File Changes for angie
switch to commits view, user indexv342_base to v343_preview (2016-12-05 to 2016-12-19) v343
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- src/hg/cartDump/cartDump.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/encode3/encodeDataWarehouse/fix/edwFixReplaced/edwFixReplaced.c
- lines changed 12, context: html, text, full: html, text
1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
Libifying isAllDigits from a handful of places into common.c.
- src/hg/encode3/importEncode2/encodeCvToDb/encodeCvToDb.c
- lines changed 10, context: html, text, full: html, text
1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
Libifying isAllDigits from a handful of places into common.c.
- src/hg/hgBlat/hgBlat.c
- lines changed 2, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgConvert/hgConvert.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgCustom/hgCustom.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgGateway/hgGateway.c
- lines changed 3, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgGene/hgGene.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgGenome/hgGenome.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgIntegrator/hgIntegrator.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgLiftOver/hgLiftOver.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgLogin/hgLogin.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- lines changed 79, context: html, text, full: html, text
e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
Better cookies and validation for hgLogin: instead of sending gbMembers.idx as
the login cookie and then never checking the value of the incoming cookie, use
a salted hash. The salt is a secret text value specified by login.cookieSalt
in hg.conf.private. For remote login, both hosts' hg.conf.private files must
specify the same login.cookieSalt. In order to avoid logging out all users,
for now the correct value of gbMembers.idx is accepted in place of the salted
hash for local logins. For remote logins without login.cookieSalt, there is
still no way to check the incoming cookie. For local logins without
login.cookieSalt, the correct gbMembers.idx is accepted.
refs #17327
- src/hg/hgLogin/hgLogin.h
- lines changed 1, context: html, text, full: html, text
e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
Better cookies and validation for hgLogin: instead of sending gbMembers.idx as
the login cookie and then never checking the value of the incoming cookie, use
a salted hash. The salt is a secret text value specified by login.cookieSalt
in hg.conf.private. For remote login, both hosts' hg.conf.private files must
specify the same login.cookieSalt. In order to avoid logging out all users,
for now the correct value of gbMembers.idx is accepted in place of the salted
hash for local logins. For remote logins without login.cookieSalt, there is
still no way to check the incoming cookie. For local logins without
login.cookieSalt, the correct gbMembers.idx is accepted.
refs #17327
- src/hg/hgPublicSessions/hgPublicSessions.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgSession/hgSession.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- lines changed 54, context: html, text, full: html, text
e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
Better cookies and validation for hgLogin: instead of sending gbMembers.idx as
the login cookie and then never checking the value of the incoming cookie, use
a salted hash. The salt is a secret text value specified by login.cookieSalt
in hg.conf.private. For remote login, both hosts' hg.conf.private files must
specify the same login.cookieSalt. In order to avoid logging out all users,
for now the correct value of gbMembers.idx is accepted in place of the salted
hash for local logins. For remote logins without login.cookieSalt, there is
still no way to check the incoming cookie. For local logins without
login.cookieSalt, the correct gbMembers.idx is accepted.
refs #17327
- src/hg/hgTables/hgTables.c
- lines changed 2, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgTracks/mainMain.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgTracks/renderMain.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgVai/hgVai.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/hgc/hgc.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/inc/autoUpgrade.h
- lines changed 2, context: html, text, full: html, text
e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
Better cookies and validation for hgLogin: instead of sending gbMembers.idx as
the login cookie and then never checking the value of the incoming cookie, use
a salted hash. The salt is a secret text value specified by login.cookieSalt
in hg.conf.private. For remote login, both hosts' hg.conf.private files must
specify the same login.cookieSalt. In order to avoid logging out all users,
for now the correct value of gbMembers.idx is accepted in place of the salted
hash for local logins. For remote logins without login.cookieSalt, there is
still no way to check the incoming cookie. For local logins without
login.cookieSalt, the correct gbMembers.idx is accepted.
refs #17327
- src/hg/inc/gpFx.h
- lines changed 3, context: html, text, full: html, text
40665f857785f2b82af4f5de26642d2be9986d1e Thu Dec 15 14:14:31 2016 -0800
If null variants (no_sequence_alteration) are not filtered out, then show them without bothering to intersect with genes. This avoids wasted time and redundant output.
- src/hg/inc/wikiLink.h
- lines changed 19, context: html, text, full: html, text
e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
Better cookies and validation for hgLogin: instead of sending gbMembers.idx as
the login cookie and then never checking the value of the incoming cookie, use
a salted hash. The salt is a secret text value specified by login.cookieSalt
in hg.conf.private. For remote login, both hosts' hg.conf.private files must
specify the same login.cookieSalt. In order to avoid logging out all users,
for now the correct value of gbMembers.idx is accepted in place of the salted
hash for local logins. For remote logins without login.cookieSalt, there is
still no way to check the incoming cookie. For local logins without
login.cookieSalt, the correct gbMembers.idx is accepted.
refs #17327
- lines changed 2, context: html, text, full: html, text
fba55c7cdca98634dd406e5a0b58ce09f98593d3 Mon Dec 12 16:46:03 2016 -0800
Having absolutely no new security is a bummer, so for now, by default, check incoming cookie vs. gbMembers.idx, but add a setting login.acceptAnyId that we can enable in case there is a problem with checking idx.
Also add a new setting login.acceptIdx that can be disabled (along with login.acceptAnyId) in order to absolutely require a login.cookieSalt match for better security.
refs #17327
- src/hg/lib/.gitignore
- lines changed 1, context: html, text, full: html, text
4feb01b9f78ef5fb72b83e9b86522dacaa47af08 Tue Nov 29 12:16:32 2016 -0800
Ignore new automatically generated .h file.
- src/hg/lib/annoGratorGpVar.c
- lines changed 48, context: html, text, full: html, text
40665f857785f2b82af4f5de26642d2be9986d1e Thu Dec 15 14:14:31 2016 -0800
If null variants (no_sequence_alteration) are not filtered out, then show them without bothering to intersect with genes. This avoids wasted time and redundant output.
- src/hg/lib/annoStreamDb.c
- lines changed 11, context: html, text, full: html, text
3668909bc45cf722a9b69e2dafbf5e161a6a87a6 Wed Dec 14 16:36:45 2016 -0800
annoStreamDb should not be hardcoded to find all.joiner in the current directory. Now, if env var ALL_JOINER_FILE exists, it will be used instead. vai.pl can now look for all.joiner in hgVai's parent directory (.../cgi-bin) and use ALL_JOINER_FILE if there is no ./all.joiner. refs #12216 note-28
- src/hg/lib/cart.c
- lines changed 3, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- lines changed 12, context: html, text, full: html, text
e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
Better cookies and validation for hgLogin: instead of sending gbMembers.idx as
the login cookie and then never checking the value of the incoming cookie, use
a salted hash. The salt is a secret text value specified by login.cookieSalt
in hg.conf.private. For remote login, both hosts' hg.conf.private files must
specify the same login.cookieSalt. In order to avoid logging out all users,
for now the correct value of gbMembers.idx is accepted in place of the salted
hash for local logins. For remote logins without login.cookieSalt, there is
still no way to check the incoming cookie. For local logins without
login.cookieSalt, the correct gbMembers.idx is accepted.
refs #17327
- lines changed 5, context: html, text, full: html, text
1363e178b292e47349dfbc7b5158ac5c1ceb0e2a Wed Dec 14 14:13:46 2016 -0800
Instead of requiring that loginValidateCookies() be called before wikiLinkUserName is called, just call it if necessary in wikiLinkUserName. Avoids clashes with other squirrelly paths to wikiLinkUserName. refs #17327, #12216#note-28
- src/hg/lib/customTrack.c
- lines changed 2, context: html, text, full: html, text
4cc51edbbb70a41e84029fc8d5334c3d3d9d2ef2 Tue Dec 6 11:39:42 2016 -0800
An unintended side effect of adding plain VCF recognition to customTrackTypeFromBigFile was that customTrackIsBigData started returning true for plain VCF, which tripped up customPp and customFactory code. Fix by excluding plain VCF from customTrackIsBigData. fixes #18503
- src/hg/lib/gpFx.c
- lines changed 1, context: html, text, full: html, text
40665f857785f2b82af4f5de26642d2be9986d1e Thu Dec 15 14:14:31 2016 -0800
If null variants (no_sequence_alteration) are not filtered out, then show them without bothering to intersect with genes. This avoids wasted time and redundant output.
- src/hg/lib/hdb.c
- lines changed 10, context: html, text, full: html, text
1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
Libifying isAllDigits from a handful of places into common.c.
- src/hg/lib/hui.c
- lines changed 6, context: html, text, full: html, text
c85802ccef6bba0d6159c20950a01094e817c56c Thu Dec 15 11:15:23 2016 -0800
Add env var UDC_CACHEDIR to override hg.conf udc.cacheDir for command-line use of CGI. Add -udcCache option to vai.pl using UDC_CACHEDIR. refs #12216 note-32
- src/hg/lib/wikiLink.c
- lines changed 281, context: html, text, full: html, text
e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
Better cookies and validation for hgLogin: instead of sending gbMembers.idx as
the login cookie and then never checking the value of the incoming cookie, use
a salted hash. The salt is a secret text value specified by login.cookieSalt
in hg.conf.private. For remote login, both hosts' hg.conf.private files must
specify the same login.cookieSalt. In order to avoid logging out all users,
for now the correct value of gbMembers.idx is accepted in place of the salted
hash for local logins. For remote logins without login.cookieSalt, there is
still no way to check the incoming cookie. For local logins without
login.cookieSalt, the correct gbMembers.idx is accepted.
refs #17327
- lines changed 33, context: html, text, full: html, text
0c450818052cb799efeab3d7d49c800378bcf3ab Mon Dec 12 13:57:55 2016 -0800
Without login.cookieSalt, don't even check ID cookie vs. gbMembers.idx because that could vary from system to system. refs #17327
- lines changed 52, context: html, text, full: html, text
fba55c7cdca98634dd406e5a0b58ce09f98593d3 Mon Dec 12 16:46:03 2016 -0800
Having absolutely no new security is a bummer, so for now, by default, check incoming cookie vs. gbMembers.idx, but add a setting login.acceptAnyId that we can enable in case there is a problem with checking idx.
Also add a new setting login.acceptIdx that can be disabled (along with login.acceptAnyId) in order to absolutely require a login.cookieSalt match for better security.
refs #17327
- lines changed 1, context: html, text, full: html, text
1363e178b292e47349dfbc7b5158ac5c1ceb0e2a Wed Dec 14 14:13:46 2016 -0800
Instead of requiring that loginValidateCookies() be called before wikiLinkUserName is called, just call it if necessary in wikiLinkUserName. Avoids clashes with other squirrelly paths to wikiLinkUserName. refs #17327, #12216#note-28
- src/hg/near/hgNear/hgNear.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/phyloPng/phyloPng.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/hg/utils/vai.pl
- lines changed 1, context: html, text, full: html, text
b546eecd8adb64a42547ccd39ae436b09d0bd167 Fri Dec 9 15:44:46 2016 -0800
Use cgi-bin by default, not cgi-bin-angie! Thanks Christopher Lee. refs #12216
- lines changed 1, context: html, text, full: html, text
4a1540ff08c68fd435e71eeefe579e368ad8211a Wed Dec 14 14:51:15 2016 -0800
Doh, an early extra close() on a filehandle... refs #12216 note-27
- lines changed 13, context: html, text, full: html, text
3668909bc45cf722a9b69e2dafbf5e161a6a87a6 Wed Dec 14 16:36:45 2016 -0800
annoStreamDb should not be hardcoded to find all.joiner in the current directory. Now, if env var ALL_JOINER_FILE exists, it will be used instead. vai.pl can now look for all.joiner in hgVai's parent directory (.../cgi-bin) and use ALL_JOINER_FILE if there is no ./all.joiner. refs #12216 note-28
- lines changed 14, context: html, text, full: html, text
b0b401942ab87c2208fec5bfbeeeb4a1cb1bc326 Wed Dec 14 16:48:38 2016 -0800
If HGDB_CONF is not set and hg.conf is not in the usual places, look for it in hgVai's parent dir and set HGDB_CONF if found. refs #12216 note-32
- lines changed 1, context: html, text, full: html, text
0239643d97af85334bfeb84c9e9732c19ae6682f Thu Dec 15 10:40:53 2016 -0800
Oops, an overly restrictive regex was preventing vai.pl from accepting --position=chrX (without the range). refs #12216 note-20
- lines changed 11, context: html, text, full: html, text
c85802ccef6bba0d6159c20950a01094e817c56c Thu Dec 15 11:15:23 2016 -0800
Add env var UDC_CACHEDIR to override hg.conf udc.cacheDir for command-line use of CGI. Add -udcCache option to vai.pl using UDC_CACHEDIR. refs #12216 note-32
- src/hg/visiGene/hgVisiGene/hgVisiGene.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
- src/inc/common.h
- lines changed 3, context: html, text, full: html, text
1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
Libifying isAllDigits from a handful of places into common.c.
- src/lib/annoStreamTab.c
- lines changed 5, context: html, text, full: html, text
1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
Libifying isAllDigits from a handful of places into common.c.
- src/lib/blastParse.c
- lines changed 11, context: html, text, full: html, text
1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
Libifying isAllDigits from a handful of places into common.c.
- src/lib/common.c
- lines changed 12, context: html, text, full: html, text
1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
Libifying isAllDigits from a handful of places into common.c.
- lines changed 3, context: html, text, full: html, text
e5c786377cee95f737ff9d4bbada817e14f94aa4 Mon Dec 12 09:25:06 2016 -0800
Better cookies and validation for hgLogin: instead of sending gbMembers.idx as
the login cookie and then never checking the value of the incoming cookie, use
a salted hash. The salt is a secret text value specified by login.cookieSalt
in hg.conf.private. For remote login, both hosts' hg.conf.private files must
specify the same login.cookieSalt. In order to avoid logging out all users,
for now the correct value of gbMembers.idx is accepted in place of the salted
hash for local logins. For remote logins without login.cookieSalt, there is
still no way to check the incoming cookie. For local logins without
login.cookieSalt, the correct gbMembers.idx is accepted.
refs #17327
- src/lib/wormdna.c
- lines changed 12, context: html, text, full: html, text
1cc8c6d3d7f2357898ad366c94b1f33a403a2aee Thu Dec 8 14:14:33 2016 -0800
Libifying isAllDigits from a handful of places into common.c.
- src/product/ex.hg.conf
- lines changed 2, context: html, text, full: html, text
89a44e5c387d7b75c46c45f84729f11a70d57597 Mon Dec 12 15:28:15 2016 -0800
Document new hg.conf(.private) setting login.cookieSalt in ex.hg.conf. refs #17327
- src/utils/newProg/newProg.c
- lines changed 1, context: html, text, full: html, text
1c77d240de04728dfcb0e0b3ef973b69c1931728 Fri Dec 9 15:06:19 2016 -0800
Instead of adding setUdcCacheDir just before every call that opens a cart, call setUdcCacheDir at the beginning of cartNew. refs #18524
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