fix(unitproc):timeNanosec:minor comment with version and author
[BK-2020-03.git] / unitproc / bkcsvjoin
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1# Date: 2020-02-21T21:23Z;
2
3# Author: Steven Baltakatei Sandoval
4
5# License: This bash script, 'bkcsvjoin.sh', is licensed under GPLv3 or
6# later by Steven Baltakatei Sandoval:
7#
8# 'bkcsvjoin.sh' sorts and joins two CSV files based on first field
9# Copyright (C) 2020 Steven Baltakatei Sandoval (baltakatei.com)
10#
11# This program is free software: you can redistribute it and/or modify
12# it under the terms of the GNU General Public License as published by
13# the Free Software Foundation, either version 3 of the License, or
14# any later version.
15#
16# This program is distributed in the hope that it will be useful,
17# but WITHOUT ANY WARRANTY; without even the implied warranty of
18# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
19# GNU General Public License for more details.
20#
21# A copy of the GNU General Public License may be found at
22# <https://www.gnu.org/licenses/>.
23
24# Description: Sorts and joins two CSV files based upon the contents
25# of the first field ("field1") in each line of CSV file. It assumes
26# the first line is a header labelling field names. It outputs several
27# files into a new directory in the working directory. Set theory
28# characters in output file names indicate file 1 elements with "A"
29# and file 2 elements with "B". Input assumes UNIX-style line
30# endings. The output files use the following numbers and definitions:
31#
32# 1. A⋃B The union of A and B. Contains all field1 elements from file 1 and 2.
33#
34# 2. A⋃(A⋂B) Contains all field1 elements of file 1 plus the matches between
35# file 1 and 2.
36#
37# 3. B⋃(B⋂A) Contains all field1 elements of file 2 plus the matches between
38# file 1 and 2.
39#
40# 4. A⋂B Contains only field1 elements present in both file 1 and file 2.
41#
42# 5. A-B Contains all field1 elements of file 1 except when a matching
43# element is present in file 2.
44#
45# 6. B-A Contains all field1 elements of file 2 except when a matching
46# element is present in file 1.
47#
48# 7. A⊖B Contains all field1 elements of file 1 and file 2 except for
49# elements which are present in both file 1 and 2.
50
51# Usage: bkcsvjoin.sh [ file1 ] [ file2 ] > fileOut.csv
52
53# Dependencies: GNU Coreutils 8.30-3 (bash, join, sort, head, tail,
54# mkdir) (see end of file for license details). Note: only tested on
55# Debian GNU/Linux 10.
56
57echoerr() { echo "$@" 1>&2; } # Function for outputing text to stderr.
58
59SCRIPT_DATE=$(date +%Y%m%dT%H%M%S%z)
60SCRIPT_PATH=$(pwd)
61
62# Create temporary working directory
63TEMP_DIRPATH="$SCRIPT_PATH"/"$SCRIPT_DATE"..temp
64mkdir "$TEMP_DIRPATH"
65
66# Read file names as input arguments
67FILE1_PATH="$1"
68FILE2_PATH="$2"
69FILE1_BASENAME=$(basename "$FILE1_PATH")
70FILE2_BASENAME=$(basename "$FILE2_PATH")
71#[[ -f "$FILE1_PATH" ]] && echoerr "DEBUG:$FILE1_PATH is file with basename $FILE1_BASENAME."
72#[[ -f "$FILE2_PATH" ]] && echoerr "DEBUG:$FILE2_PATH is file with basename $FILE2_BASENAME."
73
74# Warn and prompt if carriage return character is used.
75if [[ $(grep -Uc $'\x0D' "$FILE1_PATH") -gt 0 ]] || [[ $(grep -Uc $'\x0D' "$FILE2_PATH") -gt 0 ]]; then
76 echoerr "ERROR: Carriage Return character(s) detected. Windows text file?"
77 read -p "Do you wish to attempt to convert DOS-style line endings to UNIX-style by removing all carriage returns? (probably okay) [y/n]" choice
78 case "$choice" in
79 y|Y ) echoerr "yes"
80 OPTION_DOS2UNIX="true"
81 ;;
82 n|N ) echoerr "no"
83 OPTION_DOS2UNIX="false"
84 echoerr "WARNING:Output may contain mix of DOS-style (CRLF) and UNIX-style (LF) line endings!"
85 echoerr " See https://stackoverflow.com/a/2613834 "
86 sleep 2
87 ;;
88 * ) echo "Invalid selection."
89 echoerr "Exiting." && exit 1;;
90 esac
91fi
92
93# Sort files on field1 and write to temporary directory. See [1], and [2].
94FILE1_SORTED_PATH="$TEMP_DIRPATH"/"$FILE1_BASENAME"_SORTED.csv
95FILE2_SORTED_PATH="$TEMP_DIRPATH"/"$FILE2_BASENAME"_SORTED.csv
96( head -n1 $FILE1_PATH && tail -n+2 $FILE1_PATH | sort -t, -k1,1 | uniq ) > $FILE1_SORTED_PATH
97( head -n1 $FILE2_PATH && tail -n+2 $FILE2_PATH | sort -t, -k1,1 | uniq ) > $FILE2_SORTED_PATH
98
99# 1. A⋃B. Join files into Union of (file 1) + (file 2) (i.e. throwing nothing out). See [3], [6].
100FILES_JOINED_COMPLETE="$( join -t, -a1 -a2 -o auto --header "$FILE1_SORTED_PATH" "$FILE2_SORTED_PATH" )"
101
102# 2. A⋃(A⋂B). Join files, file 1 uniques only (omit unmatched field1 entries from file 2). See [6].
103FILES_JOINED_F1UO="$( join -t, -a1 -o auto --header "$FILE1_SORTED_PATH" "$FILE2_SORTED_PATH" )"
104
105# 3. B⋃(A⋂B). Join files, file 2 uniques only (omit unmatched field1 entries from file 1). See [6].
106FILES_JOINED_F2UO="$( join -t, -a2 -o auto --header "$FILE1_SORTED_PATH" "$FILE2_SORTED_PATH" )"
107
108# 4. A⋂B. Join files, only entries present in both file 1 and file 2 ( file 1 ⋂ file 2 ). See [6].
109FILES_JOINED_INTERSECTION="$( join -t, -o auto --header "$FILE1_SORTED_PATH" "$FILE2_SORTED_PATH" )"
110
111# 5. A-B. Join files into Relative Complement of (file 1) - (file 2) field1 entries. See See [5], [6].
112FILES_JOINED_DIFFERENCE_AB="$( join -t, -v1 -o auto --header "$FILE1_SORTED_PATH" "$FILE2_SORTED_PATH" )"
113
114# 6. B-A. Join files into Relative Complement of (file 2) - (file 1) field1 entries. See [5], [6].
115FILES_JOINED_DIFFERENCE_BA="$( join -t, -v2 -o auto --header "$FILE1_SORTED_PATH" "$FILE2_SORTED_PATH" )"
116
117# 7. A⊖B. Join files into Symmetric Difference of (file 2) ⊖ (file 1) field1 entries. See [5], [6].
118FILES_JOINED_DIFFERENCE_SYM="$( join -t, -v1 -v2 -o auto --header "$FILE1_SORTED_PATH" "$FILE2_SORTED_PATH" )"
119
120# Attempt to restore to UNIX-style line endings by removing all carriage return (CR) characters OPTION_DOS2UNIX set to true. See [7].
121if [[ $OPTION_DOS2UNIX == "true" ]]; then
122 FILES_JOINED_COMPLETE="$(echo "$FILES_JOINED_COMPLETE" | tr -d '\r')"
123 FILES_JOINED_F1UO="$(echo "$FILES_JOINED_F1UO" | tr -d '\r')"
124 FILES_JOINED_F2UO="$(echo "$FILES_JOINED_F2UO" | tr -d '\r')"
125 FILES_JOINED_INTERSECTION="$(echo "$FILES_JOINED_INTERSECTION" | tr -d '\r')"
126 FILES_JOINED_DIFFERENCE_AB="$(echo "$FILES_JOINED_DIFFERENCE_AB" | tr -d '\r')"
127 FILES_JOINED_DIFFERENCE_BA="$(echo "$FILES_JOINED_DIFFERENCE_BA" | tr -d '\r')"
128 FILES_JOINED_DIFFERENCE_SYM="$(echo "$FILES_JOINED_DIFFERENCE_SYM" | tr -d '\r')"
129fi
130
131# Output CSV files to temp directory with carriage returns ('\r') removed.
132echo "$FILES_JOINED_COMPLETE" > "$TEMP_DIRPATH"/"1.A⋃B..UNION.csv" && echoerr "1.A⋃B..UNION.csv written to $TEMP_DIRPATH"
133echo "$FILES_JOINED_F1UO" > "$TEMP_DIRPATH"/"2.A⋃(A⋂B)..FILE-1-UNIQUES-ONLY.csv" && echoerr "2.A⋃(A⋂B)..FILE-1-UNIQUES-ONLY.csv written to $TEMP_DIRPATH"
134echo "$FILES_JOINED_F2UO" > "$TEMP_DIRPATH"/"3.B⋃(A⋂B)..FILE-2-UNIQUES-ONLY.csv" && echoerr "3.B⋃(A⋂B)..FILE-2-UNIQUES-ONLY.csv written to $TEMP_DIRPATH"
135echo "$FILES_JOINED_INTERSECTION" > "$TEMP_DIRPATH"/"4.A⋂B..INTERSECTION.csv" && echoerr "4.A⋂B..INTERSECTION.csv written to $TEMP_DIRPATH"
136echo "$FILES_JOINED_DIFFERENCE_AB" > "$TEMP_DIRPATH"/"5.A-B..DIFFERENCE_A_MINUS_B.csv" && echoerr "5.A-B..DIFFERENCE_A_MINUS_B.csv written to $TEMP_DIRPATH"
137echo "$FILES_JOINED_DIFFERENCE_BA" > "$TEMP_DIRPATH"/"6.B-A..DIFFERENCE_B_MINUS_A.csv" && echoerr "6.B-A..DIFFERENCE_B_MINUS_A.csv written to $TEMP_DIRPATH"
138echo "$FILES_JOINED_DIFFERENCE_SYM" > "$TEMP_DIRPATH"/"7.A⊖B..DIFFERENCE_SYM.csv" && echoerr "7.A⊖B..DIFFERENCE_SYM.csv written to $TEMP_DIRPATH"
139
140# ==References==
141# [1]: How to sort a csv file while retaining the first line. https://stackoverflow.com/a/14562674
142# [2]: How to sort a csv file by sorting on a single field. https://stackoverflow.com/a/44744800
143# [3]: How to join multiple sorted csv files into one. https://stackoverflow.com/a/27606199
144# [4]: How to join a csv file retaining the first line, sorting by certain fields, and not omitting nonmatching fields. https://superuser.com/a/1527095
145# [5]: How to determine symmetric difference between two sorted files. https://www.gnu.org/software/coreutils/manual/html_node/Set-operations.html
146# [6]: Set theory symbols https://www.rapidtables.com/math/symbols/Set_Symbols.html
147# [7]: How to convert DOS-style to UNIX-style line endings. https://stackoverflow.com/a/2613834
148
149# ==Dependencies==
150
151 # GNU bash, version 5.0.3(1)-release (x86_64-pc-linux-gnu)
152 # Copyright (C) 2019 Free Software Foundation, Inc.
153 # License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
154
155 # This is free software; you are free to change and redistribute it.
156 # There is NO WARRANTY, to the extent permitted by law.
157
158
159 # join (GNU coreutils) 8.30
160 # Copyright (C) 2018 Free Software Foundation, Inc.
161 # License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
162 # This is free software: you are free to change and redistribute it.
163 # There is NO WARRANTY, to the extent permitted by law.
164
165 # Written by Mike Haertel.
166
167
168 # sort (GNU coreutils) 8.30
169 # Copyright (C) 2018 Free Software Foundation, Inc.
170 # License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
171 # This is free software: you are free to change and redistribute it.
172 # There is NO WARRANTY, to the extent permitted by law.
173
174 # Written by Mike Haertel and Paul Eggert.
175
176
177 # head (GNU coreutils) 8.30
178 # Copyright (C) 2018 Free Software Foundation, Inc.
179 # License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
180 # This is free software: you are free to change and redistribute it.
181 # There is NO WARRANTY, to the extent permitted by law.
182
183 # Written by David MacKenzie and Jim Meyering.
184
185
186 # tail (GNU coreutils) 8.30
187 # Copyright (C) 2018 Free Software Foundation, Inc.
188 # License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
189 # This is free software: you are free to change and redistribute it.
190 # There is NO WARRANTY, to the extent permitted by law.
191
192 # Written by Paul Rubin, David MacKenzie, Ian Lance Taylor,
193 # and Jim Meyering.
194
195
196 # mkdir (GNU coreutils) 8.30
197 # Copyright (C) 2018 Free Software Foundation, Inc.
198 # License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
199 # This is free software: you are free to change and redistribute it.
200 # There is NO WARRANTY, to the extent permitted by law.
201
202 # Written by David MacKenzie.
203
204# ==Metadata==
205# - Created in task 20200220_90eb0c7d
206