1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
|
#!/bin/csh -f
if ($#argv != 3) then
echo "usage:"
echo "embossdoc.csh srctop wwwtop booktop"
endif
set edir = $argv[1]
set wdir = $argv[2]
set bdir = $argv[3]
\rm -rf x/
mkdir x
cd x
echo >! ../efunc.out
echo >! ../efunc.check
echo >! ../edata.out
echo >! ../edata.check
touch $wdir/ajax/dummy.html
foreach x ($wdir/ajax/*html $wdir/nucleus/*html \
$wdir/datadef/*html $wdir/datadef/*empty $wdir/appsource/*html)
# echo "'$x:t'"
if ($x:t == "index.html") then
echo "Preserve index $x"
else if ($x:t == "other.html") then
echo "Preserve other $x"
else
\rm $x
endif
end
#echo "Ajax functions"
# ... skip pcre
foreach x ($edir/ajax/core/*.c $edir/ajax/graphics/*.c $edir/ajax/ajaxdb/*.c $edir/ajax/acd/*.c $edir/ajax/ensembl/*.c)
embossdoccheck.pl $x >> ../efunc.check
embossdoc.pl $x >> ../efunc.out
end
cat *.srs >! ../efunc.dat
\cp *html $wdir/ajax/
foreach x (*.book)
if(-s $x) then
\cp $x $bdir/ajax/
else
echo "$x empty"
\rm $x
endif
end
\rm *html
\rm *.srs
#echo "Ajax static datatypes"
foreach x ($edir/ajax/core/*.c $edir/ajax/graphics/*.c $edir/ajax/ajaxdb/*.c $edir/ajax/acd/*.c $edir/ajax/ensembl/*.c)
embossdatacheck.pl $x >> ../edata.check
embossdatadoc.pl $x >> ../edata.out
end
cat *.srsdata >! ../edata.dat
foreach x (*html)
if (-e $wdir/datadef/$x) then
echo "Warning: Ajax overwriting $wdir/datadef/$x"
endif
\cp $x $wdir/datadef/
end
cp *.empty $wdir/datadef/
\rm *html
\rm *.srsdata
\rm *.empty
#echo "Nucleus functions"
foreach x ($edir/nucleus/*.c)
embossdoccheck.pl $x >> ../efunc.check
embossdoc.pl $x >> ../efunc.out
end
cat *.srs >> ../efunc.dat
\cp *html $wdir/nucleus/
\rm *html
\rm *.srs
#echo "Nucleus static datatypes"
foreach x ($edir/nucleus/*.c)
embossdatacheck.pl $x >> ../edata.check
embossdatadoc.pl $x >> ../edata.out
end
cat *.srsdata >> ../edata.dat
foreach x (*html)
if (-e $wdir/datadef/$x) then
echo "Warning: Nucleus overwriting $wdir/datadef/$x"
endif
\cp $x $wdir/datadef/
end
cp *.empty $wdir/datadef/
\rm *html
\rm *.srsdata
\rm *.empty
#echo "Emboss functions"
foreach x ($edir/emboss/*.c)
embossdoccheck.pl $x >> ../efunc.check
embossdoc.pl $x >> ../efunc.out
end
cat *.srs >> ../efunc.dat
\cp *html $wdir/appsource/
\rm *html
\rm *.srs
#echo "Emboss static datatypes"
foreach x ($edir/emboss/*.c)
embossdatacheck.pl $x >> ../edata.check
embossdatadoc.pl $x >> ../edata.out
end
cat *.srsdata >> ../edata.dat
foreach x (*html)
if (-e $wdir/datadef/$x) then
echo "Warning: Emboss overwriting $wdir/datadef/$x"
endif
\cp $x $wdir/datadef/
end
\rm *html
\rm *.srsdata
#echo "Ajax datatypes"
foreach x ($edir/ajax/core/*.h $edir/ajax/graphics/*.h $edir/ajax/ajaxdb/*.h $edir/ajax/acd/*.h $edir/ajax/ensembl/*.h)
embossdatacheck.pl $x >> ../edata.check
embossdatadoc.pl $x >> ../edata.out
end
cat *.srsdata >> ../edata.dat
foreach x (*html)
if (-e $wdir/datadef/$x) then
if (-e $wdir/datadef/$x:r.empty) then
# echo "Note: Ajax headers overwriting $wdir/datadef/$x is empty"
\cp $x $wdir/datadef/
else if (-e $x:r.empty) then
# echo "Note: Ajax header $x is empty - keep previous"
# ls -al $x $x:r.empty $wdir/datadef/$x:r.empty $wdir/datadef/$x
else
echo "Warning: Ajax headers overwriting $wdir/datadef/$x"
\cp $x $wdir/datadef/
endif
else
\cp $x $wdir/datadef/
endif
end
\rm *html
\rm *.srsdata
\rm *.empty
#echo "Nucleus datatypes"
foreach x ($edir/nucleus/*.h)
embossdatacheck.pl $x >> ../edata.check
embossdatadoc.pl $x >> ../edata.out
end
foreach x (*html)
if (-e $wdir/datadef/$x) then
if (-e $wdir/datadef/$x:r.empty) then
# echo "Note: Nucleus headers overwriting $wdir/datadef/$x is empty"
\cp $x $wdir/datadef/
else if (-e $x:r.empty) then
# echo "Note: Nucleus header $x is empty - keep previous"
# ls -al $x $x:r.empty $wdir/datadef/$x:r.empty $wdir/datadef/$x
else
echo "Warning: Nucleus headers overwriting $wdir/datadef/$x"
\cp $x $wdir/datadef/
endif
else
\cp $x $wdir/datadef/
endif
end
cat *.srsdata >> ../edata.dat
\rm *html
\rm *.srsdata
\rm *.empty
cp deprecated.new ~/devemboss/deprecated.txt
cd ..
\rm -rf x/
# Check the categories are all defined
embossdoccategories.pl efunc.out edata.out >! ecat.out
#source ~/srsfunc/etc/prep_srs
#
#srsbuild efunc -nn
#srsbuild efunc -rel '2.9.0'
#
#srsbuild edata -nn
#srsbuild edata -rel '2.9.0'
#
#srsbuild -l efunc
#srsbuild -l edata
|
