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add overlooked jsonlite:: prefix to fromJson()

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hyginn 2020-09-28 18:00:45 +10:00
parent 12213b73a4
commit 12e3de439f
1 changed files with 35 additions and 29 deletions
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64
BIN-Storing_data.R
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@ -3,11 +3,12 @@
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-Storing_data unit
#
# Version: 1.3
# Version: 1.3.1
#
# Date: 2017-10 - 2020-09
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# V 1.3.1 add overlooked jsonlite:: prefix to fromJson()
# V 1.3 Made file locations more consistent. All student-edited files
# go into the myScripts directory
# V 1.2 2020 updates. Finally removed stringAsFactors :-)
@ -34,26 +35,26 @@
#TOC>
#TOC> Section Title Line
#TOC> -----------------------------------------------------------------------
#TOC> 1 A Relational Datamodel in R: review 61
#TOC> 1.1 Building a sample database structure 101
#TOC> 1.1.1 completing the database 207
#TOC> 1.2 Querying the database 240
#TOC> 1.3 Task: submit for credit (part 1/2) 271
#TOC> 2 Implementing the protein datamodel 293
#TOC> 2.1 JSON formatted source data 319
#TOC> 2.2 "Sanitizing" sequence data 360
#TOC> 2.3 Create a protein table for our data model 382
#TOC> 2.3.1 Initialize the database 384
#TOC> 2.3.2 Add data 396
#TOC> 2.4 Complete the database 416
#TOC> 2.4.1 Examples of navigating the database 443
#TOC> 2.5 Updating the database 475
#TOC> 3 Add your own data 487
#TOC> 3.1 Find a protein 495
#TOC> 3.2 Put the information into JSON files 525
#TOC> 3.3 Create an R script to create your own database 567
#TOC> 3.3.1 Check and validate 590
#TOC> 3.4 Task: submit for credit (part 2/2) 635
#TOC> 1 A Relational Datamodel in R: review 62
#TOC> 1.1 Building a sample database structure 102
#TOC> 1.1.1 completing the database 208
#TOC> 1.2 Querying the database 241
#TOC> 1.3 Task: submit for credit (part 1/2) 272
#TOC> 2 Implementing the protein datamodel 294
#TOC> 2.1 JSON formatted source data 320
#TOC> 2.2 "Sanitizing" sequence data 361
#TOC> 2.3 Create a protein table for our data model 383
#TOC> 2.3.1 Initialize the database 385
#TOC> 2.3.2 Add data 397
#TOC> 2.4 Complete the database 417
#TOC> 2.4.1 Examples of navigating the database 444
#TOC> 2.5 Updating the database 476
#TOC> 3 Add your own data 488
#TOC> 3.1 Find a protein 496
#TOC> 3.2 Put the information into JSON files 526
#TOC> 3.3 Create an R script to create your own database 568
#TOC> 3.3.1 Check and validate 596
#TOC> 3.4 Task: submit for credit (part 2/2) 641
#TOC>
#TOC> ==========================================================================
@ -573,15 +574,20 @@ if (file.exists(sprintf("./myScripts/%staxonomy.json", biCode(MYSPE)))) {
# source("./scripts/ABC-createRefDB.R")
# - than add the two commands that add your protein and taxonomy data,
# they should look like:
# myDB <- dbAddProtein( myDB, fromJSON("./myScripts/MBP1_<MYSPE>.json"))
# myDB <- dbAddTaxonomy( myDB, fromJSON("./myScripts/MYSPEtaxonomy.json"))
#
# - save the file in the ./myScripts/ folder and source() it:
# source("./myScripts/makeProteinDB.R")
# This command needs to be executed whenever you recreate
# the database. In particular, whenever you have added or modified data
# in any of the JSON files. Later you will add more information ...
# myDB <- dbAddProtein(myDB,
# jsonlite::fromJSON("./myScripts/MBP1_<MYSPE>.json"))
# myDB <- dbAddTaxonomy(myDB,
# jsonlite::fromJSON("./myScripts/<MYSPE>taxonomy.json"))
#
#
# - save the .json file in the ./myScripts/ folder and source() it:
#
# source("./myScripts/makeProteinDB.R") # <<<- This command ...
#
# ... needs to be executed whenever you recreate the database. In particular,
# whenever you have added or modified data in any of the JSON files. Later you
# will add more information.
# Remember this principle. Don't rely on objects in memory - you might
# "break" them with a code experiment. But always have a script with