From 14b76ba416ae00ef13a769724d87035bd4996c0d Mon Sep 17 00:00:00 2001
From: nicolevasilevsky <vasilevs@ohsu.edu>
Date: Fri, 22 Jan 2021 10:05:50 -0800
Subject: [PATCH] edit makefile

---
 src/ontology/cl.Makefile       |   5 +
 src/scripts/obo-simple-diff.pl | 189 +++++++++++++++++++++++++++++++++
 2 files changed, 194 insertions(+)
 create mode 100644 src/scripts/obo-simple-diff.pl

diff --git a/src/ontology/cl.Makefile b/src/ontology/cl.Makefile
index 1a0006a51..3912fc309 100644
--- a/src/ontology/cl.Makefile
+++ b/src/ontology/cl.Makefile
@@ -239,3 +239,8 @@ reports/diff_edit_%.txt: tmp/src-master-%.owl tmp/src-%.owl
 
 branch_diffs: reports/diff_edit_imports.md reports/diff_edit_noimports.md reports/diff_edit_imports.txt reports/diff_edit_noimports.txt
 
+tmp/cl-lastbuild.obo: 
+	$(ROBOT) merge -I $(CL_EDIT_GITHUB_MASTER) -o $@
+
+reports/obo-diff.txt: tmp/cl-lastbuild.obo
+	perl ../scripts/obo-simple-diff.pl $< cl.obo > $@.tmp && mv $@.tmp $@
diff --git a/src/scripts/obo-simple-diff.pl b/src/scripts/obo-simple-diff.pl
new file mode 100644
index 000000000..10612cb5f
--- /dev/null
+++ b/src/scripts/obo-simple-diff.pl
@@ -0,0 +1,189 @@
+#!/usr/bin/perl -w
+
+use strict;
+
+my $show_context;
+my %tag_h;
+while ($ARGV[0] =~ /^\-.+/) {
+    my $opt = shift @ARGV;
+    if ($opt eq '-h' || $opt eq '--help') {
+        print usage();
+        exit 0;
+    }
+    elsif ($opt eq '-c') {
+        $show_context = 1;
+    }
+    elsif ($opt eq '-l') {
+        %tag_h = 
+            (
+             is_a => 1,
+             relationship => 1
+            );
+    }
+    else {
+        die $opt;
+    }
+}
+
+my $f1 = shift @ARGV;
+my $f2 = shift @ARGV;
+
+my %ftypeh = ();
+my %nh = ();
+
+print STDERR "Parsing: $f1\n";
+my $doc1 = pdoc($f1);
+
+print STDERR "Parsing: $f2\n";
+my $doc2 = pdoc($f2);
+
+my @ids =  (keys %$doc1,
+            keys %$doc2);
+
+@ids = sort @ids;
+printf STDERR "Comparing: %d IDs\n", scalar(@ids);
+my %doneh = ();
+foreach my $id (@ids) {
+    next if $doneh{$id};
+    $doneh{$id} = 1;
+    my @plus = ();
+    my @minus = ();
+    my @u = ();
+    foreach my $v (@{$doc1->{$id}||[]}) {
+        if (grep {smatch($v,$_)} @{$doc2->{$id} || []}) {
+            push(@u, $v);
+        }
+        else {
+            push(@minus, $v);
+        }
+    }
+    foreach my $v (@{$doc2->{$id}||[]}) {
+        if (grep {smatch($v,$_)} @{$doc1->{$id} || []}) {
+            
+        }
+        else {
+            push(@plus, $v);
+        }
+    }
+    if (scalar(@plus) || scalar(@minus)) {
+        my $chg = '';
+        if (!$doc1->{$id}) {
+            $chg = '+';
+        }
+        if (!$doc2->{$id}) {
+            $chg = '-';
+        }
+        my $n = $nh{$id};
+        printf "%s[%s]\n",$chg,$ftypeh{$id};
+        print $chg."id: $id ! $n\n";
+        foreach (@minus) {
+            print "-$_\n";
+        }
+        foreach (@plus) {
+            print "+$_\n";
+        }
+        if ($show_context) {
+            foreach (@u) {
+                print '#'."$_\n";
+            }
+        }
+        print "\n";
+    }
+}
+
+
+exit 0;
+
+sub pdoc {
+    my $f = shift;
+    my $doc = {};
+    my $id;
+    my $ftype;
+    open(F,$f) || die $f;
+    while (<F>) {
+        chomp;
+        if (/^\[(\S+)\]/) {
+            $ftype = $1;
+        }
+        elsif (/^id:\s*(\S+)/) {
+            $id = $1;
+            $ftypeh{$id} = $ftype;
+            #print STDERR "$id ==> $ftype\n";
+        }
+        else {
+            if (!$id) {
+                next;
+            }
+
+            if (/^namespace:/) {
+                # TODO - make optional
+                next;
+            }
+
+            if (/^name:\s*(.*)/) {
+                my $n = $1;
+                if ($nh{$id}) {
+                    if ($nh{$id} ne $n) {
+                        $nh{$id} .= ' --> ' . $n;
+                    }
+                }
+                else {
+                    $nh{$id} = $n;
+                }
+            }
+
+            if (%tag_h) {
+                if (/^(\S+):\s*(.*)/) {
+                    if (!$tag_h{$1}) {
+                        next;
+                    }
+                }
+            }
+
+            if (/^(\S+):\s*(.*)/) {
+                push(@{$doc->{$id}}, $_);
+            }
+            else {
+                $id = '';
+            }
+        }
+    }
+    close(F);
+    return $doc;
+}
+
+sub scriptname {
+    my @p = split(/\//,$0);
+    pop @p;
+}
+
+sub smatch {
+    my ($v1,$v2) = @_;
+    $v1 = trim($v1);
+    $v2 = trim($v2);
+    return $v1 eq $v2;
+}
+
+sub trim {
+    my $x = $_[0];
+    $x =~ s/\s*\!.*//;
+    $x =~ s/\s+/ /g;
+    $x =~ s/^\s+//;
+    $x =~ s/\s+$//;
+    return $x;
+
+}
+
+sub usage {
+    my $sn = scriptname();
+
+    <<EOM;
+$sn OBO-FILE1 OBO-FILE2
+
+Compares two obo files
+
+
+
+EOM
+}
+