows
If eqstr(dr("name"), "Colonellus") Then Stop
m = getTaxrecg(dr, addon)
If childNames.IndexOf(m.taxon) < 0 Then ' new match
desc.Add(m)
childNames.Add(m.taxon)
End If
Next dr
End If
If (dballowed And 4) AndAlso tMatch.catLifeID <> "" Then
ds = getDS("select * from catlife.tax " &
"where parent = @parm1 and (namestatus = 'accepted name' or namestatus = 'provisionally accepted name');", tMatch.catLifeID)
If ds IsNot Nothing Then
For Each dr As DataRow In ds.Tables(0).Rows
m = getCatLifeTaxrec(dr, addon)
If childNames.IndexOf(m.taxon) < 0 Then ' new match
desc.Add(m)
childNames.Add(m.taxon)
End If
Next dr
End If
End If
If (dballowed And 16) AndAlso tMatch.spiderID > 0 Then
ds = getDS("select * from spidercat where parentid = @parm1;", tMatch.spiderID)
For Each dr As DataRow In ds.Tables(0).Rows
m = getspiderTaxrec(dr, addon)
If childNames.IndexOf(m.taxon) < 0 Then ' new match
desc.Add(m)
childNames.Add(m.taxon)
End If
Next dr
End If
Return desc
End Function
Function allDescendants(tMatch As taxrec, rank As String, dballowed As Integer) As List(Of taxrec)
' returns a sorted list of itis + bugguide descendant names, at rank (or all descendants if rank is "")
Dim children As New List(Of taxrec)
Dim chil As New List(Of taxrec)
Dim desc As New List(Of taxrec) ' all the descendants to return
Dim childName As New List(Of String)
Dim descName As New List(Of String)
Dim validName As String
Dim recRank As String
Dim i As Integer
children = getChildren(tMatch, True, dballowed) ' get immediate children, sources = dballowed
For i1 As Integer = children.Count - 1 To 0 Step -1
validName = validTaxon(children(i1), 0)
If validName = "" Then
recRank = children(i1).rank
If rank = "" OrElse eqstr(rank, recRank) Then
If descName.IndexOf(children(i1).taxon) < 0 Then ' add new taxrec
descName.Add(children(i1).taxon)
desc.Add(children(i1))
Else
children.RemoveAt(i1)
End If
ElseIf (itisRankID.ContainsKey(recRank) AndAlso itisRankID(rank) <= itisRankID(recRank)) Then ' rank is as low as target
children.RemoveAt(i1)
End If
End If
Next i1
For Each m As taxrec In children
If rank = "" OrElse Not eqstr(rank, m.rank) Then
chil = allDescendants(m, rank, dballowed)
For Each m2 As taxrec In chil
i = descName.IndexOf(m2.taxon)
If i < 0 Then ' add new taxrec
descName.Add(m2.taxon)
desc.Add(m2)
ElseIf m2.taxid <> "" Then
desc(i) = m2
End If
Next m2
End If
Next m
sortTaxrec(desc)
Return desc
End Function
Function getItisTaxrec(dr As DataRow, addon As Boolean) As taxrec
' get rank, taxon, authority, and tsn from Itis to a taxrec
Dim m As New taxrec
Dim s As String
If IsDBNull(dr("complete_name")) Then m.taxon = "" Else m.taxon = dr("complete_name").trim
If IsDBNull(dr("rank_id")) Then m.rank = "" Else m.rank = itisRanks(dr("rank_id"))
s = getScalar("select taxon_author from itis.taxon_authors_lkp, itis.taxonomic_units " &
"where taxon_authors_lkp.taxon_author_id = taxonomic_units.taxon_author_id and tsn = @parm1;", dr("tsn"))
If Not IsDBNull(s) AndAlso s IsNot Nothing AndAlso s <> "" Then m.authority = s Else m.authority = ""
m.authority = m.authority.Replace(" and ", " & ")
m.itistsn = dr("tsn")
m.link = ""
If Not IsDBNull(dr("parent_tsn")) Then m.parentTsn = dr("parent_tsn") Else m.parentTsn = 0
If addon Then taxrecAddon(m)
If m.taxlink = "" Then m.taxlink = "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=" & m.itistsn
Return m
End Function
Function getspiderTaxrec(dr As DataRow, addon As Boolean) As taxrec
' get rank, taxon, etc from spider to a taxrec
Dim m As New taxrec
If IsDBNull(dr("name")) Then m.taxon = "" Else m.taxon = dr("name").trim
If IsDBNull(dr("rank")) Then m.rank = "" Else m.rank = dr("rank").trim
If IsDBNull(dr("authority")) Then m.authority = "" Else m.authority = dr("authority").trim
m.authority = m.authority.Replace(" and ", " & ")
If IsDBNull(dr("idq")) Then m.spiderID = 0 Else m.spiderID = dr("idq")
If IsDBNull(dr("parentid")) Then m.spiderParent = 0 Else m.spiderParent = dr("parentid")
m.link = ""
If addon Then taxrecAddon(m)
If m.taxlink = "" Then m.taxlink = dr("url")
Return m
End Function
Function getCatLifeTaxrec(dr As DataRow, addon As Boolean) As taxrec
' get rank, taxon, etc from catlife to a taxrec
Dim m As New taxrec
If IsDBNull(dr("name")) Then m.taxon = "" Else m.taxon = dr("name").trim
If IsDBNull(dr("rank")) Then m.rank = "" Else m.rank = dr("rank")
If eqstr(m.rank, "infraspecies") Then m.rank = "Subspecies"
If IsDBNull(dr("author")) Then m.authority = "" Else m.authority = dr("author").trim
m.authority = m.authority.Replace(" and ", " & ")
If IsDBNull(dr("taxid")) Then
m.catLifeID = ""
m.link = ""
Else
m.catLifeID = dr("taxid").trim
'm.link = "http://www.catalogueoflife.org/col/browse/tree/id/" & m.catLifeID
m.link = ""
End If
If IsDBNull(dr("parent")) Then m.catLifeParentID = "" Else m.catLifeParentID = dr("parent").trim
If addon Then taxrecAddon(m)
Return m
End Function
Function eqstr(ByRef s1 As String, ByRef s2 As String) As Boolean
' case insensitive string equals
Return String.Equals(s1, s2, StringComparison.OrdinalIgnoreCase)
End Function
Function getRefrec(dr As DataRow) As refrec
Dim rec As New refrec
If Not IsDBNull(dr("refid")) Then rec.refid = dr("refid")
If Not IsDBNull(dr("reftype")) Then rec.reftype = dr("reftype").trim
If Not IsDBNull(dr("pubtype")) Then rec.pubtype = dr("pubtype").trim
If Not IsDBNull(dr("afirst")) Then rec.afirst = dr("afirst").trim
If Not IsDBNull(dr("alast")) Then rec.alast = dr("alast").trim
If Not IsDBNull(dr("efirst")) Then rec.efirst = dr("efirst").trim
If Not IsDBNull(dr("elast")) Then rec.elast = dr("elast").trim
If Not IsDBNull(dr("year")) Then rec.year = dr("year").trim
If Not IsDBNull(dr("title")) Then rec.title = dr("title").trim
If Not IsDBNull(dr("journal")) Then rec.journal = dr("journal")
If Not IsDBNull(dr("publisher")) Then rec.publisher = dr("publisher")
If Not IsDBNull(dr("series")) Then rec.series = dr("series").trim
If Not IsDBNull(dr("volume")) Then rec.volume = dr("volume").trim
If Not IsDBNull(dr("issue")) Then rec.issue = dr("issue").trim
If Not IsDBNull(dr("chapter")) Then rec.chapter = dr("chapter").trim
If Not IsDBNull(dr("pages")) Then rec.pages = dr("pages").trim
If Not IsDBNull(dr("url")) Then rec.url = dr("url").trim
If Not IsDBNull(dr("isbn")) Then rec.isbn = dr("isbn").trim
If Not IsDBNull(dr("issn")) Then rec.issn = dr("issn").trim
If Not IsDBNull(dr("doi")) Then rec.doi = dr("doi").trim
If Not IsDBNull(dr("doiaccess")) Then rec.doiaccess = dr("doiaccess").trim
If Not IsDBNull(dr("taxon")) Then rec.taxon = dr("taxon").trim
If Not IsDBNull(dr("taxonexcept")) Then rec.taxonExcept = dr("taxonexcept").trim
If Not IsDBNull(dr("bottomrank")) Then rec.bottomRank = dr("bottomrank") Else rec.bottomRank = 230
If Not IsDBNull(dr("etc")) Then rec.etc = dr("etc").trim
If Not IsDBNull(dr("comment")) Then rec.comment = dr("comment").trim
If Not IsDBNull(dr("urlaccessed")) Then rec.urlAccessed = dr("urlaccessed").trim
If Not IsDBNull(dr("updated")) Then rec.updated = dr("updated").trim
's = getScalar("select wikilink from wikipubs where pubname = @parm1;", rec.journal)
'If s IsNot Nothing Then rec.wikilink = s
Return rec
End Function
Function getWikiRefs(ancestor As List(Of taxrec)) As List(Of refrec)
' returns the refrecs for a taxrec (using taxon lookup)
Dim ds As DataSet
Dim refs As New List(Of refrec)
Dim ref As New refrec
Dim ss() As String
For i1 As Integer = 0 To ancestor.Count - 1
' this will miss a few refs that have odd-ranked taxons.
ds = getDS("select * from wikiref where taxon = @parm1;", ancestor(i1).taxon)
For Each dr As DataRow In ds.Tables(0).Rows
ref = getRefrec(dr)
If itisRankID.ContainsKey(ancestor(0).rank) AndAlso itisRankID(ancestor(0).rank) <= dr("bottomrank") Then
If ref.taxonExcept <> "" Then ' does not apply to some taxons
ss = ref.taxonExcept.Split("|")
For Each rec As String In ss
rec = rec.Trim
If rec <> "" AndAlso isAncestor(ancestor, rec, 0) Then
ref.title = "" ' exclude ref from this taxon
Exit For
End If
Next rec
End If
If ref.title <> "" Then
For Each r As refrec In refs
If eqstr(r.title, ref.title) Then ' no dups
ref.title = "" ' skip -- it's a duplicate
Exit For
End If
Next r
If ref.title <> "" Then refs.Add(ref)
End If
End If
Next dr
Next i1
Return refs
End Function
Function iucnstatus(status As String, trend As String, year As String) As String
' translates the 2-character IUCN status into english
Dim s As String
s = """" & UCase(status) & """"
Select Case LCase(status)
Case "ex"
s &= ". The species is extinct."
Case "ew"
s &= ". The species is extinct in the wild."
Case "cr"
s &= ", critically endangered. The species faces an extremely high risk of extinction in the immediate future."
Case "en"
s &= ", endangered. The species faces a high risk of extinction in the near future."
Case "vu"
s &= ", vulnerable. The species faces a high risk of endangerment in the medium term."
Case "nt"
s &= ", near threatened. The species may be considered threatened in the near future."
Case "lc"
s &= ", least concern, with no immediate threat to the species' survival."
Case "dd"
s &= ", data deficient."
Case Else
s = ""
End Select
If trend = "stable" OrElse trend = "increasing" OrElse trend = "decreasing" Then
s &= " The population is " & trend & "."
End If
If year > 0 Then s &= " The IUCN status was reviewed in " & year & "."
Return s
End Function
Function getRange(m As taxrec) As String
' returns the range in english for a wikipedia entry.
Dim ref As String
Dim s1, s2 As String
Dim i1 As Integer
Dim range As String
Dim source As String
Dim iRange As New List(Of String)
ref = ""
If m.spiderID > 0 Then ' get spidercat range
s1 = getScalar("select distribution from spidercat where name = @parm1", m.taxon)
If s1 <> "" Then
s1 = m.spiderdist
s1 = s1.Replace("Is. Introduced to", "Islands, and has been introduced into")
s1 = s1.Replace(". Introduced to", ", has been introduced into")
s1 = s1.Replace(" Is.", " Islands")
iRange = s1.Split(",").ToList
End If
End If
If iRange.Count = 0 AndAlso m.taxid <> "" Then ' check oddinfo, already formatted
s1 = getScalar("select drange from oddinfo where taxid = @parm1", m.taxid)
If s1 <> "" Then iRange = s1.Split("|").ToList
End If
If iRange.Count = 0 Then ' get gbif countries, if any
source = ""
If eqstr(m.rank, "species") OrElse eqstr(m.rank, "subspecies") Then
iRange = getgbifrange(m, source)
End If
End If
If m.spiderdist <> "" Then
For i As Integer = 0 To iRange.Count - 1
iRange(i) = iRange(i).Trim
i1 = iRange(i).IndexOf(" to ")
If i1 > 0 Then ' USA to Nicaragua
s1 = iRange(i).Substring(0, i1)
s2 = iRange(i).Substring(i1 + 4)
s1 = translocation(s1)
s2 = translocation(s2)
iRange(i) = "a range from " & s1 & " to " & s2
Else
iRange(i) = translocation(iRange(i))
If iRange(i).Contains("into USA") Or iRange(i).Contains("into Caribbean") Or iRange(i).Contains("into Far East") Or iRange(i).Contains("into Near East") Then
iRange(i) = iRange(i).Replace("introduced into ", "introduced into the ")
End If
iRange(i) = iRange(i).Replace(" USA", " United States")
End If
Next i
Else ' non-spider irange
For i As Integer = 0 To iRange.Count - 1
iRange(i) = translocation(iRange(i))
Next i
End If
For i As Integer = iRange.Count - 1 To 0 Step -1 ' remove duplicates (from translocation, etc.)
For j As Integer = i - 1 To 0 Step -1
If iRange(i) = iRange(j) Then
iRange.RemoveAt(i)
Exit For
End If
Next j
Next i
Dim locale As New List(Of String)
Dim wlink As New List(Of String)
Dim ds As DataSet
Dim iTitle As Integer
ds = getDS("select * from translocation")
For Each dr As DataRow In ds.Tables(0).Rows
s1 = dr("newlocation")
If s1.StartsWith("the ") Then s1 = s1.Substring(4)
locale.Add(s1)
wlink.Add(dr("wikilink"))
Next dr
For i As Integer = iRange.Count - 1 To 0 Step -1 ' add wikilinks for some areas
iTitle = -1
s1 = iRange(i)
If s1.StartsWith("the ") Then s1 = s1.Substring(4)
For j As Integer = 0 To locale.Count - 1 ' check full title
If eqstr(s1, locale(j)) Then
iTitle = j
Exit For
End If
Next j
If iTitle < 0 Then
For j As Integer = 0 To locale.Count - 1 ' get the longest match
If (iTitle < 0 OrElse locale(j).Length > locale(iTitle).Length) AndAlso
iRange(i).Contains(locale(j)) Then iTitle = j
Next j
End If
If iTitle >= 0 AndAlso wlink(iTitle) <> "" Then ' add a wikilink
If locale(iTitle) = wlink(iTitle) Then
iRange(i) = iRange(i).Replace(wlink(iTitle), "[[" & wlink(iTitle) & "]]")
Else ' display different text than link
iRange(i) = iRange(i).Replace(locale(iTitle), "[[" & wlink(iTitle) & "|" & locale(iTitle) & "]]")
End If
End If
Next i
range = ""
If iRange.Count > 0 Then ' have some range
If eqstr(m.rank, "species") Or eqstr(m.rank, "subspecies") Then
range = "It is found in " & formatList(iRange, "and") & "."
Else
range = "They are found in " & formatList(iRange, "and") & "."
End If
End If
If range <> "" Then range = range.Replace("found in worldwide", "found worldwide")
If range.EndsWith("..") Then range = range.Substring(0, range.Length - 1)
If range.EndsWith("..") Then range = range.Substring(0, range.Length - 1)
Return range & ref
End Function
Function getgbifrange(m As taxrec, ByRef source As String) As List(Of String)
Dim ds, ds2 As DataSet
Dim irange As New List(Of String)
Dim countrycode, locationid, location, locality As String
Dim name1, name2 As String
Dim names1 As New List(Of String)
Dim names2 As New List(Of String)
Dim i, k As Integer
If m.gbifID = "" Then Return irange
ds = getDS("select * from gbif.distribution where taxonid = @parm1", m.gbifID)
For Each dr As DataRow In ds.Tables(0).Rows
locality = dr("locality")
If locality Is Nothing Then locality = ""
countrycode = dr("countrycode")
If countrycode Is Nothing Then countrycode = ""
locationid = dr("locationid")
If locationid Is Nothing Then locationid = ""
If dr("source") = "Integrated Taxonomic Information System (ITIS)" And locationid = "" And countrycode = "" Then
' use the locality
locality = locality.Replace("""", "")
locality = translocation(locality)
If irange.IndexOf(locality) < 0 Then irange.Add(locality)
Else ' get it from name1, name2
name1 = "" : name2 = ""
If countrycode IsNot Nothing AndAlso countrycode <> "" Then ' use countrycode
ds2 = getDS("select * from glocation where countrycode = @parm1", countrycode)
ElseIf Not locationid.StartsWith("TDWG") And countrycode = "" Then ' use the locality
ds2 = getDS("select * from glocation where name = @parm1 order by idq", locality)
ElseIf locationid IsNot Nothing AndAlso locationid <> "" Then ' use locationid
If locationid.StartsWith("TDWG:") Then locationid = locationid.Substring(5)
ds2 = getDS("select * from glocation where code = @parm1", locationid)
Else
ds2 = Nothing
End If
If ds2 IsNot Nothing AndAlso ds2.Tables(0).Rows.Count > 0 Then
name1 = ds2.Tables(0).Rows(0)("name1")
name2 = ds2.Tables(0).Rows(0)("name2")
name1 = translocation(name1)
name2 = translocation(name2)
End If
If name1 <> "" Then
If name2.Contains("United States") Then name2 = "the United States"
If name2.Contains("Canada") Then name2 = "Canada"
If name2.Contains("Atlantic Ocean") Then name2 = "the Atlantic Ocean"
If name2.Contains("Tropical Africa") Then name2 = "Tropical Africa"
End If
If name1.Contains("Europe &") OrElse name2.Contains("Europe &") Then Stop
Select Case name2
Case "the Caribbean",
"Central America",
"Mexico",
"China",
"Western Asia",
"Indo-China",
"the Indian Subcontinent",
"Australia",
"New Zealand"
' use name2
Case "the southwestern Pacific",
"the south-central Pacific",
"south-central Pacific",
"the northwestern Pacific",
"the north-central Pacific",
"north-central Pacific"
name1 = "the Pacific Ocean"
name2 = ""
Case Else
name2 = ""
End Select
i = names1.IndexOf(name1)
If i < 0 Then
names1.Add(name1)
names2.Add(name2)
ElseIf names2(i) <> name2 Then
names2(i) = "" ' go with continent if there's more than one country in it.
End If
If name1 IsNot Nothing AndAlso name1 <> "" Then
Select Case (dr("source"))
Case "Integrated Taxonomic Information System (ITIS)"
' source = "itis"
Case "Catalogue of Life"
' source = "catlife"
Case "World Register of Marine Species"
source = "worms"
End Select
End If
End If
Next dr
' combine temperate and tropical Asia into a single continent.
i = names1.IndexOf("temperate Asia")
k = names1.IndexOf("tropical Asia")
If i >= 0 AndAlso k >= 0 Then
names1(i) = "Asia" : names2(i) = ""
names1.RemoveAt(k) : names2.RemoveAt(k)
End If
' special case for Europe & itis
If irange.IndexOf("Europe & Northern Asia (excluding China)") >= 0 Then
i = names1.IndexOf("Europe")
If i >= 0 Then
names1.RemoveAt(i)
names2.RemoveAt(i)
End If
End If
For i1 As Integer = 0 To names1.Count - 1
If names2(i1) <> "" Then location = names2(i1) Else location = names1(i1)
If location <> "" AndAlso irange.IndexOf(location) < 0 Then irange.Add(location)
Next i1
Return irange
End Function
Function translocation(locality As String)
' translate locality to better form
Dim s As String
s = getScalar("select newlocation from translocation where original = @parm1", locality)
If s Is Nothing OrElse s = "" Then Return locality
Return s
End Function
Function formatList(ss As List(Of String), separator As String) As String
' add commas and ", and" to a list, return a single string
' separator is "and" or "or"
Dim s = ""
If ss.Count = 1 Then
s = ss(0)
ElseIf ss.Count = 2 Then
s = ss(0) & " " & separator & " " & ss(1)
Else
For i As Integer = 0 To ss.Count - 1
If i = ss.Count - 1 Then ' done
s &= ss(i)
ElseIf i = ss.Count - 2 Then ' next to last
s &= ss(i) & ", " & separator & " "
Else
s &= ss(i) & ", " ' others
End If
Next i
End If
Return s
End Function
Function loadMatch(sTaxon As String, addon As Boolean) As taxrec
' load a taxrec from the database for a taxon
Dim match As New taxrec
Dim ds As New DataSet
ds = TaxonkeySearch(sTaxon)
If ds IsNot Nothing Then
For Each dr As DataRow In ds.Tables(0).Rows
match = getTaxrec(dr, addon)
If eqstr(match.taxon, sTaxon) AndAlso match.rank <> "" AndAlso
itisRankID.ContainsKey(match.rank) Then Exit For
Next dr ' should only be one
End If
If match.taxid = "" AndAlso match.gbifID = "" Then ' check gbif
ds = getDS("select * from gbif.tax where name = @parm1 and usable <> ''", sTaxon)
'ds = getDS("select * from gbif.tax join taxa.gbifplus using (taxid) where name = @parm1 and usable <> ''", sTaxon)
If ds.Tables(0).Rows.Count = 1 Then match = getTaxrecg(ds.Tables(0).Rows(0), addon)
End If
If match.taxid = "" AndAlso match.catLifeID = "" Then ' check catlife
ds = getDS("select * from catlife.tax where name = @parm1 and namestatus = 'accepted name'", sTaxon)
If ds.Tables(0).Rows.Count = 1 Then match = getCatLifeTaxrec(ds.Tables(0).Rows(0), addon)
End If
If match.taxid = "" AndAlso match.spiderID <= 0 Then ' check spidercat
ds = getDS("select * from spidercat where name = @parm1", sTaxon)
If ds.Tables(0).Rows.Count = 1 Then match = getspiderTaxrec(ds.Tables(0).Rows(0), addon)
End If
Return match
End Function
Function loadGbifMatch(sTaxon As String, addon As Boolean) As taxrec
' like loadmatch, except for gbif including accepted and doubtful taxa.
Dim match As New taxrec
Dim ds As New DataSet
ds = getDS("select * from gbif.tax " &
" where name = @parm1 and (status = 'accepted' or status = 'doubtful')", sTaxon)
If ds.Tables(0).Rows.Count = 1 Then
match = getTaxrecg(ds.Tables(0).Rows(0), addon)
Return match
ElseIf ds.Tables(0).Rows.Count > 1 Then
For Each dr As DataRow In ds.Tables(0).Rows
If dr("usable") = "ok" Then
match = getTaxrecg(dr, addon)
Return match
End If
Next dr
For Each dr As DataRow In ds.Tables(0).Rows
If dr("status") = "accepted" Then
match = getTaxrecg(dr, addon)
Return match
End If
Next dr
match = getTaxrecg(ds.Tables(0).Rows(0), addon)
End If
Return match
End Function
Sub MergeSort(ByRef v As Object, ByRef ix As List(Of Integer), min As Integer, max As Integer)
' use for in-place sorting.
Dim half As Integer
Dim isString As Boolean
Dim j, i, k As Integer
If v.count - 1 < min Then Exit Sub
isString = TypeOf v(min) Is String
If max - min > 1 Then
Dim tix As New List(Of Integer)
tix.AddRange(ix) ' copy index array
half = (max + min) * 0.5
If min < half Then MergeSort(v, tix, min, half) ' sort lower half
If half + 1 < max Then MergeSort(v, tix, half + 1, max) ' sort upper half
' now merge the two sorted halves
i = min : j = half + 1 : k = min - 1
Do While i <= half Or j <= max
k = k + 1
If j > max Then
ix(k) = tix(i)
i = i + 1
ElseIf i > half Then
ix(k) = tix(j)
j = j + 1
' ignore case when comparing strings
ElseIf (isString AndAlso String.Compare(v(tix(i)), v(tix(j)), True) <= 0) OrElse _
(Not isString AndAlso v(tix(i)) <= v(tix(j))) Then
ix(k) = tix(i)
i = i + 1
Else
ix(k) = tix(j)
j = j + 1
End If
Loop
Else ' 1 or 2 elements -- do by hand
If max - min >= 1 Then
k = min
' If v(ix(k)) > v(ix(k + 1)) Then ' compare first and second items
If isString AndAlso String.Compare(v(ix(k)), v(ix(k + 1)), True) > 0 OrElse _
(Not isString) AndAlso v(ix(k)) > v(ix(k + 1)) Then
i = ix(k) : ix(k) = ix(k + 1) : ix(k + 1) = i ' swap
End If
End If
End If
End Sub
Function abbreviate(s1 As String)
' abbreviates the genus in a species or subspecies combination
Dim k As Integer
k = s1.IndexOf(" ")
If k >= 0 And k < s1.Length Then
Return UCase(s1.Substring(0, 1)) & ". " & s1.Substring(k + 1)
Else
Return s1
End If
End Function
Function getUrlDomain(s As String) As String
' get the domain of a url.
Dim i As Integer
If s Is Nothing OrElse s = "" Then Return ""
s = s.Replace("https://", "")
s = s.Replace("http://", "")
If s.StartsWith("www.") Then s = s.Replace("www.", "")
i = s.IndexOf("/")
If i < 0 Then i = s.IndexOf("?")
If i < 0 Then i = s.IndexOf("#")
If i < 0 Then i = s.IndexOf("|")
If i >= 0 Then s = s.Substring(0, i)
Return s
End Function
Function binsearch(ByRef ss As List(Of String), s As String, i1 As Integer, i2 As Integer) As Integer
Dim ihalf As Integer
Dim i As Integer
If s = ss(i2) Then Return i2
If i1 = i2 OrElse i1 + 1 = i2 Then Return -1
ihalf = (i1 + i2) \ 2
i = String.Compare(s, ss(ihalf), True)
If i > 0 Then
Return binsearch(ss, s, ihalf, i2)
ElseIf i < 0 Then
Return binsearch(ss, s, i1, ihalf)
Else
Return ihalf
End If
End Function
Sub gardener(PageID As String, ByRef inPages As List(Of String), ByRef level As Integer,
max As Integer, maxlev As Integer)
' check for walled garden
' returns a list of pages that link here, along with their incoming links, and theirs, etc.
' aborts when inpages.count reaches max or recursion level (no-repeats) reaches maxlev.
Dim s, s1 As String
Dim incoming As New List(Of String)
Dim ss As New List(Of String)
Dim r1 As HttpResponseMessage
Dim qcontent As FormUrlEncodedContent
Dim parms As Dictionary(Of String, String)
Dim jq As JObject
Dim jtt As List(Of JToken)
level += 1
If level > maxlev Then level = -1
If level < 0 Then Exit Sub
parms = New Dictionary(Of String, String)
parms.Add("action", "query")
parms.Add("pageids", PageID)
parms.Add("prop", "linkshere")
parms.Add("lhnamespace", "0")
parms.Add("lhlimit", max)
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
ss = New List(Of String)
r1 = qClient.PostAsync(urlWikiPedia, qcontent).Result
s = r1.Content.ReadAsStringAsync().Result
jq = JObject.Parse(s)
If jq.SelectToken("query.pages." & PageID & ".linkshere") IsNot Nothing Then
jtt = jq.SelectToken("query.pages." & PageID & ".linkshere").ToList
For Each jt As JToken In jtt
s1 = jt("pageid")
If inPages.IndexOf(s1) < 0 Then
ss.Add(s1)
inPages.Add(s1)
If inPages.Count >= max Then Exit Sub
End If
Next jt
For Each s1 In ss
gardener(s1, inPages, level, max, maxlev)
If level < 0 Or inPages.Count >= max Then Exit Sub
Next s1
End If
level -= 1
End Sub
Function getQnumber(m As taxrec, ancestor As List(Of taxrec)) As String
' get the wikidata qnumber of an animal.
Dim s, s1, s2, s3 As String
Dim sb As New StringBuilder
Dim qNumber As String
Dim jq As JObject
Dim jz, jz2, jt As JToken
Dim parms As New Dictionary(Of String, String)
Dim r1 As HttpResponseMessage
Dim qcontent As FormUrlEncodedContent
Dim pageID As String
Dim parentTaxon As String
's = getWikiDataPage(m.taxon, urlWikiData)
parms = New Dictionary(Of String, String)
parms.Add("action", "wbsearchentities")
parms.Add("search", m.taxon) ' "File:Aeoloplides turnbulli P1490124a.jpg"
parms.Add("language", "en")
parms.Add("limit", "50")
parms.Add("continue", "0")
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(urlWikiData, qcontent).Result
s = r1.Content.ReadAsStringAsync().Result
jq = JObject.Parse(s)
jz = jq.SelectToken("search")
qNumber = ""
For i1 As Integer = 0 To jz.Count - 1
Try
s1 = jz(i1).SelectToken("match.type").ToString
s2 = jz(i1).SelectToken("match.language").ToString
s3 = jz(i1).SelectToken("match.text").ToString
Catch ex As Exception
s1 = "" : s2 = "" : s3 = ""
End Try
pageID = jz(i1).SelectToken("title").ToString
If s1 = "label" And s2 = "en" And eqstr(s3, m.taxon) Then
pageID = jz(i1).SelectToken("title").ToString
parms = New Dictionary(Of String, String)
parms.Add("action", "wbgetentities")
parms.Add("ids", pageID) ' "File:Aeoloplides turnbulli P1490124a.jpg"
parms.Add("props", "claims") ' P815 P2464 = bugguide
parms.Add("languages", "en") ' P815
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(urlWikiData, qcontent).Result
s = r1.Content.ReadAsStringAsync().Result
jq = JObject.Parse(s)
jz2 = jq.SelectToken("entities." & pageID & ".claims") ' 109216
' P171 is parent
' P105 is rank
jt = jz2.SelectToken("P171") ' parent
If jt IsNot Nothing Then
s2 = jt.ToList(0)("mainsnak")("datavalue")("value")("id").ToString ' parent qnumber
If s2 <> "" Then
parms = New Dictionary(Of String, String)
parms.Add("action", "wbgetentities")
parms.Add("ids", s2) ' "File:Aeoloplides turnbulli P1490124a.jpg"
parms.Add("props", "claims") ' P815 P2464 = bugguide
parms.Add("languages", "en") ' P815
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(urlWikiData, qcontent).Result
s3 = r1.Content.ReadAsStringAsync().Result
jq = JObject.Parse(s3)
jz2 = jq.SelectToken("entities." & s2 & ".claims")
jt = jz2.SelectToken("P225") ' value
parentTaxon = jt.ToList(0)("mainsnak")("datavalue")("value").ToString ' parent qnumber
If isAncestor(ancestor, parentTaxon, 0) Then Return pageID
End If
jt = jz2.SelectToken("P171") ' grandparent
If jt IsNot Nothing Then
s2 = jt.ToList(0)("mainsnak")("datavalue")("value")("id").ToString ' parent qnumber
If s2 <> "" Then
parms = New Dictionary(Of String, String)
parms.Add("action", "wbgetentities")
parms.Add("ids", s2) ' "File:Aeoloplides turnbulli P1490124a.jpg"
parms.Add("props", "claims") ' P815 P2464 = bugguide
parms.Add("languages", "en") ' P815
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(urlWikiData, qcontent).Result
s3 = r1.Content.ReadAsStringAsync().Result
jq = JObject.Parse(s3)
jz2 = jq.SelectToken("entities." & s2 & ".claims")
jt = jz2.SelectToken("P225") ' value
parentTaxon = jt.ToList(0)("mainsnak")("datavalue")("value").ToString ' parent qnumber
If isAncestor(ancestor, parentTaxon, 0) Then Return pageID
End If
End If
End If
End If
Next i1
Return ""
End Function
Function addInitialPeriods(s As String) As String
' puts periods at initials in reference names.
Dim s1 As String
If s Is Nothing OrElse s = "" Then Return ""
s1 = s.Trim
s1 = Regex.Replace(s1, "([^A-Za-z\-\'’]|^)([A-Z])([^A-Za-z\.\-\'’]|$)", "$1$2.$3") ' A '
s1 = Regex.Replace(s1, "([^A-Za-z\-\'’]|^)([A-Z])([^A-Za-z\.\-\'’]|$)", "$1$2.$3") ' A '
s1 = Regex.Replace(s1, "([^A-Za-z\-\'’]|^)([A-Z])([A-Z])([^A-Za-z\.\-\'’]|$)", "$1$2.$3.$4") ' AA '
s1 = Regex.Replace(s1, "([^A-Za-z\-\'’]|^)([A-Z])([A-Z])([^A-Za-z\.\-\'’]|$)", "$1$2.$3.$4") ' AA '
s1 = Regex.Replace(s1, "([^A-Za-z\-\'’]|^)([A-Z])([A-Z])([A-Z])([^A-Za-z\.\-\'’]|$)", "$1$2.$3.$4.$5") 'AAA'
s1 = Regex.Replace(s1, "([^A-Za-z\-\'’]|^)([A-Z])([A-Z])([A-Z])([^A-Za-z\.\-\'’]|$)", "$1$2.$3.$4.$5") 'AAA'
s1 = Regex.Replace(s1, "([^A-Za-z\-\'’]|^)(Jr)([^A-Za-z\.\-\'’]|$)", "$1$2.$3")
s1 = s1.Replace(" |", "|")
Return s1.Trim
End Function
Sub appendPageTitle(pageTitle As String)
' write to qbug.txt
Dim fname As String
Dim sq() As String = Nothing
fname = Path.ChangeExtension(My.Settings.logfile, "txt")
If pageTitle.StartsWith("orphan") Then
sq = pageTitle.Split(vbTab)
For i1 As Integer = 1 To sq.Count - 1
File.AppendAllText(fname, "* " & Format(Now, "yyyy-MM-dd HH:mm:ss") & " orphan, check parent: " & "[[" & sq(i1) & "]]" & vbCrLf)
Next i1
ElseIf pageTitle = "" Then
File.AppendAllText(fname, "* " & vbCrLf & "* " & Format(Now, "yyyy-MM-dd HH:mm:ss") & vbCrLf)
Else
File.AppendAllText(fname, "* " & Format(Now, "yyyy-MM-dd HH:mm:ss") & " [[" & pageTitle & "]]" & vbCrLf)
End If
End Sub
Sub outLog(s As String)
File.AppendAllText(My.Settings.logfile, Format(Now, "yyyy-MM-dd HH:mm:ss") & vbTab & s & vbCrLf)
End Sub
Function citation(ref As refrec) As String
' returns a citation in {{cite...}} format
Dim afirst() As String
Dim alast() As String = {}
Dim efirst() As String
Dim elast() As String
Dim cit As String = ""
Dim maxAuthors As Integer = 4
Dim s1 As String
Dim sq() As String
If ref.pubtype <> "" Then
cit = "{{Cite " & ref.pubtype.ToLower
ElseIf ref.journal = "" And ref.url <> "" And ref.chapter = "" Then
cit = "{{Cite web"
Else
cit = "{{Cite journal"
End If
If ref.comment <> "" Then cit &= " " & ref.comment
cit &= vbCrLf
If cit.Contains("Cite web") AndAlso ref.urlAccessed <> "" Then cit &= "| accessdate = " & ref.urlAccessed & vbCrLf
If ref.title <> "" Then cit &= "| title = " & ref.title & vbCrLf
If ref.year <> "" Then cit &= "| date = " & ref.year & vbCrLf
If ref.alast <> "" Then
afirst = ref.afirst.Split("|")
alast = ref.alast.Split("|")
For i As Integer = 0 To afirst.Count - 1
If alast(i) <> "" Then cit &= "| last" & i + 1 & " = " & alast(i) & " | first" & i + 1 & " = " & afirst(i) & vbCrLf
Next i
End If
If ref.elast <> "" Then
efirst = ref.efirst.Split("|")
elast = ref.elast.Split("|")
For i As Integer = 0 To efirst.Count - 1
If elast(i) <> "" Then cit &= "| editor-last" & i + 1 & " = " & elast(i) & " | editor-first" & i + 1 & " = " & efirst(i) & vbCrLf
Next i
End If
If alast.Count > maxAuthors Then cit &= "| display-authors = " & maxAuthors & vbCrLf
If ref.journal <> "" Then cit &= "| journal = " & ref.journal & vbCrLf
If ref.publisher <> "" Then cit &= "| publisher = " & ref.publisher & vbCrLf
s1 = ""
If ref.series <> "" Then s1 &= "| series = " & ref.series
If ref.volume <> "" Then s1 &= "| volume = " & ref.volume
If ref.issue <> "" Then s1 &= "| issue = " & ref.issue
If ref.chapter <> "" Then s1 &= "| chapter = " & ref.chapter
If ref.pages <> "" Then
If ref.pages.Contains("-") Or ref.pages <> "–" Or ref.pages = "," Then
s1 &= "| pages = " & ref.pages
Else
s1 &= "| page = " & ref.pages
End If
End If
If s1 <> "" Then cit &= s1 & vbCrLf
If ref.isbn <> "" Then cit &= "| isbn = " & ref.isbn & vbCrLf
If ref.issn <> "" Then cit &= "| issn = " & ref.issn & vbCrLf
If ref.url <> "" Then cit &= "| url = " & ref.url & vbCrLf ' url not necessary with doi? Sometimes only the URL works.
If ref.doi <> "" Then
cit &= "| doi = " & ref.doi
If ref.doiaccess <> "" Then cit &= "| doi-access = " & ref.doiaccess
cit &= vbCrLf
End If
sq = ref.etc.Split("|".ToCharArray, StringSplitOptions.RemoveEmptyEntries)
For Each s2 As String In sq
If s2.Trim <> "" Then cit &= "| " & s2.Trim & vbCrLf
Next s2
cit &= "}}"
Return cit
End Function
Function getTaxAmbig(taxon As String) As String
If taxAmbig.ContainsKey(taxon) Then Return taxAmbig(taxon)
Return taxon
End Function
Function orphanCheck(pageTitle As String) As List(Of String)
' returns the incoming links in mainspace
Dim parms As New Dictionary(Of String, String)
Dim r1 As HttpResponseMessage
Dim qcontent As FormUrlEncodedContent
Dim jq As JObject
Dim s As String
Dim cont As String
Dim pages As List(Of String)
parms = New Dictionary(Of String, String)
parms.Add("action", "query")
parms.Add("titles", pageTitle) ' "File:Aeoloplides turnbulli P1490124a.jpg"
parms.Add("prop", "linkshere")
parms.Add("lhlimit", "500")
parms.Add("lhnamespace", "0")
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(urlWikiPedia, qcontent).Result
s = r1.Content.ReadAsStringAsync().Result
jq = JObject.Parse(s)
pages = New List(Of String)
If jq.SelectToken("query.pages.*.linkshere") IsNot Nothing Then
For i1 As Integer = 0 To jq.SelectToken("query.pages.*.linkshere").Count - 1
s = jq.SelectToken("query.pages.*.linkshere")(i1)("title")
pages.Add(s)
Next i1
End If
cont = jq.SelectToken("continue.lhcontinue")
parms = New Dictionary(Of String, String)
parms.Add("action", "query")
parms.Add("titles", pageTitle) ' "File:Aeoloplides turnbulli P1490124a.jpg"
parms.Add("prop", "linkshere")
parms.Add("lhlimit", "500")
parms.Add("lhnamespace", "0")
parms.Add("lhcontinue", cont)
parms.Add("format", "json")
qcontent = New FormUrlEncodedContent(parms)
r1 = qClient.PostAsync(urlWikiPedia, qcontent).Result
s = r1.Content.ReadAsStringAsync().Result
jq = JObject.Parse(s)
If jq.SelectToken("query.pages.*.linkshere") IsNot Nothing Then
For i1 As Integer = 0 To jq.SelectToken("query.pages.*.linkshere").Count - 1
s = jq.SelectToken("query.pages.*.linkshere")(i1)("title")
pages.Add(s)
Next i1
End If
cont = jq.SelectToken("continue.lhcontinue")
Return pages
End Function
Class references
Dim name As New List(Of String)
Dim reference As New List(Of String)
Dim used As New List(Of Boolean)
Dim k As Integer
Function refExists(rname As String, ref As String) As Integer
' return 2 if reference itself exists, 1 if the ref name exists, 0 if clear
If reference.Contains(ref) Then Return 2
If name.Contains(rname) Then Return 1
Return 0
End Function
Function Ref(rname As String) As String
' <ref name=name/>
' sets used = true
k = name.IndexOf(rname)
If k >= 0 Then
used(k) = True
Return "<ref name=" & rname & "/>"
Else
Return ""
End If
End Function
Function longRef(rname As String) As String
' does not include <ref> and </ref>
' does not set used = true
k = name.IndexOf(rname)
If k >= 0 Then
Return reference(k)
Else
Return ""
End If
End Function
Sub addref(rname As String, ref As String)
' adds a references, sets used to false
If refExists(rname, ref) = 0 Then
name.Add(rname)
reference.Add(ref)
used.Add(False)
End If
End Sub
Function allRefs() As String
' returns a string of all the used references, with <ref name=> and </ref>
Dim s As String = ""
For i As Integer = 0 To name.Count - 1
If used(i) Then
If s <> "" Then s &= vbCrLf ' blank line between references
s &= "<ref name=" & name(i) & ">" & vbCrLf & reference(i) & "</ref>" & vbCrLf
End If
Next i
Return s
End Function
End Class
Function formatchildren(m As taxrec, children As List(Of taxrec), refs As references,
ancestor As List(Of taxrec), showSource As Boolean) As String
' returns a formatted list of children, either in a sentence or a table.
Dim subrank As String
Dim s, s1, s2 As String
Dim ss As New List(Of String)
Dim sq As New List(Of String)
Dim sTaxon As String
Dim childred As New List(Of taxrec)
Dim source As String
Dim sourceUsed As Boolean = False
Dim spiderflag As Boolean
Dim bugref As String
If children.Count <= 1 Then Return ""
sTaxon = m.taxon
If eqstr(m.rank, "species") Or eqstr(m.rank, "genus") Or eqstr(m.rank, "subspecies") Then sTaxon = "''" & sTaxon & "''"
For i1 As Integer = 0 To children.Count - 1
s1 = getDisambig(children(i1))
If s1 = "" Then
s1 = children(i1).taxon
If (eqstr(children(i1).rank, "species") Or eqstr(children(i1).rank, "subspecies")) And children.Count = 1 Then s1 = abbreviate(s1)
Else
s1 = s1 & "|" & children(i1).taxon ' should not happen for species or subspecies, so abbreviation won't matter
End If
If eqstr(children(i1).rank, "species") Or eqstr(children(i1).rank, "genus") Then
s1 = "''[[" & s1.Trim & "]]''"
ElseIf eqstr(children(i1).rank, "subspecies") Then
s1 = "''" & s1.Trim & "''"
Else
s1 = "[[" & s1.Trim & "]]"
End If
If children(i1).taxon = "Mesagyrtoides" Then Stop
If children(i1).extinct Then s1 = "† " & s1
If m.spiderID > 0 And children(i1).spiderID <= 0 Then
s1 = "* (" & s1 & ")"
spiderflag = True
Else
s1 = "* " & s1
End If
If children(i1).authority IsNot Nothing AndAlso children(i1).authority.Trim <> "" Then
s1 &= " <small>" & children(i1).authority & "</small>"
End If
source = ""
If showSource Then
If children(i1).itistsn > 0 Then source &= " i"
If children(i1).catLifeID IsNot Nothing AndAlso children(i1).catLifeID <> "" Then source &= " c"
If children(i1).gbifID <> "" Then source &= " g"
If LCase(children(i1).link) IsNot Nothing AndAlso LCase(children(i1).link).Contains("bugguide") Then source &= " b"
If children(i1).spiderID > 0 Then source &= " s"
If source <> "" Then
s1 &= "<span style=""color:gray""><sup>" & source & "</sup></span>"
sourceUsed = True
End If
End If
s2 = firstCommon(children(i1).taxid)
If s2 <> "" Then s1 &= " (" & s2 & ")"
ss.Add(s1)
Next i1
subrank = LCase(children(0).rank)
ss.Sort()
subrank = pluralRank(subrank)
s = "==" & UCase(subrank.Chars(0)) & subrank.Substring(1) & "==" & vbCrLf
If children.Count < 10 Then
s1 = numeral(children.Count)
Else
s1 = children.Count
End If
s &= "These " & s1 & " " & subrank & " belong to the " & LCase(m.rank) & " " & sTaxon & ":" & vbCrLf
If children.Count >= maxColumn Then
If itisRankID(children(0).rank) >= 220 Then
s &= "{{Div col|colwidth=29em}}" & vbCrLf ' species or subspecies
Else
s &= "{{Div col|colwidth=22em}}" & vbCrLf ' single word taxon
End If
End If
spiderflag = False
For i1 As Integer = 0 To children.Count - 1
s &= ss(i1) & vbCrLf
Next i1
If s.EndsWith(vbCrLf) Then s = s.Substring(0, s.Length - 2)
If children.Count >= maxColumn Then s &= vbCrLf & "{{Div col end}}"
If refs.refExists("bugguide", "") > 0 Then ' name exists - use generic bugguide ref
bugref = refs.Ref("bugguide")
Else
bugref = refs.Ref("buglink") ' specific reference
End If
If sourceUsed Then
If isAncestor(ancestor, "Araneae", 0) Then ' spider
s &= "<small>Data sources: i = ITIS," & refs.Ref("itis") & " c = Catalogue of Life," & refs.Ref("catlife") &
" g = GBIF," & refs.Ref("gbif") & " b = BugGuide.net," & bugref &
" s = World Spider Catalog" & refs.Ref("spidercat") & "</small>"
If spiderflag Then s &= vbCrLf & "<small>" & StrConv(m.rank, VbStrConv.ProperCase) & "names in parentheses may no longer be valid.</small>"
Else
s &= vbCrLf & "<small>Data sources: i = ITIS," & refs.Ref("itis") & " c = Catalogue of Life," & refs.Ref("catlife") &
" g = GBIF," & refs.Ref("gbif") & " b = BugGuide.net" & bugref & "</small>"
End If
s &= vbCrLf
End If
Return s
End Function
Function firstCommon(taxonID As String) As String
' select the first common name (the best one, lower case) from wiki.
Dim ss() As String
Dim s As String
If taxonID <> "" Then
s = getScalar("select commonnames from oddinfo where taxid = @parm1", taxonID)
Else
s = ""
End If
If s IsNot Nothing Then
ss = s.Split("|")
If ss.Count >= 1 Then Return ss(0)
End If
Return ""
End Function
Function getDisambig(m As taxrec) As String
' get a disambig link for a taxon, if there is one.
' "" (for no change) or a page title, normally the same but sometimes with (genus) or something added
Dim s1 As String
If m.taxid <> "" Then
s1 = getScalar("select ambiglink from oddinfo where taxid = @parm1", m.taxid)
Else
s1 = ""
End If
If s1 = "" Then s1 = getScalar("select ambiglink from oddinfo where name = @parm1", m.taxon)
Return s1
End Function
Sub defineRefs(tmatch As taxrec, ancestor As List(Of taxrec), bugname As String,
refs As references, showSource As Boolean)
' define the "automatic" references (not in wikirefs) in case they're needed later
Dim s, s1 As String
Dim prec As paleorec
s1 = ""
If tmatch.itistsn > 0 Then
s = "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=" & tmatch.itistsn
s = citeweb(s, bugname & " Report", "Integrated Taxonomic Information System")
'If tmatch.itiscomments IsNot Nothing AndAlso tmatch.itiscomments.Count > 0 Then s &= "{{PD-notice}}"
refs.addref("itis", s)
Else
' define a generic itis ref
s = citeweb("https://www.itis.gov/", "ITIS, Integrated Taxonomic Information System", "")
refs.addref("itis", s)
End If
If tmatch.hodges <> "" AndAlso isAncestor(ancestor, "lepidoptera", 0) Then
s = "http://mothphotographersgroup.msstate.edu/species.php?hodges=" & tmatch.hodges
s1 = tmatch.taxon
If eqstr(tmatch.rank, "species") Or eqstr(tmatch.rank, "genus") Or eqstr(tmatch.rank, "subspecies") Then s1 = "''" & s1 & "''"
s = citeweb(s, "North American Moth Photographers Group, " & s1, "")
refs.addref("mpg", s)
End If
If tmatch.catLifeID <> "" Then
If eqstr(tmatch.rank, "species") Or eqstr(tmatch.rank, "subspecies") Then
s = "http://www.catalogueoflife.org/col/details/species/id/" & tmatch.catLifeID
s = citeweb(s, bugname & " species details", "Catalogue of Life")
refs.addref("catlife", s)
Else
s = "http://www.catalogueoflife.org/col/browse/tree/id/" & tmatch.catLifeID
s = citeweb(s, "Browse " & bugname, "Catalogue of Life")
refs.addref("catlife", s)
End If
ElseIf showSource Then
' define a generic webref
s = citeweb("http://www.catalogueoflife.org/", "Catalogue of Life", "")
refs.addref("catlife", s)
End If
If tmatch.gbifID <> "" Then
s = "https://www.gbif.org/species/" & tmatch.gbifID
s = citeweb(s, bugname, "GBIF")
refs.addref("gbif", s)
ElseIf showSource Then
' define a generic webref
s = citeweb("https://www.gbif.org/", "GBIF", "")
refs.addref("gbif", s)
End If
If tmatch.spiderlink <> "" Then
s = citeweb(tmatch.spiderlink, bugname, "NMBE World Spider Catalog")
refs.addref("spidercat", s)
End If
If tmatch.iucnID <> "" Then
s = "http://oldredlist.iucnredlist.org/details/" & tmatch.iucnID ' http://www.iucnredlist.org/details/42685/0
s = citeweb(s, bugname & " Red List status", "IUCN Red List")
refs.addref("iucn", s)
End If
If tmatch.taxid <> "" Then
s = citeweb("https://xpda.com/bugs/showQuery.aspx?taxon=" & tmatch.taxon.Replace(" ", "%20"),
" Images and collection data for " & bugname, "Pictures from Earth")
refs.addref("xp01", s)
End If
If tmatch.link <> "" Then
If Not LCase(tmatch.link).StartsWith("wsc.") Or tmatch.spiderlink = "" Then ' use the domain
s1 = getUrlDomain(tmatch.link).Trim
If s1 <> "" Then
If s1.Contains("paleobiodb.org") Then
s = citeweb(tmatch.link, "The Paleobiology Database, " & tmatch.rank & " " & bugname, "")
refs.addref("buglink", s)
Else
If s1 = "bugguide.net" Then s1 = "BugGuide.net"
s = citeweb(tmatch.link, bugname & " " & tmatch.rank & " Information", s1)
refs.addref("buglink", s)
End If
End If
If showSource AndAlso Not tmatch.link.ToLower.Contains("bugguide") Then ' add generic bugguide reference, for data source
s = citeweb("https://bugguide.net/", "BugGuide.net", "")
refs.addref("bugguide", s)
End If
End If
End If
If tmatch.extinct AndAlso (Not s1.Contains("paleobiodb")) Then
' add paleo reference
prec = getPaleo(tmatch)
If prec.pID > 0 Then
s = citeweb("https://paleobiodb.org/classic/basicTaxonInfo?taxon_no=" & prec.pID, "The Paleobiology Database, " & tmatch.rank & " " & bugname, "")
refs.addref("paleo", s)
End If
End If
End Sub
Function citeweb(url As String, title As String, site As String) As String
' returns a citation in {{cite web...] format
Dim s As String
' "{{cite web|url=" & text & "|title=" & webtitle & "|website=" & substring text & "|accessdate= format(date, "yyyy-MM-dd") & "}}"
s = "{{Cite web| title=" & title & vbCrLf
s &= "| url=" & url & vbCrLf
If site <> "" Then s &= "| website=" & site & vbCrLf
s &= "| accessdate=" & Format(CDate(Today), "yyyy-MM-dd") & vbCrLf
s &= "}}"
Return s
End Function
Function createTaxTemplate(m As taxrec, parent As String) As String
' create a taxonomy template for taxrec
Dim sb As StringBuilder
'{{Don't edit this line {{{machine code|}}}
'|rank=
'|link={{subst:#titleparts:{{subst:PAGENAME}}|2|2}}
'|parent=
'|refs=<!--Shown on this page only; don't include <ref> tags -->
'}}
sb = New StringBuilder
sb.AppendLine("{{Don't edit this line {{{machine code|}}}")
sb.AppendLine("|rank=" & latinRank(m.rank))
If m.ambigLink <> "" Then
sb.AppendLine("|link=" & m.ambigLink & "|" & m.taxon)
Else
sb.AppendLine("|link=" & m.taxon)
End If
sb.AppendLine("|parent=" & parent)
If m.extinct Then sb.AppendLine("|extinct=yes")
If (m.spiderlink <> "") Then
sb.AppendLine("|refs=" & m.spiderlink)
ElseIf m.taxlink <> "" Then
sb.AppendLine("|refs=" & m.taxlink)
ElseIf m.itistsn > 0 Then
sb.AppendLine("|refs=https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=" & m.itistsn)
ElseIf (m.gbifID <> "" And m.gbifID <> "0") Then
sb.AppendLine("|refs=" & "https://www.gbif.org/species/" & m.gbifID)
ElseIf m.catLifeID <> "" Then
sb.AppendLine("|refs=" & "http://www.catalogueoflife.org/col/browse/tree/id/" & m.catLifeID)
Else
Return ""
End If
sb.AppendLine("}}")
Return sb.ToString
End Function
Class paleorec
Public pID As Integer = 0
Public name As String = ""
Public rank As String = ""
Public authority As String = ""
Public commonname As String = ""
Public parentID As Integer = 0
Public parentName As String = ""
Public extant As String = ""
Public nOccurences As Integer = 0
Public firstMaxma As String = ""
Public firstMinma As String = ""
Public lastMaxma As String = ""
Public lastMinma As String = ""
Public earlyinterval As String = ""
Public lateinterval As String = ""
Public nDesc As Integer = 0
Public nExtant As Integer = 0
Public phylum As String = ""
Public cclass As String = ""
Public order As String = ""
Public family As String = ""
Public genus As String = ""
Public imageID As Integer = 0
End Class
Function getPaleoRec(dr As DataRow) As paleorec
Dim prec As New paleorec
If IsDBNull(dr("orig_no")) Then prec.pID = "" Else prec.pID = dr("orig_no")
If IsDBNull(dr("taxon_name")) Then prec.name = "" Else prec.name = dr("taxon_name")
If IsDBNull(dr("taxon_rank")) Then prec.rank = "" Else prec.rank = dr("taxon_rank")
If IsDBNull(dr("taxon_attr")) Then prec.authority = "" Else prec.authority = dr("taxon_attr")
prec.authority = prec.authority.Replace(" and ", " & ")
If IsDBNull(dr("common_name")) Then prec.commonname = "" Else prec.commonname = dr("common_name")
If IsDBNull(dr("parent_no")) Then prec.parentID = "" Else prec.parentID = dr("parent_no")
If IsDBNull(dr("parent_name")) Then prec.parentName = "" Else prec.parentName = dr("parent_name")
If IsDBNull(dr("is_extant")) Then prec.extant = "" Else prec.extant = dr("is_extant")
If IsDBNull(dr("n_occs")) Then prec.nOccurences = "" Else prec.nOccurences = dr("n_occs")
If IsDBNull(dr("firstapp_max_ma")) Then prec.firstMaxma = "" Else prec.firstMaxma = dr("firstapp_max_ma")
If IsDBNull(dr("firstapp_min_ma")) Then prec.firstMinma = "" Else prec.firstMinma = dr("firstapp_min_ma")
If IsDBNull(dr("lastapp_max_ma")) Then prec.lastMaxma = "" Else prec.lastMaxma = dr("lastapp_max_ma")
If IsDBNull(dr("lastapp_min_ma")) Then prec.lastMinma = "" Else prec.lastMinma = dr("lastapp_min_ma")
If IsDBNull(dr("early_interval")) Then prec.earlyinterval = "" Else prec.earlyinterval = dr("early_interval")
If IsDBNull(dr("late_interval")) Then prec.lateinterval = "" Else prec.lateinterval = dr("late_interval")
If IsDBNull(dr("taxon_size")) Then prec.nDesc = "" Else prec.nDesc = dr("taxon_size")
If IsDBNull(dr("extant_size")) Then prec.nExtant = "" Else prec.nExtant = dr("extant_size")
If IsDBNull(dr("phylum")) Then prec.phylum = "" Else prec.phylum = dr("phylum")
If IsDBNull(dr("class")) Then prec.cclass = "" Else prec.cclass = dr("class")
If IsDBNull(dr("oorder")) Then prec.order = "" Else prec.order = dr("oorder")
If IsDBNull(dr("family")) Then prec.family = "" Else prec.family = dr("family")
If IsDBNull(dr("genus")) Then prec.genus = "" Else prec.genus = dr("genus")
If IsDBNull(dr("image_no")) Then prec.imageID = "" Else prec.imageID = dr("image_no")
Return prec
End Function
Function getPaleo(m As taxrec) As paleorec
' get a matching paleo orig_no.
Dim ds As DataSet
Dim author, year, mauthor, myear As String
Dim rm As RegularExpressions.Match
Dim anc As List(Of taxrec)
Dim prec As New paleorec
ds = getDS("select * from paleo.tax where taxon_name = @parm1 and taxon_rank = @parm2 and parent_name <> ''", m.taxon, m.rank)
If ds.Tables(0).Rows.Count = 0 Then Return New paleorec
For Each dr As DataRow In ds.Tables(0).Rows
prec = getPaleoRec(dr)
rm = Regex.Match(dr("taxon_attr"), "^.*?([\p{L}\-\.]+?),? ([0-9]{4})\)?$")
If rm.Groups.Count = 3 Then
author = rm.Groups(1).Value
year = rm.Groups(2).Value
Else
author = ""
year = ""
End If
rm = Regex.Match(m.authority, "^.*?([a-zA-Z\-\.]+?),? ([0-9]{4})\)?$")
If rm.Groups.Count = 3 Then
mauthor = rm.Groups(1).Value
myear = rm.Groups(2).Value
Else
mauthor = ""
myear = ""
End If
If year <> "" And year = myear OrElse author <> "" And
String.Compare(mauthor, author, StringComparison.OrdinalIgnoreCase) = 0 Then Return prec
' check ancestor
anc = getancestors(m, 1, False, "kingdom")
If isAncestor(anc, dr("parent_name"), 0) Then Return prec
If dr("family") <> "" Then
If isAncestor(anc, dr("family"), 0) Then Return prec
Else ' family blank
If isAncestor(anc, dr("oorder"), 0) Then Return prec
End If
Next dr
Return New paleorec
End Function
End Module