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Revision 1.5 - (show annotations) (download)
Thu Jul 14 05:34:44 2005 UTC (15 years ago) by brinkley
Branch: MAIN
CVS Tags: wirm_2_1, wirm_2_2, HEAD
Changes since 1.4: +110 -0 lines
Switched main trunk to be sig-vivalog-merge-branch. Merge with vivalog
code is now the main development trunk. See ChangeLog for details.

1 2005-07-13 Jim Brinkley <brinkley@foote>
2
3 * Switched HEAD to be sig-vivalog-merge-branch:
4 Tagged last version of HEAD branch before switch to be wirm_1_5.
5 Checked out clean version of HEAD branch
6 In checked out version,
7 For each subdirectory
8 Locally removed all files except CVS sub-directories
9 cvs update -j sig-vivalog-merge-branch
10 Then did the same at the top level
11 To check did cvs diff -r sig-vivalog-merge-branch
12 Showed no difference between main branch and sig-vivalog-merge-branch
13 Committed changes back to HEAD branch.
14
15
16 2004-07-31 Jim Brinkley <brinkley@caudate>
17
18 * Added code to check that repo is specified before trying to contact database. All of merge should be done now,
19 but need to test. Also added repo_required to wrm/cgi scripts to prevent some of them from used when no repo
20 is set.
21
22 2004-07-30 Jim Brinkley <brinkley@caudate>
23
24 * Merged HT_emit_header, HT_carry_context and repo_read_context. But also had to modify to fix
25 what seem like bugs: cgi/user-login.pl and user-logout.pl were not setting the proper cookies since they
26 were specifying the wrong -path parameter. When I fixed that there seemed to be no need to keep the
27 cookie from htdocs created in HT_emit_header, nor does there seem to be any use for creating a new
28 Session in repo_read_context, at least for what I have tested. So these have been removed. Further testing
29 may require them to be in place. All seems to work now except when wrm routines are called outside of a repo.
30 Fixing this will require adding checks to be sure the repo is set, which was not done in the vivalog branch.
31 So at this point the merge is complete except for new code needed to check for the repo.
32 Tag:merge-all-but-check-repo.
33
34 2004-07-27 Jim Brinkley <brinkley@caudate>
35
36 * Merged HT_url and Session_new. On closer look these don't do much with context.
37 The only routines now not merged are html.pl: HT_emit_header and HT_carry_context, and
38 gateway.pl: repo_read_context. The key is that these routines always contact the database
39 to carry or read context. But if we don't always want to do that a condition needs to be added so
40 that the database is only opened if a repo is set.
41
42
43 2004-07-27 Jim Brinkley <brinkley@caudate>
44
45 * Merged cgi, htdocs and all of wrm.pl, html.pl and gateway.pl except those sections that deal
46 with carrying context. The vivalog branch requires that all context be carried in the database,
47 which means that the database has to be connected to in wrm.pl before anything else and the wrm
48 toolkit needs to be in the repo_cgi directory, not just as a link. This is incompatible with
49 the current SIG approach of having more than one repo on the same server using the same copy of
50 wrm. All other changes seem to work so far, will look more into vivalog methods for carrying
51 context.
52 Tag:merge-all-but-context
53
54 2004-07-15 Jim Brinkley <brinkley@caudate>
55
56 * Merged repo.pl vivalog changes into SIG version
57 Accepted all vivalog changes, which mainly manaage object metadata.
58 Kept changes by SIG to handle sets and enums and to fix bug in repo_evolve - added
59 %drop local variable.
60 Tag: merge-repo
61
62 2004-07-02 Jim Brinkley <brinkley@caudate>
63
64 * Merged viz.pl vivalog changes into SIG version
65 Accepted all vivalog changes, which mainly add support for psd image type.
66 Kept one change made by SIG in viv_convert to fix a bug: check for existence of source before
67 trying to convert.
68 Tag: merge-viz
69
70 2004-07-02 Jim Brinkley <brinkley@caudate>
71
72 * Merged fci.pl vivalog changes into SIG version
73 Accepted all vivalog changes. Only one significant change:
74 - file_path() now returns locator field rather than path in
75 WirmFsaIndex. This is only used in fci.pl, and the database for both image_repo
76 and bmap_repo shows the paths are the same if the file is in the fsa, so there
77 shold be no effect.
78 Tag: merge-fci
79
80 2004-07-02 Jim Brinkley <brinkley@caudate>
81
82 * Merged db.pl vivalog changes into SIG version.
83 Accepted all vivalog changes, kept SIG additional datatypes
84 - db_make_sql now appends object metadata
85 - db_valid_type adds vivalog datetime, and keeps SIG enum and set
86 - a few minor changes
87 One minor change in db_make_sql caused me to have to redo some code in bmap_repo:
88 - filter is now surrounded by (). I had some filters to repo_query that
89 were of the form "condition ORDER by var". This is a bug in my code, but
90 was not caught until this change. Should have been $filter = "condition",
91 $order = "variable".
92 Tag: merge-db
93
94
95 2004-07-01 Jim Brinkley <brinkley@caudate>
96
97 * Merged wrm.pl vivalog changes into SIG version.
98 Accepted all vivalog changes except lines 120-121 and 176 in
99 vivalog-branch, in which $WRM_CONF{wrm_cgi} is being set to
100 $WRM_CONF{repo_cgi}/wrm. This doesn't work for installed SIG repos
101 so will need to reconcile later with Vivalog. Main incorporated changes are:
102 - sets repo if in the repo directory at startup
103 - adds WRM_CONF variables instance, static, repo_templates
104 I don't know what these are for but they don't hurt anything
105 - functions to load proprietary code if it exists.
106 Modifed wrm/lib/conf/README to descbir the delta scripts that need to be
107 run to update database.
108 Tag: merge-wrm
109
110
111 2004-06-22 Jim Brinkley <brinkley@caudate>
112
113 * Started merge of Vivalog fork of wrm toolkit with SIG version. Vivalog
114 created their own source tree at the point tagged FINAL_SIG_WIRM. They then
115 added new functionality that is not completely backward compatible. Since
116 then SIG added some new functionality to the existing fork at SIG (any
117 commits after FINAL_SIG_WIRM. Approach to doing the merge is as follows:
118 Tag latest version of SIG tree as
119 sig-vivalog-merge-branchpoint
120 Main trunk will remain the SIG tree until merge has been tested.
121 Create two new branches at this point
122 vivalog-branch
123 sig-vivalog-merge-branch
124 Vivalog-branch will contain two revisions of the Vivalog fork, as sent to
125 SIG by Rex and Mark Shanahan. These will be tagged as
126 vivalog-11-18-2003
127 vivalog-06-09-2004
128 Sig-vivalog-merge-branch will contain the results of the merge, with
129 various tag points reflecting different stages of the merge. Once the final
130 merge is complete and tested on our existing report this branch will be
131 switched over to the main trunk.
132
133 2001-03-09 Jim Brinkley <brinkley@foote.biostr.washington.edu>
134
135 * CVS tag wirm_1_4
136 Moved to DBI and mysql rather than msql
137 Removed hashes for schema, repo_types and fsa index. These are now
138 three new tables in the database. Modified backup and restore
139 scripts to not use hashes.
140 New script nodbm.pl in lib/etc. This is for converting from
141 a pre 1.4 repo to one without the hashes.
142
143 2000-04-28 Jim Brinkley <brinkley@synapse.biostr.washington.edu>
144
145 * CVS tag wirm_1_3
146 Minor changes, mostly optional arguments tocvs
147 existing functions. No change in API.
148 Overview of Changes:
149 - Moved this changeLog to wirm from wirm/wrm, in
150 preparation for removing specific repos from distribution.
151 Distribution will be then be entire wirm tree. Specific
152 repos will then be installed under repos.
153 - Allow only a single table and no banner
154 to be shown in schema-view
155 - Optional constraints and omit paramters for repo-edit and
156 repo-make. Constraints define fixed values for fields,
157 omit defines fields which should not be shown in prompts
158 - Optional target frame for navigation links
159 - Optional repo-specific configuration file
160 - Added another group, EDITOR1, for selective authoring,
161 as opposed to PRIVILEGED, which can modify anything.
162 Specific changes:
163 wirm/
164 Moved ChangeLog from wrm to top level
165 Added COPYING file containing GNU license
166 wirm/wrm/cgi
167 schema-view.pl
168 Added class and nobanner parameters. If these are not
169 present behaves the same as before. If nobanner is present
170 the banner is not displayed. If class is present only
171 the specified class schema is shown.
172 repo-edit.pl
173 Added parameters constraints and omit, passed to
174 repo.pl:repo_edit. Constraints sets fixed values for
175 one or more fields, omit removes field from list of edit.
176 repo-make.pl
177 Added parameters constraints and omit, passed to
178 repo.pl:repo_make. Same meaning as in repo-edit.
179 wirm/wrm/lib
180 gateway.pl
181 repo_make and repo_mlink
182 Added constraints and omit parameters
183 repo_edit and repo_elink
184 Added constraints and omit parameters
185 repo_attributes_prompt
186 Added constraints and omit parameters
187 Default_make, Default_make_prompt
188 Added constraints and omit parameters
189 Default_edit, Default_edit_prompt
190 Added constraints and omit parameters
191 Default_remove, Default_remove_prompt
192 Slightly changed wording in warnings
193 User_view_label
194 Added optional target frame so user page can be
195 viewed in a different frame. Used when banner
196 is in one frame and want to view full user
197 page in top frame.
198 repo.pl
199 repo_evolve
200 Added local variables to fix bug because of
201 unitialized variables
202 html.pl
203 HT_href
204 Added optional target frame name
205 HT_nav
206 Added optional target frame name
207 HT_month_prompt
208 Added Unknown month as an option
209 HT_date_prompt
210 Added default unknown date
211 HT_date_parse
212 Return undef if unknown is in date string
213 wrm.pl
214 repo_config
215 Added include repo-specific configuration
216 file if present.
217 wirm/wrm/lib/backup/
218 repo-restore.pl
219 Remove existing tables before restore.
220
221 2000-01-31 Jim Brinkley <brinkley@foote.biostr.washington.edu>
222
223 * CVS tag wirm_1_2
224 Added minimal permissions facility. In wrm.pl created a global
225 variable called WRM_GROUPS, with 4 ordered group levels, starting
226 with ADMINISTRATOR (level 0), ending with PUBLIC. user-setgroup.pl
227 now selects from this list to assign group to a user (can only be
228 done by someone in the administrator group). Scripts callable from
229 wrm console call wrm.pl:check-permissions, with parameter of highest
230 level group required to call that script. If user is not at that
231 level the script exits. Finer control can be obtained in a given
232 repo by using the context mechanism to change views or actions
233 depending on the group.
234
235 Also removed list of users from login screen in user-login.pl.
236 Providing a list of users gives a hacker an unfair advantage. Now
237 users must remember their login name. (But anyone can still register
238 as a public user).
239
240 The purpose of this minimal facility is to allow us to make some
241 of our repos (specifically the brain map repo) more widely avaialble,
242 without compromising the database. But we need a finer-grained
243 mechanism that allows arbitrary groups to be created for a given
244 repo, for users to be assigned to these groups, and for read
245 write privileges to be assigned to each object class visible to a
246 a group. This is standard for a commercial RDB - we should look
247 at this again when we move from msql to DBI.
248
249 1999-12-17 Jim Brinkley <brinkley@foote.biostr.washington.edu>
250
251 * CVS tag wirm_1_1
252 Fixed up scripts to work with the new directory
253 organization. Scripts do not need be copied to be installed since
254 all absolute pathnames in "use lib" directives are
255 replaced by pathnames relative to wrm/lib directory, assuming a
256 uniform directory organization. Module FindBin used to find
257 directory which which the cgi script was being run, after
258 resolving symbolic links. Multiple repositories also enabled by
259 collecting together all connections to repo-specific files and
260 database in wrm.pl, creating subroutines to set the repo in
261 wrm.pl, and adding a new context variable, cx_repo to pass the
262 current repo between cgi invocations. Install script now just
263 links cgi and htdocs directories to configurable server cgi and
264 htdocs locations, using conf.pl, a new file that is required by
265 wrm.pl. Backup and restore scripts added in a new directory
266 wrm/lib/backup, which allow backup and restore of all data for a
267 repo. This allows data to be moved from instance of a repo to
268 another, for example from a development version to a production
269 version.
270
271 * Specific changes:
272 All cgi files in wrm/cgi, use lib ~rex... replaced by use lib
273 $RealBin/../lib, where $RealBin is defined by use
274 FindBin. Also replaced these files in wrm/lib/conf/* and
275 anywhere else hardcoded paths appeared.
276
277 wrm/cgi. All scripts now begin with repo_required(), defined
278 in wrm/lib/wrm.pl, which checks the context to see if a repo
279 has been defined. If not sets a link to new script
280 set_repo.pl, which is used to set the repo.
281
282 wrm/htdocs. Modified docs to reflect new organization. Added
283 repos.html to describe methods for setting, installing,
284 backing up and restoring repositories. Extensively modified
285 wrm-pod/wrm.html (as derived from pod in wrm.pl) to reflect
286 added functionality for repository management.
287
288 wrm/lib/conf. Removed CONF and conf dbm hash. Instead made
289 %WRM_CONF set directly by wrm.pl and conf.pl. Extensively
290 modified install.pl to mainly just create links to wrm/cgi and
291 wrm/htdocs. Wrote db-init.pl, which requires root, for
292 dropping and creating an msql db prior to repo-init. Deleted
293 wrm-init, replaced with repo-init.pl, which takes a repo name
294 and either creates it if it doesn't already exist, or
295 initializes it (removes all data) if it does, and created
296 links to repo cgi and htdocs directories, as specified in
297 conf.pl file.
298
299 wrm/lib. All connections to dbm hashes and msql database moved
300 to wrm.pl. wrm.pl extensively modified to set %WRM_CONF
301 programmatically rather than via hash. First requires conf.pl,
302 which must be edited for each installation from a copy of
303 conf.pl.sample, which defines installation-specific cgi and
304 htdocs locations. wrm.pl also sets the repo context to be the
305 name of the repo if it was required from a repo
306 driectory. html.pl read_context checks for cx_repo parameter
307 and sets repo if present.
308
309 1999-11-24 Jim Brinkley <brinkley@synapse>
310
311 * CVS tag wirm_1_0
312 Initial creation of wrm toolkit directory, copied from
313 ~rex/wrm-latest. This will not work as initially copied, but
314 serves as a starting point that can get us back to Rex's original
315 work while using directory names expected in future developments
316 (since it is hard to change directory names in CVS).
317
318 * Note that wirm was originally developed by Rex Jakobovits for
319 his PhD thesis in computer science.
320
321 * Reorganized subdirectories to reflect 3 basic locations: cgi for
322 cgi scripts, lib for library scripts outside of www, and htdocs
323 for html and images that should be directly visible to the web
324 browser. This is in anticipation of removing the need for
325 hardcoded pathnames. When this is done the install script will
326 create symbolic links to these subdirectories. Some names also
327 changed to move to uniform directory naming scheme for both wrm
328 toolkit and repos.
329
330 * Specific changes from wrm-latest to wirm/wrm
331 wrm-cgi renamed to cgi, otherwise same content
332 wrm-lib renamed to lib
333 Removed pod2html-dircache and pod2html-itemcache
334 wrm-viz renamed to htdocs
335 Removed repos subdirectory Added docs from top level
336 doc moved to htdocs subdirectory
337 Removed wrm-install.tar since the entire wirm/wrm directory
338 will be the tar file.
339 demo_repo copied from broca. See ChangeLog in this
340 directory. This will be a demo repo included with the
341 distribution, that is also described in the tutorial.
342
343
344

brinkley@uw.edu
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