My current work.

BIN-Storing_data.R

@@ -33,7 +33,7 @@
 
 
 #TOC> ==========================================================================
-#TOC> 
+#TOC>
 #TOC>   Section  Title                                                   Line
 #TOC> -----------------------------------------------------------------------
 #TOC>   1        A Relational Datamodel in R: review                       63
@@ -56,7 +56,7 @@
 #TOC>   3.3        Create an R script to create your own database         572
 #TOC>   3.3.1          Check and validate                                 600
 #TOC>   3.4        Task: submit for credit (part 2/2)                     645
-#TOC> 
+#TOC>
 #TOC> ==========================================================================
 
 
@@ -206,7 +206,7 @@ str(philDB)
 # go back, re-read, play with it, and ask for help. These are the foundations.
 
 
-# ===   1.1.1  completing the database                       
+# ===   1.1.1  completing the database
 
 
 # Next I'll add one more person, and create the other two tables:
@@ -293,6 +293,47 @@ for (ID in pID) {
 #    BUT COPY THE EXACT, COMPLETE  OUTPUT, PASTE IT INTO YOUR SUBMISSION,
 #    AND FORMAT IT CORRECTLY.
 
+# == Submission - Code to add another philosopher to the datamodel:
+
+pID <- autoincrement(philDB$person)
+immanuelKant <- data.frame(id = pID,
+                           name = "Immanuel Kant",
+                           born = "1724",
+                           died = "1804",
+                           school = "Enlightenment Philosophy")
+philDB$person <- rbind(philDB$person, immanuelKant)
+
+bID = autoincrement(philDB$books)
+immanuelKantWork <- data.frame(id = bID,
+                               title = "Critique of Pure Reason",
+                               published = "1781")
+philDB$books <- rbind(philDB$books, immanuelKantWork)
+philDB$works <- rbind(philDB$works, data.frame(id = autoincrement(philDB$works), personID = pID, bookID = bID))
+
+bID = autoincrement(philDB$books)
+immanuelKantWork <- data.frame(id = bID,
+                               title = "Critique of Judgement",
+                               published = "1790")
+philDB$books <- rbind(philDB$books, immanuelKantWork)
+philDB$works <- rbind(philDB$works, data.frame(id = autoincrement(philDB$works), personID = pID, bookID = bID))
+
+# == Submission: Code to list the philosophical schools in alphabetical order as well as their respective books in alphabetical order.
+
+schools <- unique(philDB$person$school)
+schools <- sort(schools)
+
+for (s in schools) {
+  cat(sprintf("%s\n", s))
+  authors = which(philDB$person$school == s)
+  for (author in authors) {
+    works = which(philDB$works$personID == author)
+    for (work in works) {
+      bookId = which(philDB$books$id == philDB$works$bookID[work])
+      cat(sprintf("\t%s - (%s)\n", philDB$books$title[bookId], philDB$books$published[bookId]))
+    }
+  }
+}
+
 
 # =    2  Implementing the protein datamodel  ==================================
 
@@ -385,7 +426,7 @@ dbSanitizeSequence(x)
 
 # ==   2.3  Create a protein table for our data model  =========================
 
-# ===   2.3.1  Initialize the database                       
+# ===   2.3.1  Initialize the database
 
 
 # The function dbInit contains all the code to return a list of empty
@@ -397,7 +438,7 @@ myDB <- dbInit()
 str(myDB)
 
 
-# ===   2.3.2  Add data                                      
+# ===   2.3.2  Add data
 
 
 # fromJSON() returns a dataframe that we can readily process to add data
@@ -444,7 +485,7 @@ source("./scripts/ABC-createRefDB.R")
 str(myDB)
 
 
-# ===   2.4.1  Examples of navigating the database           
+# ===   2.4.1  Examples of navigating the database
 
 
 # You can look at the contents of the tables in the usual way we access
@@ -597,7 +638,7 @@ if (file.exists(sprintf("./myScripts/%staxonomy.json", biCode(MYSPE)))) {
 # "break" them with a code experiment. But always have a script with
 # which you can create what you need.
 
-# ===   3.3.1  Check and validate                            
+# ===   3.3.1  Check and validate
 
 
 # Is your protein named according to the pattern "MBP1_MYSPE"? It should be.

myScripts/.myProfile.R

@@ -14,7 +14,8 @@
 # ==============================================================================
 # options(stringsAsFactors = FALSE)
 
-myEMail <- "<your-e-mail-address-here>"        # e.g. "u.franklin@utoronto.ca"
+myEMail <- "yh.deng@mail.utoronto.ca"        # e.g. "u.franklin@utoronto.ca"
-myStudentNumber <- <your-student-number-here>  # e.g. 1003141592
+myStudentNumber <- 1005845285  # e.g. 1003141592
+MYSPE <- "Cutaneotrichosporon oleaginosum" 
 
 # [END]

myScripts/CUTOLTaxonomy.json

@@ -0,0 +1,4 @@
+[{
+	"ID": 879819,
+	"species": "Cutaneotrichosporon oleaginosum"}
+]

myScripts/MBP1_CUTOL.json

@@ -0,0 +1,19 @@
+[
+  { "name" : "MBP1_CUTOL",
+    "RefSeqID" : "XP_018278493.1",
+    "UniProtID" : "A0A0J0XLN0",
+    "taxonomyID" : 879819,
+    "sequence" : [
+       "MGKKAAAAGDGGPNTIYKATYSGVPVFEFICRNVAVMRRRSDAYLNATQILKVAGFDKPQRTRVLEREVQ",
+       "KGEHEKVQGGYGKYQGTWVPIERGLALAKQYNVEDLLRPIIDFVPRESVSPPPAPKHAVAPPTKRNKEPK",
+       "PKEGLVPIKSAGVLSGTGRHQTPDSVGEDVESEVMDDMSESQTPSPLNGTSLLPAVDERSIDGMDIDGFS",
+       "MMNGGGHARKRSAAMMDDEDEYEQLKRARGNSAVHTPPPPGQSPRYGGMQHPLTQDEYNDIVLNYFVSEA",
+       "TQIPAVMTNPPYNWDPNGIIDDDHHTALHWAAAMGRTRVIKLLLSAGARIFDKNNLDQTPLMRSVMFTNN",
+       "YDLRKFPEVFELLHRSTLNIDKNNRTVFHHIANLALYKGKTHAARYYMEVILSRLADYPQELADVINFAD",
+       "EDGETALTLAARARSKRIVKALLDHGADPKLRNRDHKSAEDYILEDERFRSSPDVMLNRTQPSAAPRNPT",
+       "SLGAAVFSQGLPPQLYNSEAARLASGPHSSDILQQMQALARSFEAEKLNKERDVLEAKAMLTSIHTEVND",
+       "AGRTLHNLGEQMKPLEAKQGELDGLVERLQSKLQKDLARGARKWKAADEGRENRWKNGDDPSQAGEDYSD",
+       "LPELTAIPDNAEAEEERLRGEIEKMRARRGELVTRLVKAQTQTGTTDKMAQYRRLITAGCGGDINPGEID",
+       "DIVGQLLDMLENEAQSGRPAPPPQAAPSWVTS"]
+  }
+]

myScripts/makeProteinDB.R

@@ -0,0 +1,4 @@
+source("./scripts/ABC-createRefDB.R")
+
+myDB <- dbAddProtein(myDB, jsonlite::fromJSON("./myScripts/MBP1_CUTOL.json"))
+myDB <- dbAddTaxonomy(myDB, jsonlite::fromJSON("./myScripts/CUTOLtaxonomy.json"))

myScripts/myScript.R

@@ -0,0 +1,38 @@
+# myScript.R
+#
+# --- As you work with this file, you can delete the instructions below --------
+# Write your notes and code experiments into this document. Save it
+# from time to time - however I recommend that you do not _commit_
+# your saved version.
+#
+# As long as you do not _commit_ this script to version control,
+# you can _pull_ updated versions of the entire project from GitHub
+# by using the RStudio version control interface. However, once
+# you _commit_ any file in your local version, RStudio will require
+# you to resolve conflicts before you can _pull_ updates.
+# --- As you work with this file, you can delete the instructions above --------
+#
+## Purpose: <...>
+#
+# Version: <...>
+#
+# Date:    <...>
+# Author:  <Name> (<namee@mail.utoronto.ca>)
+#
+# Versions:
+#
+#   <number>    <Features>
+#
+# TODO:
+#   <...>
+#
+# ====================================================================
+
+
+
+
+
+
+
+# [END]
+