mirror of
https://github.com/galaxyproject/galaxy.git
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Merged galaxy/galaxy-central into default
This commit is contained in:
Martin Cech
+13
-47
@@ -1,88 +1,54 @@
|
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;
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; Config for building eggs for distribution (via a site such as
|
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; eggs.g2.bx.psu.edu). Probably only useful to Galaxy developers at
|
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; Penn State. This file is used by scripts/dist-scramble.py
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; eggs.galaxyproject.org). Probably only useful to members of the Galaxy Team
|
||||
; building eggs for distribution. This file is used by
|
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; scripts/dist-scramble.py
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||||
;
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||||
; More information: http://wiki.g2.bx.psu.edu/Admin/Config/Eggs
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; More information: http://wiki.galaxyproject.org/Admin/Config/Eggs
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;
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[hosts]
|
||||
py2.5-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.5
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py2.5-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.5
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py2.6-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.6
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py2.6-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.6
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py2.7-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.7
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py2.7-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.7
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py2.5-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.5
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py2.5-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.5
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py2.6-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.6
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py2.6-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6
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py2.7-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.7
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py2.7-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.7
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py2.5-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /Library/Frameworks/Python.framework/Versions/2.5/bin/python2.5
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py2.6-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6
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py2.7-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
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py2.6-macosx-10.6-universal-ucs2 = lion.bx.psu.edu /usr/bin/python2.6
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py2.7-macosx-10.6-intel-ucs2 = lion.bx.psu.edu /usr/local/bin/python2.7
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py2.5-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.5
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py2.6-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.6
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py2.7-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.7
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py2.5-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.5
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py2.6-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.6
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py2.7-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.7
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py2.5-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.5
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py2.6-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.6
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py2.7-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.7
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py2.5-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u_64-ucs2/bin/python2.5
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py2.6-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u_64-ucs2/bin/python2.6
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py2.7-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u_64-ucs2/bin/python2.7
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;
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; these hosts are used to build eggs with no C extensions
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py2.5 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.5
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py2.6 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6
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py2.7 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.7
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[groups]
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py2.5-linux-i686 = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4
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py2.5-linux-x86_64 = py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4
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py2.6-linux-i686 = py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4
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py2.6-linux-x86_64 = py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4
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py2.7-linux-i686 = py2.7-linux-i686-ucs2 py2.7-linux-i686-ucs4
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py2.7-linux-x86_64 = py2.7-linux-x86_64-ucs2 py2.7-linux-x86_64-ucs4
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py2.5-linux = py2.5-linux-i686 py2.5-linux-x86_64
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py2.6-linux = py2.6-linux-i686 py2.6-linux-x86_64
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py2.7-linux = py2.7-linux-i686 py2.7-linux-x86_64
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linux-i686 = py2.5-linux-i686 py2.6-linux-i686 py2.7-linux-i686
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linux-x86_64 = py2.5-linux-x86_64 py2.6-linux-x86_64 py2.7-linux-x86_64
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linux-i686 = py2.6-linux-i686 py2.7-linux-i686
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linux-x86_64 = py2.6-linux-x86_64 py2.7-linux-x86_64
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linux = linux-i686 linux-x86_64
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py2.5-macosx = py2.5-macosx-10.3-fat-ucs2
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py2.6-macosx = py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2
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py2.7-macosx = py2.7-macosx-10.3-fat-ucs2 py2.7-macosx-10.6-intel-ucs2
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macosx = py2.5-macosx py2.6-macosx py2.7-macosx
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py2.5-solaris-i86pc = py2.5-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2
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py2.6-solaris-i86pc = py2.6-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2
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py2.7-solaris-i86pc = py2.7-solaris-2.10-i86pc_32-ucs2 py2.7-solaris-2.10-i86pc_64-ucs2
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py2.5-solaris-sun4u = py2.5-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2
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py2.6-solaris-sun4u = py2.6-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2
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py2.7-solaris-sun4u = py2.7-solaris-2.10-sun4u_32-ucs2 py2.7-solaris-2.10-sun4u_64-ucs2
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py2.5-solaris = py2.5-solaris-i86pc py2.5-solaris-sun4u
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py2.6-solaris = py2.6-solaris-i86pc py2.6-solaris-sun4u
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py2.7-solaris = py2.7-solaris-i86pc py2.7-solaris-sun4u
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solaris-i86pc = py2.5-solaris-i86pc py2.6-solaris-i86pc py2.7-solaris-i86pc
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solaris-sun4u = py2.5-solaris-sun4u py2.6-solaris-sun4u py2.7-solaris-sun4u
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solaris = solaris-i86pc solaris-sun4u
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py2.5-all = py2.5-linux py2.5-macosx py2.5-solaris
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py2.6-all = py2.6-linux py2.6-macosx py2.6-solaris
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py2.7-all = py2.7-linux py2.7-macosx py2.7-solaris
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macosx = py2.6-macosx py2.7-macosx
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py2.6-all = py2.6-linux py2.6-macosx
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py2.7-all = py2.7-linux py2.7-macosx
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; the 'all' key is used internally by the build system to specify which hosts
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; to build on when no hosts are specified on the dist-eggs.py command line.
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all = linux macosx solaris
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all = linux macosx
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; the 'noplatform' key, likewise, is for which build hosts should be used when
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; building pure python (noplatform) eggs.
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noplatform = py2.5 py2.6 py2.7
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noplatform = py2.6 py2.7
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; don't build these eggs on these platforms:
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[ignore]
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ctypes = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 py2.7-linux-i686-ucs2 py2.7-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 py2.7-linux-x86_64-ucs2 py2.7-linux-x86_64-ucs4 py2.5-macosx-10.3-fat-ucs2 py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 py2.7-macosx-10.3-fat-ucs2 py2.5-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_32-ucs2 py2.7-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 py2.7-solaris-2.10-i86pc_64-ucs2 py2.5-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_32-ucs2 py2.7-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 py2.7-solaris-2.10-sun4u_64-ucs2
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;ctypes =
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@@ -21,7 +21,7 @@ MySQL_python = 1.2.3c1
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PyRods = 3.2.4
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numpy = 1.6.0
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pbs_python = 4.3.5
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psycopg2 = 2.0.13
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psycopg2 = 2.5.1
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pycrypto = 2.5
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pysam = 0.4.2
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pysqlite = 2.5.6
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@@ -38,7 +38,7 @@ Beaker = 1.4
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boto = 2.5.2
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decorator = 3.1.2
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docutils = 0.7
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drmaa = 0.4b3
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drmaa = 0.6
|
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elementtree = 1.2.6_20050316
|
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Fabric = 1.7.0
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GeneTrack = 2.0.0_beta_1
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@@ -72,7 +72,7 @@ raven = 3.1.8
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|
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; extra version information
|
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[tags]
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psycopg2 = _8.4.2_static
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psycopg2 = _9.2.4_static
|
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pysqlite = _3.6.17_static
|
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MySQL_python = _5.1.41_static
|
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bx_python = _7b95ff194725
|
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@@ -83,7 +83,7 @@ pysam = _kanwei_b10f6e722e9a
|
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; the wiki page above
|
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[source]
|
||||
MySQL_python = mysql-5.1.41
|
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psycopg2 = postgresql-8.4.2
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psycopg2 = postgresql-9.2.4
|
||||
pysqlite = sqlite-amalgamation-3_6_17
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[dependencies]
|
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|
||||
@@ -100,19 +100,14 @@ def get_installed_repositories_from_repository_dependencies( trans, repository_d
|
||||
continue
|
||||
# rd_key is something like: 'http://localhost:9009__ESEP__package_rdkit_2012_12__ESEP__test__ESEP__d635ffb9c665__ESEP__True'
|
||||
# rd_val is something like: [['http://localhost:9009', 'package_numpy_1_7', 'test', 'cddd64ecd985', 'True']]
|
||||
try:
|
||||
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
|
||||
container_util.get_components_from_key( rd_key )
|
||||
except:
|
||||
tool_shed, name, owner, changeset_revision = container_util.get_components_from_key( rd_val )
|
||||
repository_components_tuple = container_util.get_components_from_key( rd_key )
|
||||
components_list = suc.extract_components_from_tuple( repository_components_tuple )
|
||||
tool_shed, name, owner, changeset_revision = components_list[ 0:4 ]
|
||||
installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed, name, owner, changeset_revision )
|
||||
if installed_repository not in installed_repositories:
|
||||
installed_repositories.append( installed_repository )
|
||||
for rd_val in rd_vals:
|
||||
try:
|
||||
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_val
|
||||
except:
|
||||
tool_shed, name, owner, changeset_revision = rd_val
|
||||
tool_shed, name, owner, changeset_revision = rd_val[ 0:4 ]
|
||||
installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed, name, owner, changeset_revision )
|
||||
if installed_repository not in installed_repositories:
|
||||
installed_repositories.append( installed_repository )
|
||||
@@ -631,13 +626,10 @@ def merge_containers_dicts_for_new_install( containers_dicts ):
|
||||
# Change the folder id so it won't confict with others being merged.
|
||||
old_container_repository_dependencies_folder.id = folder_id
|
||||
folder_id += 1
|
||||
repository_components_tuple = container_util.get_components_from_key( old_container_repository_dependencies_folder.key )
|
||||
components_list = suc.extract_components_from_tuple( repository_components_tuple )
|
||||
name = components_list[ 1 ]
|
||||
# Generate the label by retrieving the repository name.
|
||||
try:
|
||||
toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
|
||||
container_util.get_components_from_key( old_container_repository_dependencies_folder.key )
|
||||
except ValueError:
|
||||
# For backward compatibility to the 12/20/12 Galaxy release.
|
||||
toolshed, name, owner, changeset_revision = container_util.get_components_from_key( old_container_repository_dependencies_folder.key )
|
||||
old_container_repository_dependencies_folder.label = str( name )
|
||||
repository_dependencies_folder.folders.append( old_container_repository_dependencies_folder )
|
||||
# Merge tool_dependencies.
|
||||
|
||||
@@ -352,19 +352,20 @@ def get_required_repo_info_dicts( trans, tool_shed_url, repo_info_dicts ):
|
||||
for key, val in repository_dependencies.items():
|
||||
if key in [ 'root_key', 'description' ]:
|
||||
continue
|
||||
try:
|
||||
toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
|
||||
container_util.get_components_from_key( key )
|
||||
components_list = [ toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td ]
|
||||
except ValueError:
|
||||
# For backward compatibility to the 12/20/12 Galaxy release, default prior_installation_required and only_if_compiling_contained_td
|
||||
# to False in the caller.
|
||||
toolshed, name, owner, changeset_revision = container_util.get_components_from_key( key )
|
||||
components_list = [ toolshed, name, owner, changeset_revision ]
|
||||
only_if_compiling_contained_td = 'False'
|
||||
repository_components_tuple = container_util.get_components_from_key( key )
|
||||
components_list = suc.extract_components_from_tuple( repository_components_tuple )
|
||||
# Skip listing a repository dependency if it is required only to compile a tool dependency defined for the dependent repository since
|
||||
# in this case, the repository dependency is really a dependency of the dependent repository's contained tool dependency, and only if
|
||||
# that tool dependency requires compilation.
|
||||
# For backward compatibility to the 12/20/12 Galaxy release.
|
||||
prior_installation_required = 'False'
|
||||
only_if_compiling_contained_td = 'False'
|
||||
if len( components_list ) == 4:
|
||||
prior_installation_required = 'False'
|
||||
only_if_compiling_contained_td = 'False'
|
||||
elif len( components_list ) == 5:
|
||||
prior_installation_required = components_list[ 4 ]
|
||||
only_if_compiling_contained_td = 'False'
|
||||
if not util.asbool( only_if_compiling_contained_td ):
|
||||
if components_list not in required_repository_tups:
|
||||
required_repository_tups.append( components_list )
|
||||
|
||||
@@ -855,7 +855,7 @@ def build_repository_containers_for_tool_shed( trans, repository, changeset_revi
|
||||
folder_id, data_managers_root_folder = build_invalid_data_managers_folder( trans, folder_id, data_managers, error_messages, label="Invalid Data Managers" )
|
||||
containers_dict[ 'invalid_data_managers' ] = data_managers_root_folder
|
||||
except Exception, e:
|
||||
log.debug( "Exception in build_repository_containers_for_tool_shed: %s" % str( e ) )
|
||||
log.exception( "Exception in build_repository_containers_for_tool_shed: %s" % str( e ) )
|
||||
finally:
|
||||
lock.release()
|
||||
return containers_dict
|
||||
@@ -1325,29 +1325,31 @@ def get_components_from_key( key ):
|
||||
repository_name = items[ 1 ]
|
||||
repository_owner = items[ 2 ]
|
||||
changeset_revision = items[ 3 ]
|
||||
if len( items ) >= 5:
|
||||
try:
|
||||
prior_installation_required = items[ 4 ]
|
||||
except:
|
||||
prior_installation_required = 'False'
|
||||
try:
|
||||
only_if_compiling_contained_td = items[ 5 ]
|
||||
except:
|
||||
only_if_compiling_contained_td = 'False'
|
||||
if len( items ) == 5:
|
||||
prior_installation_required = items[ 4 ]
|
||||
return toolshed_base_url, repository_name, repository_owner, changeset_revision, prior_installation_required
|
||||
elif len( items ) == 6:
|
||||
prior_installation_required = items[ 4 ]
|
||||
only_if_compiling_contained_td = items[ 5 ]
|
||||
return toolshed_base_url, repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td
|
||||
else:
|
||||
# For backward compatibility to the 12/20/12 Galaxy release we have to return the following, and callers must handle exceptions.
|
||||
return toolshed_base_url, repository_name, repository_owner, changeset_revision
|
||||
|
||||
def handle_repository_dependencies_container_entry( trans, repository_dependencies_folder, rd_key, rd_value, folder_id, repository_dependency_id, folder_keys ):
|
||||
try:
|
||||
toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
|
||||
get_components_from_key( rd_key )
|
||||
except ValueError:
|
||||
# For backward compatibility to the 12/20/12 Galaxy release, default prior_installation_required and only_if_compiling_contained_td to 'False'.
|
||||
toolshed, repository_name, repository_owner, changeset_revision = get_components_from_key( rd_key )
|
||||
repository_components_tuple = get_components_from_key( rd_key )
|
||||
components_list = suc.extract_components_from_tuple( repository_components_tuple )
|
||||
toolshed, repository_name, repository_owner, changeset_revision = components_list[ 0:4 ]
|
||||
# For backward compatibility to the 12/20/12 Galaxy release.
|
||||
if len( components_list ) == 4:
|
||||
prior_installation_required = 'False'
|
||||
only_if_compiling_contained_td = 'False'
|
||||
elif len( components_list ) == 5:
|
||||
prior_installation_required = components_list[ 4 ]
|
||||
only_if_compiling_contained_td = 'False'
|
||||
elif len( components_list ) == 6:
|
||||
prior_installation_required = components_list[ 4 ]
|
||||
only_if_compiling_contained_td = components_list[ 5 ]
|
||||
folder = get_folder( repository_dependencies_folder, rd_key )
|
||||
label = generate_repository_dependencies_folder_label_from_key( repository_name,
|
||||
repository_owner,
|
||||
@@ -1416,14 +1418,19 @@ def is_subfolder_of( folder, repository_dependency ):
|
||||
return False
|
||||
|
||||
def key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, key ):
|
||||
try:
|
||||
toolshed_base_url, key_name, key_owner, key_changeset_revision, key_prior_installation_required, key_only_if_compiling_contained_td = \
|
||||
get_components_from_key( key )
|
||||
except ValueError:
|
||||
# For backward compatibility to the 12/20/12 Galaxy release, default key_prior_installation_required to False.
|
||||
toolshed_base_url, key_name, key_owner, key_changeset_revision = get_components_from_key( key )
|
||||
repository_components_tuple = get_components_from_key( key )
|
||||
components_list = suc.extract_components_from_tuple( repository_components_tuple )
|
||||
toolshed, key_name, key_owner, key_changeset_revision = components_list[ 0:4 ]
|
||||
# For backward compatibility to the 12/20/12 Galaxy release.
|
||||
if len( components_list ) == 4:
|
||||
key_prior_installation_required = 'False'
|
||||
key_only_if_compiling_contained_td = 'False'
|
||||
elif len( components_list ) == 5:
|
||||
key_prior_installation_required = components_list[ 4 ]
|
||||
key_only_if_compiling_contained_td = 'False'
|
||||
elif len( components_list ) == 6:
|
||||
key_prior_installation_required = components_list[ 4 ]
|
||||
key_only_if_compiling_contained_td = components_list[ 5 ]
|
||||
if repository_name == key_name and \
|
||||
repository_owner == key_owner and \
|
||||
changeset_revision == key_changeset_revision and \
|
||||
|
||||
@@ -36,12 +36,9 @@ def build_repository_dependency_relationships( trans, repo_info_dicts, tool_shed
|
||||
if key in [ 'root_key', 'description' ]:
|
||||
continue
|
||||
d_repository = None
|
||||
try:
|
||||
d_toolshed, d_name, d_owner, d_changeset_revision, d_prior_installation_required, d_only_if_compiling_contained_td = \
|
||||
container_util.get_components_from_key( key )
|
||||
except ValueError:
|
||||
# For backward compatibility to the 12/20/12 Galaxy release.
|
||||
d_toolshed, d_name, d_owner, d_changeset_revision = container_util.get_components_from_key( key )
|
||||
repository_components_tuple = container_util.get_components_from_key( key )
|
||||
components_list = suc.extract_components_from_tuple( repository_components_tuple )
|
||||
d_toolshed, d_name, d_owner, d_changeset_revision = components_list[ 0:4 ]
|
||||
for tsr in tool_shed_repositories:
|
||||
# Get the the tool_shed_repository defined by name, owner and changeset_revision. This is the repository that will be
|
||||
# dependent upon each of the tool shed repositories contained in val. We'll need to check tool_shed_repository.tool_shed
|
||||
@@ -437,22 +434,22 @@ def get_updated_changeset_revisions_for_repository_dependencies( trans, key_rd_d
|
||||
# We have the updated changset revision.
|
||||
updated_key_rd_dicts.append( new_key_rd_dict )
|
||||
else:
|
||||
try:
|
||||
toolshed, repository_name, repository_owner, repository_changeset_revision, prior_installation_required, rd_only_if_compiling_contained_td = \
|
||||
container_util.get_components_from_key( key )
|
||||
except ValueError:
|
||||
# For backward compatibility to the 12/20/12 Galaxy release.
|
||||
toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key )
|
||||
repository_components_tuple = container_util.get_components_from_key( key )
|
||||
components_list = suc.extract_components_from_tuple( repository_components_tuple )
|
||||
toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[ 0:4 ]
|
||||
# For backward compatibility to the 12/20/12 Galaxy release.
|
||||
if len( components_list ) == 4:
|
||||
prior_installation_required = 'False'
|
||||
rd_only_if_compiling_contained_td = 'False'
|
||||
elif len( components_list ) == 5:
|
||||
rd_only_if_compiling_contained_td = 'False'
|
||||
message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \
|
||||
( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) )
|
||||
log.debug( message )
|
||||
else:
|
||||
try:
|
||||
toolshed, repository_name, repository_owner, repository_changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
|
||||
container_util.get_components_from_key( key )
|
||||
except ValueError:
|
||||
# For backward compatibility to the 12/20/12 Galaxy release.
|
||||
toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key )
|
||||
repository_components_tuple = container_util.get_components_from_key( key )
|
||||
components_list = suc.extract_components_from_tuple( repository_components_tuple )
|
||||
toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[ 0:4 ]
|
||||
message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \
|
||||
( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) )
|
||||
log.debug( message )
|
||||
|
||||
@@ -307,6 +307,21 @@ def create_or_update_tool_shed_repository( app, name, description, installed_cha
|
||||
sa_session.flush()
|
||||
return tool_shed_repository
|
||||
|
||||
def extract_components_from_tuple( repository_components_tuple ):
|
||||
'''Extract the repository components from the provided tuple in a backward-compatible manner.'''
|
||||
toolshed = repository_components_tuple[ 0 ]
|
||||
name = repository_components_tuple[ 1 ]
|
||||
owner = repository_components_tuple[ 2 ]
|
||||
changeset_revision = repository_components_tuple[ 3 ]
|
||||
components_list = [ toolshed, name, owner, changeset_revision ]
|
||||
if len( repository_components_tuple ) == 5:
|
||||
toolshed, name, owner, changeset_revision, prior_installation_required = repository_components_tuple
|
||||
components_list = [ toolshed, name, owner, changeset_revision, prior_installation_required ]
|
||||
elif len( repository_components_tuple ) == 6:
|
||||
toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = repository_components_tuple
|
||||
components_list = [ toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td ]
|
||||
return components_list
|
||||
|
||||
def generate_clone_url_for_installed_repository( app, repository ):
|
||||
"""Generate the URL for cloning a repository that has been installed into a Galaxy instance."""
|
||||
tool_shed_url = get_url_from_tool_shed( app, repository.tool_shed )
|
||||
|
||||
+228
-136
@@ -17,6 +17,34 @@ var GalaxyUpload = Backbone.View.extend(
|
||||
// upload mod
|
||||
uploadbox: null,
|
||||
|
||||
// extension types
|
||||
select_extension : {
|
||||
'' : 'Auto-detect',
|
||||
'bed' : 'bed',
|
||||
'ab1' : 'ab1'
|
||||
},
|
||||
|
||||
// states
|
||||
state : {
|
||||
init : 'fa-icon-trash',
|
||||
done : 'fa-icon-caret-down'
|
||||
},
|
||||
|
||||
// counter
|
||||
counter : {
|
||||
// stats
|
||||
announce : 0,
|
||||
success : 0,
|
||||
error : 0,
|
||||
running : 0,
|
||||
|
||||
// reset stats
|
||||
reset : function()
|
||||
{
|
||||
this.announce = this.success = this.error = this.running = 0;
|
||||
}
|
||||
},
|
||||
|
||||
// initialize
|
||||
initialize : function()
|
||||
{
|
||||
@@ -58,21 +86,18 @@ var GalaxyUpload = Backbone.View.extend(
|
||||
event_mouseleave : function (e)
|
||||
{
|
||||
},
|
||||
|
||||
|
||||
// start
|
||||
event_announce : function(index, file, message)
|
||||
{
|
||||
// hide info
|
||||
this.uploadbox.info().hide();
|
||||
|
||||
// make id
|
||||
var id = '#upload-' + index;
|
||||
|
||||
|
||||
// add upload item
|
||||
$(this.el).append(this.template_file(id));
|
||||
$(this.el).append(this.template_file(id, this.select_extension));
|
||||
|
||||
// scroll to bottom
|
||||
$(this.el).scrollTop($(this.el).prop('scrollHeight'));
|
||||
//$(this.el).scrollTop($(this.el).prop('scrollHeight'));
|
||||
|
||||
// access upload item
|
||||
var it = this.get_upload_item(index);
|
||||
@@ -84,59 +109,27 @@ var GalaxyUpload = Backbone.View.extend(
|
||||
it.find('.title').html(file.name);
|
||||
|
||||
// configure select field
|
||||
it.find('#extension').select2(
|
||||
{
|
||||
placeholder: 'Auto-detect',
|
||||
width: 'copy',
|
||||
ajax: {
|
||||
url: "http://www.weighttraining.com/sm/search",
|
||||
dataType: 'jsonp',
|
||||
quietMillis: 100,
|
||||
data: function(term, page)
|
||||
{
|
||||
return {
|
||||
types: ["exercise"],
|
||||
limit: -1,
|
||||
term: term
|
||||
};
|
||||
},
|
||||
results: function(data, page)
|
||||
{
|
||||
return { results: data.results.exercise }
|
||||
}
|
||||
},
|
||||
formatResult: function(exercise)
|
||||
{
|
||||
return "<div class='select2-user-result'>" + exercise.term + "</div>";
|
||||
},
|
||||
formatSelection: function(exercise)
|
||||
{
|
||||
return exercise.term;
|
||||
},
|
||||
initSelection : function (element, callback)
|
||||
{
|
||||
var elementText = $(element).attr('data-init-text');
|
||||
callback({"term":elementText});
|
||||
}
|
||||
});
|
||||
//it.find('#extension').select2();
|
||||
|
||||
// add functionality to remove button
|
||||
var self = this;
|
||||
it.find('.remove').on('click', function() { self.event_remove (index) });
|
||||
it.find('.symbol').on('click', function() { self.event_remove (index) });
|
||||
|
||||
// initialize progress
|
||||
this.event_progress(index, file, 0);
|
||||
|
||||
// update button status
|
||||
this.modal.enable('Upload');
|
||||
this.modal.enable('Reset');
|
||||
// update counter
|
||||
this.counter.announce++;
|
||||
|
||||
// update screen
|
||||
this.update_screen();
|
||||
},
|
||||
|
||||
// start
|
||||
event_initialize : function(index, file, message)
|
||||
{
|
||||
// update on screen counter
|
||||
this.button_show.number(message);
|
||||
this.button_show.number(this.counter.announce);
|
||||
|
||||
// get element
|
||||
var it = this.get_upload_item(index);
|
||||
@@ -168,16 +161,9 @@ var GalaxyUpload = Backbone.View.extend(
|
||||
it.find('.info').html(percentage + '% of ' + this.size_to_string (file.size));
|
||||
},
|
||||
|
||||
// end
|
||||
// success
|
||||
event_success : function(index, file, message)
|
||||
{
|
||||
// get element
|
||||
var it = this.get_upload_item(index);
|
||||
|
||||
// update progress frame
|
||||
it.addClass('panel-success');
|
||||
it.removeClass('panel-default');
|
||||
|
||||
{
|
||||
// update galaxy history
|
||||
Galaxy.currHistoryPanel.refresh();
|
||||
|
||||
@@ -186,11 +172,46 @@ var GalaxyUpload = Backbone.View.extend(
|
||||
|
||||
// update on screen counter
|
||||
this.button_show.number('');
|
||||
|
||||
// update counter
|
||||
this.counter.announce--;
|
||||
this.counter.success++;
|
||||
|
||||
// update on screen info
|
||||
this.update_screen();
|
||||
|
||||
// get element
|
||||
var it = this.get_upload_item(index);
|
||||
|
||||
// update progress frame
|
||||
it.addClass('panel-success');
|
||||
it.removeClass('panel-default');
|
||||
|
||||
// update icon
|
||||
var sy = it.find('.symbol');
|
||||
sy.removeClass('fa-icon-spin');
|
||||
sy.removeClass('fa-icon-spinner');
|
||||
|
||||
// set status
|
||||
sy.addClass(this.state.done);
|
||||
},
|
||||
|
||||
// end
|
||||
// error
|
||||
event_error : function(index, file, message)
|
||||
{
|
||||
// make sure progress is shown correctly
|
||||
this.event_progress(index, file, 0);
|
||||
|
||||
// update on screen counter
|
||||
this.button_show.number('');
|
||||
|
||||
// update counter
|
||||
this.counter.announce--;
|
||||
this.counter.error++;
|
||||
|
||||
// update on screen info
|
||||
this.update_screen();
|
||||
|
||||
// get element
|
||||
var it = this.get_upload_item(index);
|
||||
|
||||
@@ -204,29 +225,41 @@ var GalaxyUpload = Backbone.View.extend(
|
||||
// write error message
|
||||
it.find('.error').html('<strong>Failed:</strong> ' + message);
|
||||
|
||||
// make sure progress is shown correctly
|
||||
this.event_progress(index, file, 0);
|
||||
// update icon
|
||||
var sy = it.find('.symbol');
|
||||
sy.removeClass('fa-icon-spin');
|
||||
sy.removeClass('fa-icon-spinner');
|
||||
|
||||
// update on screen counter
|
||||
this.button_show.number('');
|
||||
// set status
|
||||
sy.addClass(this.state.done);
|
||||
},
|
||||
|
||||
// start upload process
|
||||
event_upload : function()
|
||||
{
|
||||
// check
|
||||
if (this.counter.announce == 0 || this.counter.running > 0)
|
||||
return;
|
||||
|
||||
// switch icons for new uploads
|
||||
var self = this;
|
||||
$(this.el).find('.symbol').each(function()
|
||||
{
|
||||
if($(this).hasClass(self.state.init))
|
||||
{
|
||||
$(this).removeClass(self.state.init);
|
||||
$(this).addClass('fa-icon-spinner');
|
||||
$(this).addClass('fa-icon-spin');
|
||||
}
|
||||
});
|
||||
|
||||
// hide configuration
|
||||
$(this.el).find('.panel-body').hide();
|
||||
|
||||
// switch icon
|
||||
$(this.el).find('.remove').each(function()
|
||||
{
|
||||
$(this).removeClass('fa-icon-trash');
|
||||
$(this).addClass('fa-icon-caret-down');
|
||||
});
|
||||
|
||||
// update button status
|
||||
this.modal.disable('Upload');
|
||||
|
||||
// update running
|
||||
this.counter.running = this.counter.announce;
|
||||
this.update_screen();
|
||||
|
||||
// configure url
|
||||
var current_history = Galaxy.currHistoryPanel.model.get('id');
|
||||
this.uploadbox.configure({url : galaxy_config.root + "api/histories/" + current_history + "/contents"});
|
||||
@@ -235,62 +268,62 @@ var GalaxyUpload = Backbone.View.extend(
|
||||
this.uploadbox.upload();
|
||||
},
|
||||
|
||||
// queue is done
|
||||
event_complete: function()
|
||||
{
|
||||
// update running
|
||||
this.counter.running = 0;
|
||||
this.update_screen();
|
||||
},
|
||||
|
||||
// remove all
|
||||
event_reset : function()
|
||||
{
|
||||
// remove from screen
|
||||
var panels = $(this.el).find('.panel');
|
||||
var self = this;
|
||||
panels.fadeOut({complete: function()
|
||||
// make sure queue is not running
|
||||
if (this.counter.running == 0)
|
||||
{
|
||||
// remove panels
|
||||
panels.remove();
|
||||
|
||||
// remove from screen
|
||||
var panels = $(this.el).find('.panel');
|
||||
panels.fadeOut({complete: function() { panels.remove(); }});
|
||||
|
||||
// reset counter
|
||||
this.counter.reset();
|
||||
|
||||
// show on screen info
|
||||
self.uploadbox.info().fadeIn();
|
||||
}});
|
||||
|
||||
// update button status
|
||||
this.modal.disable('Upload');
|
||||
this.modal.disable('Reset');
|
||||
|
||||
// remove from queue
|
||||
this.uploadbox.reset();
|
||||
this.update_screen();
|
||||
|
||||
// remove from queue
|
||||
this.uploadbox.reset();
|
||||
}
|
||||
},
|
||||
|
||||
// remove item from upload list
|
||||
event_remove : function(index)
|
||||
{
|
||||
// remove
|
||||
var self = this;
|
||||
// get item
|
||||
var it = this.get_upload_item(index);
|
||||
|
||||
// fade out and update button status
|
||||
it.fadeOut({complete: function()
|
||||
{
|
||||
// remove from screen
|
||||
it.remove();
|
||||
|
||||
// remove from queue
|
||||
self.uploadbox.remove(index);
|
||||
|
||||
// update reset button
|
||||
if ($(self.el).find('.panel').length > 0)
|
||||
self.modal.enable('Reset');
|
||||
else {
|
||||
// disable reset button
|
||||
self.modal.disable('Reset');
|
||||
var sy = it.find('.symbol');
|
||||
|
||||
// show on screen info
|
||||
self.uploadbox.info().fadeIn();
|
||||
}
|
||||
// only remove from queue if not in processing line
|
||||
if (sy.hasClass(this.state.init) || sy.hasClass(this.state.done))
|
||||
{
|
||||
// reduce counter
|
||||
if (it.hasClass('panel-default'))
|
||||
this.counter.announce--;
|
||||
else if (it.hasClass('panel-success'))
|
||||
this.counter.success--;
|
||||
else if (it.hasClass('panel-danger'))
|
||||
this.counter.error--;
|
||||
|
||||
// update upload button
|
||||
if (self.uploadbox.length() > 0)
|
||||
self.modal.enable('Upload');
|
||||
else
|
||||
self.modal.disable('Upload');
|
||||
}});
|
||||
// show on screen info
|
||||
this.update_screen();
|
||||
|
||||
// remove from queue
|
||||
this.uploadbox.remove(index);
|
||||
|
||||
// remove element
|
||||
it.remove();
|
||||
}
|
||||
},
|
||||
|
||||
// show/hide upload frame
|
||||
@@ -330,11 +363,11 @@ var GalaxyUpload = Backbone.View.extend(
|
||||
success : function(index, file, message) { self.event_success(index, file, message) },
|
||||
progress : function(index, file, message) { self.event_progress(index, file, message) },
|
||||
error : function(index, file, message) { self.event_error(index, file, message) },
|
||||
complete : function() { self.event_complete() },
|
||||
});
|
||||
|
||||
// update button status
|
||||
this.modal.disable('Upload');
|
||||
this.modal.disable('Reset');
|
||||
// setup info
|
||||
this.update_screen();
|
||||
}
|
||||
|
||||
// show modal
|
||||
@@ -362,34 +395,93 @@ var GalaxyUpload = Backbone.View.extend(
|
||||
return "<strong>" + (Math.round(size) / 10) + "</strong> " + unit;
|
||||
},
|
||||
|
||||
// set screen
|
||||
update_screen: function ()
|
||||
{
|
||||
/*
|
||||
update on screen info
|
||||
*/
|
||||
|
||||
// check default message
|
||||
if(this.counter.announce == 0)
|
||||
{
|
||||
if (this.uploadbox.compatible)
|
||||
message = 'Drag&drop files into this box or click \'Select\' to select files!';
|
||||
else
|
||||
message = 'Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.'
|
||||
} else {
|
||||
if (this.counter.running == 0)
|
||||
message = 'You added ' + this.counter.announce + ' file(s) to the queue. Add more files or click "Upload" to proceed.';
|
||||
else
|
||||
message = 'Please wait...' + this.counter.announce + ' out of ' + this.counter.running + ' remaining.';
|
||||
}
|
||||
|
||||
// set html content
|
||||
$('#upload-info').html(message);
|
||||
|
||||
/*
|
||||
update button status
|
||||
*/
|
||||
|
||||
// update reset button
|
||||
if (this.counter.running == 0 && this.counter.announce + this.counter.success + this.counter.error > 0)
|
||||
this.modal.enable('Reset');
|
||||
else
|
||||
this.modal.disable('Reset');
|
||||
|
||||
// update upload button
|
||||
if (this.counter.running == 0 && this.counter.announce > 0)
|
||||
this.modal.enable('Upload');
|
||||
else
|
||||
this.modal.disable('Upload');
|
||||
|
||||
// select upload button
|
||||
if (this.counter.running == 0)
|
||||
this.modal.enable('Select');
|
||||
else
|
||||
this.modal.disable('Select');
|
||||
},
|
||||
|
||||
// load html template
|
||||
template: function(id)
|
||||
{
|
||||
return '<div id="' + id + '" class="upload-box"></div>';
|
||||
return '<div id="' + id + '" class="upload-box"></div><h6 id="upload-info" class="upload-info"></h6>';
|
||||
},
|
||||
|
||||
// load html template
|
||||
template_file: function(id)
|
||||
template_file: function(id, select_extension)
|
||||
{
|
||||
return '<div id="' + id.substr(1) + '" class="panel panel-default">' +
|
||||
'<div class="panel-heading">' +
|
||||
'<h5 class="title"></h5>' +
|
||||
'<h5 class="info"></h5>' +
|
||||
'<div class="remove fa-icon-trash"></div>' +
|
||||
'</div>' +
|
||||
'<div class="panel-body">' +
|
||||
'<div class="menu">' +
|
||||
//'<input id="extension" type="hidden" width="10px"/> ' +
|
||||
'<span><input id="space_to_tabs" type="checkbox">Convert spaces to tabs</input></span>' +
|
||||
// start template
|
||||
var tmpl = '<div id="' + id.substr(1) + '" class="panel panel-default">' +
|
||||
'<div class="panel-heading">' +
|
||||
'<h5 class="title"></h5>' +
|
||||
'<h5 class="info"></h5>' +
|
||||
'<div class="symbol ' + this.state.init + '"></div>' +
|
||||
'</div>' +
|
||||
'</div>' +
|
||||
'<div class="panel-footer">' +
|
||||
'<div class="progress">' +
|
||||
'<div class="progress-bar progress-bar-success"></div>' +
|
||||
'<div class="panel-body">' +
|
||||
'<div class="menu">' +
|
||||
'Select file type: ' +
|
||||
'<select id="extension">';
|
||||
|
||||
// add file types to selection
|
||||
for (key in select_extension)
|
||||
tmpl += '<option value="' + key + '">' + select_extension[key] + '</option>';
|
||||
|
||||
// continue template
|
||||
tmpl += '</select>, ' +
|
||||
'<span>Convert space to tabs: <input id="space_to_tabs" type="checkbox"></input></span>' +
|
||||
'</div>' +
|
||||
'</div>' +
|
||||
'<h6 class="error"></h6>' +
|
||||
'</div>' +
|
||||
'</div>';
|
||||
'<div class="panel-footer">' +
|
||||
'<div class="progress">' +
|
||||
'<div class="progress-bar progress-bar-success"></div>' +
|
||||
'</div>' +
|
||||
'<h6 class="error"></h6>' +
|
||||
'</div>' +
|
||||
'</div>';
|
||||
|
||||
// return html string
|
||||
return tmpl;
|
||||
}
|
||||
});
|
||||
|
||||
|
||||
+28
-24
@@ -1,7 +1,7 @@
|
||||
/*
|
||||
Copyright 2012 Igor Vaynberg
|
||||
|
||||
Version: 3.4.2 Timestamp: Mon Aug 12 15:04:12 PDT 2013
|
||||
Version: 3.4.3 Timestamp: Tue Sep 17 06:47:14 PDT 2013
|
||||
|
||||
This software is licensed under the Apache License, Version 2.0 (the "Apache License") or the GNU
|
||||
General Public License version 2 (the "GPL License"). You may choose either license to govern your
|
||||
@@ -688,15 +688,19 @@ the specific language governing permissions and limitations under the Apache Lic
|
||||
this.opts.element
|
||||
.data("select2", this)
|
||||
.attr("tabindex", "-1")
|
||||
.before(this.container);
|
||||
.before(this.container)
|
||||
.on("click.select2", killEvent); // do not leak click events
|
||||
|
||||
this.container.data("select2", this);
|
||||
|
||||
this.dropdown = this.container.find(".select2-drop");
|
||||
this.dropdown.addClass(evaluate(opts.dropdownCssClass));
|
||||
this.dropdown.data("select2", this);
|
||||
|
||||
syncCssClasses(this.dropdown, this.opts.element, this.opts.adaptDropdownCssClass);
|
||||
|
||||
this.dropdown.addClass(evaluate(opts.dropdownCssClass));
|
||||
this.dropdown.data("select2", this);
|
||||
this.dropdown.on("click", killEvent);
|
||||
|
||||
this.results = results = this.container.find(resultsSelector);
|
||||
this.search = search = this.container.find("input.select2-input");
|
||||
|
||||
@@ -707,6 +711,8 @@ the specific language governing permissions and limitations under the Apache Lic
|
||||
// initialize the container
|
||||
this.initContainer();
|
||||
|
||||
this.container.on("click", killEvent);
|
||||
|
||||
installFilteredMouseMove(this.results);
|
||||
this.dropdown.on("mousemove-filtered touchstart touchmove touchend", resultsSelector, this.bind(this.highlightUnderEvent));
|
||||
|
||||
@@ -968,10 +974,11 @@ the specific language governing permissions and limitations under the Apache Lic
|
||||
opts.initSelection = function (element, callback) {
|
||||
var data = [];
|
||||
$(splitVal(element.val(), opts.separator)).each(function () {
|
||||
var id = this, text = this, tags=opts.tags;
|
||||
var obj = { id: this, text: this },
|
||||
tags = opts.tags;
|
||||
if ($.isFunction(tags)) tags=tags();
|
||||
$(tags).each(function() { if (equal(this.id, id)) { text = this.text; return false; } });
|
||||
data.push({id: id, text: text});
|
||||
$(tags).each(function() { if (equal(this.id, obj.id)) { obj = this; return false; } });
|
||||
data.push(obj);
|
||||
});
|
||||
|
||||
callback(data);
|
||||
@@ -1320,7 +1327,7 @@ the specific language governing permissions and limitations under the Apache Lic
|
||||
$("#select2-drop-mask").hide();
|
||||
this.dropdown.removeAttr("id"); // only the active dropdown has the select2-drop id
|
||||
this.dropdown.hide();
|
||||
this.container.removeClass("select2-dropdown-open");
|
||||
this.container.removeClass("select2-dropdown-open").removeClass("select2-container-active");
|
||||
this.results.empty();
|
||||
|
||||
|
||||
@@ -1395,7 +1402,7 @@ the specific language governing permissions and limitations under the Apache Lic
|
||||
|
||||
// abstract
|
||||
findHighlightableChoices: function() {
|
||||
return this.results.find(".select2-result-selectable:not(.select2-selected):not(.select2-disabled)");
|
||||
return this.results.find(".select2-result-selectable:not(.select2-disabled)");
|
||||
},
|
||||
|
||||
// abstract
|
||||
@@ -1926,10 +1933,7 @@ the specific language governing permissions and limitations under the Apache Lic
|
||||
killEvent(e);
|
||||
return;
|
||||
case KEY.TAB:
|
||||
// if selectOnBlur == true, select the currently highlighted option
|
||||
if (this.opts.selectOnBlur) {
|
||||
this.selectHighlighted({noFocus: true});
|
||||
}
|
||||
this.selectHighlighted({noFocus: true});
|
||||
return;
|
||||
case KEY.ESC:
|
||||
this.cancel(e);
|
||||
@@ -2046,6 +2050,11 @@ the specific language governing permissions and limitations under the Apache Lic
|
||||
clear: function(triggerChange) {
|
||||
var data=this.selection.data("select2-data");
|
||||
if (data) { // guard against queued quick consecutive clicks
|
||||
var evt = $.Event("select2-clearing");
|
||||
this.opts.element.trigger(evt);
|
||||
if (evt.isDefaultPrevented()) {
|
||||
return;
|
||||
}
|
||||
var placeholderOption = this.getPlaceholderOption();
|
||||
this.opts.element.val(placeholderOption ? placeholderOption.val() : "");
|
||||
this.selection.find(".select2-chosen").empty();
|
||||
@@ -2083,7 +2092,7 @@ the specific language governing permissions and limitations under the Apache Lic
|
||||
|
||||
isPlaceholderOptionSelected: function() {
|
||||
var placeholderOption;
|
||||
if (!this.opts.placeholder) return false; // no placeholder specified so no option should be considered
|
||||
if (!this.getPlaceholder()) return false; // no placeholder specified so no option should be considered
|
||||
return ((placeholderOption = this.getPlaceholderOption()) !== undefined && placeholderOption.is(':selected'))
|
||||
|| (this.opts.element.val() === "")
|
||||
|| (this.opts.element.val() === undefined)
|
||||
@@ -2216,7 +2225,7 @@ the specific language governing permissions and limitations under the Apache Lic
|
||||
this.close();
|
||||
|
||||
if (!options || !options.noFocus)
|
||||
this.selection.focus();
|
||||
this.focusser.focus();
|
||||
|
||||
if (!equal(old, this.id(data))) { this.triggerChange({added:data,removed:oldData}); }
|
||||
},
|
||||
@@ -2442,7 +2451,7 @@ the specific language governing permissions and limitations under the Apache Lic
|
||||
this.selection = selection = this.container.find(selector);
|
||||
|
||||
var _this = this;
|
||||
this.selection.on("click", ".select2-search-choice", function (e) {
|
||||
this.selection.on("click", ".select2-search-choice:not(.select2-locked)", function (e) {
|
||||
//killEvent(e);
|
||||
_this.search[0].focus();
|
||||
_this.selectChoice($(this));
|
||||
@@ -2521,10 +2530,7 @@ the specific language governing permissions and limitations under the Apache Lic
|
||||
killEvent(e);
|
||||
return;
|
||||
case KEY.TAB:
|
||||
// if selectOnBlur == true, select the currently highlighted option
|
||||
if (this.opts.selectOnBlur) {
|
||||
this.selectHighlighted({noFocus:true});
|
||||
}
|
||||
this.selectHighlighted({noFocus:true});
|
||||
this.close();
|
||||
return;
|
||||
case KEY.ESC:
|
||||
@@ -2842,9 +2848,7 @@ the specific language governing permissions and limitations under the Apache Lic
|
||||
return;
|
||||
}
|
||||
|
||||
index = indexOf(this.id(data), val);
|
||||
|
||||
if (index >= 0) {
|
||||
while((index = indexOf(this.id(data), val)) >= 0) {
|
||||
val.splice(index, 1);
|
||||
this.setVal(val);
|
||||
if (this.select) this.postprocessResults();
|
||||
@@ -2925,7 +2929,7 @@ the specific language governing permissions and limitations under the Apache Lic
|
||||
searchWidth = minimumWidth;
|
||||
}
|
||||
|
||||
this.search.width(searchWidth);
|
||||
this.search.width(Math.floor(searchWidth));
|
||||
},
|
||||
|
||||
// multi
|
||||
|
||||
@@ -82,6 +82,10 @@ var HDABaseView = Backbone.View.extend( LoggableMixin ).extend(
|
||||
|
||||
this.$el.attr( 'id', 'historyItemContainer-' + id );
|
||||
|
||||
//HACK: hover exit doesn't seem to be called on prev. tooltips when RE-rendering - so: no tooltip hide
|
||||
// handle that here by removing previous view's tooltips
|
||||
this.$el.find("[title]").tooltip( "destroy" );
|
||||
|
||||
/** web controller urls for functions relating to this hda.
|
||||
* These are rendered from urlTemplates using the model data. */
|
||||
this.urls = this._renderUrls( this.urlTemplates, this.model.toJSON() );
|
||||
@@ -247,7 +251,7 @@ var HDABaseView = Backbone.View.extend( LoggableMixin ).extend(
|
||||
var self = this;
|
||||
displayBtnData.on_click = function(){
|
||||
Galaxy.frame_manager.frame_new({
|
||||
title : "Data Viewer",
|
||||
title : "Data Viewer: " + self.model.get('name'),
|
||||
type : "url",
|
||||
location: "center",
|
||||
content : self.urls.display
|
||||
|
||||
@@ -166,6 +166,7 @@ var HDAEditView = HDABaseView.extend( LoggableMixin ).extend(
|
||||
success: function() {
|
||||
// FIXME: setting model attribute causes re-rendering, which is unnecessary.
|
||||
//self.$el.remove();
|
||||
|
||||
self.model.set({ deleted: true });
|
||||
}
|
||||
});
|
||||
|
||||
File diff suppressed because one or more lines are too long
@@ -1 +1 @@
|
||||
define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({el_main:"#everything",options:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b);$(this.el).hide()}},show:function(b){if(b){this.create(b)}this.$el.fadeIn("fast")},hide:function(){this.$el.fadeOut("fast")},create:function(c){this.$el.remove();if(!c){c=this.options}else{c=_.defaults(c,this.options)}this.setElement(this.template(c.title,c.body));$(this.el_main).append($(this.el));var d=(this.$el).find(".buttons");var b=this;if(c.buttons){$.each(c.buttons,function(e,f){d.append($("<button></button>").text(e).click(f)).append(" ")})}else{d.append($("<button></button>").text("Close").click(function(){b.hide()})).append(" ")}},template:function(c,b){return'<div class="modal in"><div class="modal-backdrop in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><span><h3 class="title">'+c+'</h3></span></div><div class="modal-body style="min-width: 540px; max-height: 445px;">'+b+'</div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}});
|
||||
define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({el_main:"#everything",options:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b);$(this.el).hide()}},show:function(b){if(b){this.create(b)}this.$el.fadeIn("fast")},hide:function(){this.$el.fadeOut("fast")},create:function(c){this.$el.remove();if(!c){c=this.options}else{c=_.defaults(c,this.options)}this.setElement(this.template(c.title,c.body));$(this.el_main).append($(this.el));var d=(this.$el).find(".buttons");var b=this;if(c.buttons){$.each(c.buttons,function(e,f){d.append($('<button id="'+String(e).toLowerCase()+'"></button>').text(e).click(f)).append(" ")})}else{d.append($("<button></button>").text("Close").click(function(){b.hide()})).append(" ")}},enable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",false)},disable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",true)},template:function(c,b){return'<div class="modal in"><div class="modal-backdrop in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><span><h3 class="title">'+c+'</h3></span></div><div class="modal-body style="min-width: 540px; max-height: 445px;">'+b+'</div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}});
|
||||
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
+1
-1
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@@ -1 +1 @@
|
||||
(function(d){jQuery.event.props.push("dataTransfer");var c={url:"",paramname:"content",maxfilesize:2048,data:{},dragover:function(){},dragleave:function(){},initialize:function(){},start:function(){},progress:function(){},success:function(){},error:function(f,g,h){alert(h)},error_browser:"Your browser does not support drag-and-drop file uploads.",error_filesize:"This file is too large. Please use an FTP client to upload it.",error_default:"The upload failed. Please make sure the file is available and accessible.",text_default:"Drag&drop files here or click to browse your local drive.",text_degrade:"Click here to browse your local drive. <br><br>Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."};var a=[];var b=-1;var e=false;d.fn.uploadbox=function(n){var f=d.extend({},c,n);var l=window.File&&window.FileReader&&window.FormData&&window.XMLHttpRequest;this.append('<input id="uploadbox_input" type="file" style="display: none" multiple>');this.append('<div id="uploadbox_info"></div>');if(l){this.find("#uploadbox_info").html(f.text_default)}else{this.find("#uploadbox_info").html(f.text_degrade)}this.on("drop",i);this.on("dragover",j);this.on("dragleave",m);this.on("click",function(p){p.stopPropagation();d("#uploadbox_input").trigger(p)});d("#uploadbox_input").change(function(q){var p=q.target.files;o(p)});function i(q){if(!q.dataTransfer){return}var p=q.dataTransfer.files;o(p);q.preventDefault();return false}function j(p){p.preventDefault();f.dragover.call(this,p)}function m(p){p.stopPropagation();f.dragleave.call(this,p)}function g(p){if(p.lengthComputable){f.progress(this.index,this.file,Math.round((p.loaded*100)/p.total))}}function o(r){var q=a.length;for(var p=0;p<r.length;p++){a.push(r[p])}for(var p=q;p<a.length;p++){f.start(p,a[p],"")}if(!e){h()}}function h(){if(b+1==a.length){e=false;return}e=true;var s=++b;try{var q=new FileReader();var t=a[s];var r=t.size;var p=1048576*f.maxfilesize;q.index=s;if(r<p){q.onloadend=function(v){k(s,t)};q.onerror=function(v){f.error(s,t,f.error_default);e=false};q.readAsDataURL(t)}else{f.error(s,t,f.error_filesize);h()}}catch(u){f.error(s,t,u)}}function k(p,r){var s=new FormData();for(var q in f.data){s.append(q,f.data[q])}s.append(f.paramname,r,r.name);var t=new XMLHttpRequest();t.upload.index=p;t.upload.file=r;t.upload.addEventListener("progress",g,false);t.open("POST",f.url,true);t.setRequestHeader("Accept","application/json");t.setRequestHeader("Cache-Control","no-cache");t.setRequestHeader("X-Requested-With","XMLHttpRequest");t.send(s);t.onloadend=function(){var u=null;if(t.responseText){try{u=jQuery.parseJSON(t.responseText)}catch(v){u=t.responseText}}if(t.status<200||t.status>299){f.error(p,r,t.statusText+" (Server Code "+t.status+")");e=false}else{f.success(p,r,u);h()}}}return this}})(jQuery);
|
||||
(function(g){jQuery.event.props.push("dataTransfer");var c={url:"",paramname:"content",maxfilesize:250,dragover:function(){},dragleave:function(){},announce:function(){},initialize:function(){},progress:function(){},success:function(){},error:function(i,j,k){alert(k)},complete:function(){},error_browser:"Your browser does not support drag-and-drop file uploads.",error_filesize:"This file is too large (>250MB). Please use an FTP client to upload it.",error_default:"Please make sure the file is available."};var f={};var a={};var b=0;var d=0;var h=false;var e=null;g.fn.uploadbox=function(x){f=g.extend({},c,x);e=this;e.append('<input id="uploadbox_input" type="file" style="display: none" multiple>');e.on("drop",l);e.on("dragover",m);e.on("dragleave",t);g("#uploadbox_input").change(function(y){v(y.target.files)});function l(y){if(!y.dataTransfer){return}v(y.dataTransfer.files);y.preventDefault();return false}function m(y){y.preventDefault();f.dragover.call(y)}function t(y){y.stopPropagation();f.dragleave.call(y)}function i(y){if(y.lengthComputable){f.progress(this.index,this.file,Math.round((y.loaded*100)/y.total))}}function v(A){if(h){return}for(var z=0;z<A.length;z++){var y=String(b++);a[y]=A[z];d++;f.announce(y,a[y],"")}}function o(y){if(a[y]){delete a[y];d--}}function j(){if(d==0){h=false;f.complete();return}else{h=true}var B=-1;for(var D in a){B=D;break}var C=a[B];o(B);var F=f.initialize(B,C);try{var z=new FileReader();var A=C.size;var y=1048576*f.maxfilesize;z.index=B;if(A<y){z.onload=function(G){n(B,C,F)};z.onerror=function(G){r(B,C,f.error_default)};z.readAsDataURL(C)}else{r(B,C,f.error_filesize)}}catch(E){r(B,C,E)}}function n(y,A,B){var C=new FormData();for(var z in B){C.append(z,B[z])}C.append(f.paramname,A,A.name);var D=new XMLHttpRequest();D.upload.index=y;D.upload.file=A;D.upload.addEventListener("progress",i,false);D.open("POST",f.url,true);D.setRequestHeader("Accept","application/json");D.setRequestHeader("Cache-Control","no-cache");D.setRequestHeader("X-Requested-With","XMLHttpRequest");D.send(C);D.onloadend=function(){var E=null;if(D.responseText){try{E=jQuery.parseJSON(D.responseText)}catch(F){E=D.responseText}}if(D.status<200||D.status>299){var G=D.statusText;if(!D.statusText){G=f.error_default}r(y,A,G+" (Server Code "+D.status+")")}else{u(y,A,E)}}}function u(y,z,A){f.success(y,z,A);j()}function r(y,z,A){f.error(y,z,A);j()}function s(){g("#uploadbox_input").trigger("click")}function q(y){for(y in a){o(y)}}function w(){if(!h){j()}}function k(y){f=g.extend({},f,y);return f}function p(){return window.File&&window.FileReader&&window.FormData&&window.XMLHttpRequest}return{select:s,remove:o,upload:w,reset:q,configure:k,compatible:p}}})(jQuery);
|
||||
@@ -19,11 +19,10 @@
|
||||
progress : function() {},
|
||||
success : function() {},
|
||||
error : function(index, file, message) { alert(message); },
|
||||
complete : function() {},
|
||||
error_browser : "Your browser does not support drag-and-drop file uploads.",
|
||||
error_filesize : "This file is too large (>250MB). Please use an FTP client to upload it.",
|
||||
error_default : "Please make sure the file is available.",
|
||||
text_default : "Drag&drop files into this box or click 'Select' to select files!",
|
||||
text_degrade : "Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."
|
||||
error_default : "Please make sure the file is available."
|
||||
}
|
||||
|
||||
// options
|
||||
@@ -32,7 +31,7 @@
|
||||
// file queue
|
||||
var queue = {};
|
||||
|
||||
// counter for file being currently processed
|
||||
// queue index counter
|
||||
var queue_index = 0;
|
||||
|
||||
// queue length
|
||||
@@ -50,21 +49,11 @@
|
||||
// parse options
|
||||
opts = $.extend({}, default_opts, options);
|
||||
|
||||
// compatibility
|
||||
var mode = window.File && window.FileReader && window.FormData && window.XMLHttpRequest;
|
||||
|
||||
// element
|
||||
el = this;
|
||||
|
||||
// append upload button
|
||||
el.append('<input id="uploadbox_input" type="file" style="display: none" multiple>');
|
||||
el.append('<div id="uploadbox_info"></div>');
|
||||
|
||||
// set info text
|
||||
if (mode)
|
||||
el.find('#uploadbox_info').html(opts.text_default);
|
||||
else
|
||||
el.find('#uploadbox_info').html(opts.text_degrade);
|
||||
|
||||
// attach events
|
||||
el.on('drop', drop);
|
||||
@@ -76,6 +65,9 @@
|
||||
{
|
||||
// add files to queue
|
||||
add(e.target.files);
|
||||
|
||||
// reset
|
||||
$(this).val('');
|
||||
});
|
||||
|
||||
// drop event
|
||||
@@ -120,11 +112,15 @@
|
||||
// respond to an upload request
|
||||
function add(files)
|
||||
{
|
||||
// only allow adding file if current batch is complete
|
||||
if (queue_status)
|
||||
return;
|
||||
|
||||
// add new files to queue
|
||||
for (var i = 0; i < files.length; i++)
|
||||
{
|
||||
// new identifier
|
||||
var index = String(++queue_index);
|
||||
var index = String(queue_index++);
|
||||
|
||||
// add to queue
|
||||
queue[index] = files[i];
|
||||
@@ -153,6 +149,15 @@
|
||||
// process an upload, recursive
|
||||
function process()
|
||||
{
|
||||
// validate
|
||||
if (queue_length == 0)
|
||||
{
|
||||
queue_status = false;
|
||||
opts.complete();
|
||||
return;
|
||||
} else
|
||||
queue_status = true;
|
||||
|
||||
// get an identifier from the queue
|
||||
var index = -1;
|
||||
for (var key in queue)
|
||||
@@ -161,10 +166,6 @@
|
||||
break;
|
||||
}
|
||||
|
||||
// validate
|
||||
if (queue_length == 0)
|
||||
return;
|
||||
|
||||
// get current file from queue
|
||||
var file = queue[index];
|
||||
|
||||
@@ -172,7 +173,7 @@
|
||||
remove(index)
|
||||
|
||||
// start
|
||||
var data = opts.initialize(index, file, length);
|
||||
var data = opts.initialize(index, file);
|
||||
|
||||
// add file to queue
|
||||
try
|
||||
@@ -312,12 +313,6 @@
|
||||
process();
|
||||
}
|
||||
|
||||
// current queue length
|
||||
function length()
|
||||
{
|
||||
return queue_length;
|
||||
}
|
||||
|
||||
// set options
|
||||
function configure(options)
|
||||
{
|
||||
@@ -328,21 +323,20 @@
|
||||
return opts;
|
||||
}
|
||||
|
||||
// visibility of on screen information
|
||||
function info()
|
||||
// verify browser compatibility
|
||||
function compatible()
|
||||
{
|
||||
return el.find('#uploadbox_info');
|
||||
return window.File && window.FileReader && window.FormData && window.XMLHttpRequest && window.FileList;
|
||||
}
|
||||
|
||||
// export functions
|
||||
return {
|
||||
'select' : select,
|
||||
'remove' : remove,
|
||||
'upload' : upload,
|
||||
'reset' : reset,
|
||||
'length' : length,
|
||||
'configure' : configure,
|
||||
'info' : info
|
||||
'select' : select,
|
||||
'remove' : remove,
|
||||
'upload' : upload,
|
||||
'reset' : reset,
|
||||
'configure' : configure,
|
||||
'compatible' : compatible
|
||||
};
|
||||
}
|
||||
})(jQuery);
|
||||
@@ -1116,16 +1116,17 @@ ul.icons{list-style-type:none;text-indent:-0.75em}ul.icons li [class^="fa-icon-"
|
||||
.galaxy-frame .frame{z-index:1002;overflow:hidden;position:absolute;background:#fff;border:1px solid #888;-webkit-box-shadow:0 0 5px rgba(0,0,0,0.3);}.galaxy-frame .frame .f-content{position:absolute;overflow:hidden;background:#fff;border:none;top:24px;bottom:3px;left:3px;right:3px}
|
||||
.galaxy-frame .frame .f-cover{position:absolute;display:none;top:0px;left:0px;height:100%;width:100%;opacity:0.0;background:#fff}
|
||||
.galaxy-frame .frame .f-iframe{border:none;width:100%;height:100%}
|
||||
.galaxy-frame .frame .f-header{height:17px;margin:2px;cursor:pointer;border:1px solid #000;background:#2c3143;color:#fff;font-weight:bold}
|
||||
.galaxy-frame .frame .f-header{height:17px;margin:2px;cursor:pointer;border:1px solid #000;background:#2c3143;color:#fff}
|
||||
.galaxy-frame .frame .f-title{position:absolute;top:2px;left:16px;right:16px;font-size:12px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;text-align:center}
|
||||
.galaxy-frame .frame .f-icon{position:absolute;cursor:pointer;font-style:normal}
|
||||
.galaxy-frame .frame .f-icon{position:absolute;cursor:pointer}
|
||||
.galaxy-frame .frame .f-not-allowed{cursor:not-allowed}
|
||||
.galaxy-frame .frame .f-close{right:5px;top:1px}
|
||||
.galaxy-frame .frame .f-pin{left:6px;top:1px}
|
||||
.galaxy-frame .frame .f-resize{background:#fff;width:16px;height:16px;color:#2c3143;right:0px;bottom:0px;text-align:center;line-height:16px;border:0px}
|
||||
.upload-info{font-weight:normal;text-align:center}
|
||||
.upload-box{width:100%;height:250px;max-height:250px;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:20px}.upload-box .panel{display:none}.upload-box .panel .panel-heading{position:relative;height:19px;padding:5px}.upload-box .panel .panel-heading .title{position:absolute;top:2px;font-weight:normal;text-align:left;margin:0px;max-width:300px;overflow:hidden}
|
||||
.upload-box .panel .panel-heading .info{position:absolute;top:3px;font-weight:normal;right:20px;text-align:right;margin:0px}
|
||||
.upload-box .panel .panel-heading .remove{position:absolute;cursor:pointer;top:0px;right:3px}
|
||||
.upload-box .panel .panel-heading .symbol{position:absolute;cursor:pointer;top:0px;right:3px}
|
||||
.upload-box .panel .panel-body{position:relative;padding:5px}
|
||||
.upload-box .panel .panel-footer{position:relative;height:20px;padding:0px}.upload-box .panel .panel-footer .progress{height:10px;margin:5px}
|
||||
.upload-box .panel .panel-footer .error{font-weight:normal;margin:2px}
|
||||
@@ -1168,12 +1169,12 @@ div.unified-panel-body{position:absolute;top:30px;bottom:0;width:100%}
|
||||
.panel-warning-message{background-image:url(warn_small.png);background-color:#fce1ba}
|
||||
.panel-done-message{background-image:url(ok_small.png);background-color:#aff1af}
|
||||
.panel-info-message{background-image:url(info_small.png);background-color:#a6e4f7}
|
||||
#masthead{position:absolute;top:0;left:0;width:100%;min-width:980px;padding:0}#masthead .nav{z-index:15001}
|
||||
#masthead{position:absolute;top:0;left:0;width:100%;min-width:990px;padding:0}#masthead .nav{z-index:15001}
|
||||
#masthead .nav>li>a{cursor:pointer;text-decoration:none}#masthead .nav>li>a:hover{color:gold}
|
||||
#masthead li.dropdown>a:hover .caret{border-top-color:gold;border-bottom-color:gold}
|
||||
#masthead .navbar-brand{position:absolute;left:0;top:0;font-family:verdana;font-weight:bold;font-size:20px;line-height:1;color:white;padding:5px 20px 12px;margin-left:-15px;z-index:2000}#masthead .navbar-brand img{display:inline;width:26px;vertical-align:top}
|
||||
#masthead .navbar-brand a{color:white;text-decoration:none}
|
||||
#masthead .iconbar{position:absolute;top:2px;right:110px;cursor:pointer;color:#999;overflow:hidden}#masthead .iconbar .symbol{float:left;margin:0px 8px}
|
||||
#masthead .iconbar{position:absolute;top:2px;right:110px;cursor:pointer;color:#999;overflow:hidden}#masthead .iconbar .symbol{float:left;margin:0px 10px}
|
||||
#masthead .iconbar .symbol .number{font-weight:bold;font-size:12px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;position:relative;left:23px;top:-18px}
|
||||
#masthead .iconbar .toggle{color:#BCC800}
|
||||
.quota-meter-container{position:absolute;top:0;right:0;height:32px}
|
||||
@@ -1246,9 +1247,10 @@ input[type="submit"].disabled,button.disabled,input[type="submit"][disabled],but
|
||||
.errormessage .alert-link,.warningmessage .alert-link,.donemessage .alert-link,.infomessage .alert-link,.errormessagesmall .alert-link,.warningmessagesmall .alert-link,.donemessagesmall .alert-link,.infomessagesmall .alert-link{font-weight:bold}
|
||||
.errormessage>p,.warningmessage>p,.donemessage>p,.infomessage>p,.errormessagesmall>p,.warningmessagesmall>p,.donemessagesmall>p,.infomessagesmall>p,.errormessage>ul,.warningmessage>ul,.donemessage>ul,.infomessage>ul,.errormessagesmall>ul,.warningmessagesmall>ul,.donemessagesmall>ul,.infomessagesmall>ul{margin-bottom:0}
|
||||
.errormessage>p+p,.warningmessage>p+p,.donemessage>p+p,.infomessage>p+p,.errormessagesmall>p+p,.warningmessagesmall>p+p,.donemessagesmall>p+p,.infomessagesmall>p+p{margin-top:5px}
|
||||
.errormessage{background-color:#f9c7c5;border-color:#dd1c15;color:#7e2a27}.errormessage hr{border-top-color:#c61913}
|
||||
.errormessage .alert-link{color:#571d1b}
|
||||
.warningmessage,.warningmessagesmall{background-image:url(warn_small.png)}
|
||||
.errormessage,.errormessagesmall{background-color:#f9c7c5;border-color:#dd1c15;color:#7e2a27}.errormessage hr,.errormessagesmall hr{border-top-color:#c61913}
|
||||
.errormessage .alert-link,.errormessagesmall .alert-link{color:#571d1b}
|
||||
.warningmessage,.warningmessagesmall{background-color:#fce1ba;border-color:#e28709;color:#80571e;background-image:url(warn_small.png)}.warningmessage hr,.warningmessagesmall hr{border-top-color:#c97908}
|
||||
.warningmessage .alert-link,.warningmessagesmall .alert-link{color:#573b14}
|
||||
.donemessage,.donemessagesmall{background-color:#aff1af;border-color:#20b420;color:#295f29;background-image:url(ok_small.png)}.donemessage hr,.donemessagesmall hr{border-top-color:#1c9e1c}
|
||||
.donemessage .alert-link,.donemessagesmall .alert-link{color:#193b19}
|
||||
.infomessage,.infomessagesmall{background-color:#a6e4f7;border-color:#1197c0;color:#1f5566;background-image:url(info_small.png)}.infomessage hr,.infomessagesmall hr{border-top-color:#0f85a8}
|
||||
|
||||
@@ -335,7 +335,7 @@ div.unified-panel-body {
|
||||
top:0;
|
||||
left:0;
|
||||
width:100%;
|
||||
min-width:980px;
|
||||
min-width:990px;
|
||||
padding: 0;
|
||||
|
||||
.nav {
|
||||
@@ -398,7 +398,7 @@ div.unified-panel-body {
|
||||
.symbol
|
||||
{
|
||||
float : left;
|
||||
margin : 0px 8px;
|
||||
margin : 0px 10px;
|
||||
}
|
||||
|
||||
.symbol .number
|
||||
@@ -770,28 +770,23 @@ input[type="submit"], button {
|
||||
background-position: 5px 5px;
|
||||
}
|
||||
|
||||
.errormessage {
|
||||
.errormessage, .errormessagesmall {
|
||||
.alert-danger();
|
||||
}
|
||||
|
||||
.warningmessage, .warningmessagesmall {
|
||||
.alert-warning();
|
||||
background-image: url(warn_small.png);
|
||||
//border-color: @warn_message_border;
|
||||
//background-color: @warn_message_bg;
|
||||
}
|
||||
|
||||
.donemessage, .donemessagesmall {
|
||||
.alert-success();
|
||||
background-image: url(ok_small.png);
|
||||
// border-color: @done_message_border;
|
||||
// background-color: @done_message_bg;
|
||||
}
|
||||
|
||||
.infomessage, .infomessagesmall {
|
||||
.alert-info();
|
||||
background-image: url(info_small.png);
|
||||
//border-color: @info_message_border;
|
||||
//background-color: @info_message_bg;
|
||||
}
|
||||
|
||||
.errormark, .warningmark, .donemark, .infomark, .ok_bgr, .err_bgr {
|
||||
|
||||
@@ -111,7 +111,6 @@
|
||||
border : 1px solid @black;
|
||||
background : @base-color-1;
|
||||
color : @white;
|
||||
font-weight : bold;
|
||||
}
|
||||
|
||||
.f-title
|
||||
@@ -133,7 +132,6 @@
|
||||
{
|
||||
position : absolute;
|
||||
cursor : pointer;
|
||||
font-style : normal;
|
||||
}
|
||||
|
||||
.f-not-allowed
|
||||
|
||||
@@ -1,3 +1,9 @@
|
||||
.upload-info
|
||||
{
|
||||
font-weight: normal;
|
||||
text-align: center;
|
||||
}
|
||||
|
||||
.upload-box
|
||||
{
|
||||
width : 100%;
|
||||
@@ -43,7 +49,7 @@
|
||||
margin: 0px;
|
||||
}
|
||||
|
||||
.remove
|
||||
.symbol
|
||||
{
|
||||
position: absolute;
|
||||
cursor: pointer;
|
||||
|
||||
@@ -254,6 +254,49 @@ def execute_uninstall_method( app, deactivate_only=False ):
|
||||
success = result.wasSuccessful()
|
||||
return success
|
||||
|
||||
def extract_log_data( test_result, from_tool_test=True ):
|
||||
'''Extract any useful data from the test_result.failures and test_result.errors attributes.'''
|
||||
for failure in test_result.failures + test_result.errors:
|
||||
# Record the twill test identifier and information about the tool, so the repository owner can discover which test is failing.
|
||||
test_id = str( failure[0] )
|
||||
if not from_tool_test:
|
||||
tool_id = None
|
||||
tool_version = None
|
||||
else:
|
||||
tool_id, tool_version = get_tool_info_from_test_id( test_id )
|
||||
test_status = dict( test_id=test_id, tool_id=tool_id, tool_version=tool_version )
|
||||
log_output = failure[1].replace( '\\n', '\n' )
|
||||
# Remove debug output that the reviewer or owner doesn't need.
|
||||
log_output = re.sub( r'control \d+:.+', r'', log_output )
|
||||
log_output = re.sub( r'\n+', r'\n', log_output )
|
||||
appending_to = 'output'
|
||||
tmp_output = {}
|
||||
output = {}
|
||||
# Iterate through the functional test output and extract only the important data. Captured logging and stdout are not recorded.
|
||||
for line in log_output.split( '\n' ):
|
||||
if line.startswith( 'Traceback' ):
|
||||
appending_to = 'traceback'
|
||||
elif '>> end captured' in line or '>> end tool' in line:
|
||||
continue
|
||||
elif 'request returned None from get_history' in line:
|
||||
continue
|
||||
elif '>> begin captured logging <<' in line:
|
||||
appending_to = 'logging'
|
||||
continue
|
||||
elif '>> begin captured stdout <<' in line:
|
||||
appending_to = 'stdout'
|
||||
continue
|
||||
elif '>> begin captured stderr <<' in line or '>> begin tool stderr <<' in line:
|
||||
appending_to = 'stderr'
|
||||
continue
|
||||
if appending_to not in tmp_output:
|
||||
tmp_output[ appending_to ] = []
|
||||
tmp_output[ appending_to ].append( line )
|
||||
for output_type in [ 'stderr', 'traceback' ]:
|
||||
if output_type in tmp_output:
|
||||
test_status[ output_type ] = '\n'.join( tmp_output[ output_type ] )
|
||||
return test_status
|
||||
|
||||
def get_api_url( base, parts=[], params=None, key=None ):
|
||||
if 'api' in parts and parts.index( 'api' ) != 0:
|
||||
parts.pop( parts.index( 'api' ) )
|
||||
@@ -1054,43 +1097,7 @@ def main():
|
||||
params )
|
||||
log.debug( 'Revision %s of repository %s installed and passed functional tests.', changeset_revision, name )
|
||||
else:
|
||||
# If the functional tests fail, log the output and update the failed changeset revision's metadata record in the tool shed via the API.
|
||||
for failure in result.failures + result.errors:
|
||||
# Record the twill test identifier and information about the tool, so the repository owner can discover which test is failing.
|
||||
test_id = str( failure[0] )
|
||||
tool_id, tool_version = get_tool_info_from_test_id( test_id )
|
||||
test_status = dict( test_id=test_id, tool_id=tool_id, tool_version=tool_version )
|
||||
log_output = failure[1].replace( '\\n', '\n' )
|
||||
# Remove debug output that the reviewer or owner doesn't need.
|
||||
log_output = re.sub( r'control \d+:.+', r'', log_output )
|
||||
log_output = re.sub( r'\n+', r'\n', log_output )
|
||||
appending_to = 'output'
|
||||
tmp_output = {}
|
||||
output = {}
|
||||
# Iterate through the functional test output and extract only the important data. Captured logging and stdout are not recorded.
|
||||
for line in log_output.split( '\n' ):
|
||||
if line.startswith( 'Traceback' ):
|
||||
appending_to = 'traceback'
|
||||
elif '>> end captured' in line or '>> end tool' in line:
|
||||
continue
|
||||
elif 'request returned None from get_history' in line:
|
||||
continue
|
||||
elif '>> begin captured logging <<' in line:
|
||||
appending_to = 'logging'
|
||||
continue
|
||||
elif '>> begin captured stdout <<' in line:
|
||||
appending_to = 'stdout'
|
||||
continue
|
||||
elif '>> begin captured stderr <<' in line or '>> begin tool stderr <<' in line:
|
||||
appending_to = 'stderr'
|
||||
continue
|
||||
if appending_to not in tmp_output:
|
||||
tmp_output[ appending_to ] = []
|
||||
tmp_output[ appending_to ].append( line )
|
||||
for output_type in [ 'stderr', 'traceback' ]:
|
||||
if output_type in tmp_output:
|
||||
test_status[ output_type ] = '\n'.join( tmp_output[ output_type ] )
|
||||
repository_status[ 'failed_tests' ].append( test_status )
|
||||
repository_status[ 'failed_tests' ] = extract_log_data( result, from_tool_test=True )
|
||||
# Call the register_test_result method, which executes a PUT request to the repository_revisions API controller with the outcome
|
||||
# of the tests, and updates tool_test_results with the relevant log data.
|
||||
# This also sets the do_not_test and tools_functionally correct flags to the appropriate values, and updates the time_last_tested
|
||||
@@ -1129,7 +1136,7 @@ def main():
|
||||
name=repository.name,
|
||||
owner=repository.owner,
|
||||
changeset_revision=repository.changeset_revision,
|
||||
error_message=repository.error_message )
|
||||
error_message=extract_log_data( result, from_tool_test=False ) )
|
||||
repository_status[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result )
|
||||
params[ 'tools_functionally_correct' ] = False
|
||||
params[ 'test_install_error' ] = True
|
||||
|
||||
@@ -38,7 +38,7 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
category = test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' )
|
||||
strings_displayed = [ 'Repository %s' % "'%s'" % repository_name,
|
||||
'Repository %s has been created' % "'%s'" % repository_name ]
|
||||
'Repository %s has been created' % "<b>%s</b>" % repository_name ]
|
||||
self.get_or_create_repository( name=repository_name,
|
||||
description=repository_description,
|
||||
long_description=repository_long_description,
|
||||
|
||||
@@ -58,7 +58,7 @@ class TestRepositoryMultipleOwners( ShedTwillTestCase ):
|
||||
self.logout()
|
||||
self.login( email=common.test_user_2_email, username=common.test_user_2_name )
|
||||
strings_displayed = [ 'Repository %s' % "'%s'" % datatypes_repository_name,
|
||||
'Repository %s has been created' % "'%s'" % datatypes_repository_name ]
|
||||
'Repository %s has been created' % "<b>%s</b>" % datatypes_repository_name ]
|
||||
repository = self.get_or_create_repository( name=datatypes_repository_name,
|
||||
description=datatypes_repository_description,
|
||||
long_description=datatypes_repository_long_description,
|
||||
@@ -98,7 +98,7 @@ class TestRepositoryMultipleOwners( ShedTwillTestCase ):
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
strings_displayed = [ 'Repository %s' % "'%s'" % tool_repository_name,
|
||||
'Repository %s has been created' % "'%s'" % tool_repository_name ]
|
||||
'Repository %s has been created' % "<b>%s</b>" % tool_repository_name ]
|
||||
repository = self.get_or_create_repository( name=tool_repository_name,
|
||||
description=tool_repository_description,
|
||||
long_description=tool_repository_long_description,
|
||||
|
||||
@@ -93,7 +93,7 @@ class TestRepositoryComponentReviews( ShedTwillTestCase ):
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
strings_displayed = [ 'Repository %s' % "'%s'" % repository_name,
|
||||
'Repository %s has been created' % "'%s'" % repository_name ]
|
||||
'Repository %s has been created' % "<b>%s</b>" % repository_name ]
|
||||
repository = self.get_or_create_repository( name=repository_name,
|
||||
description=repository_description,
|
||||
long_description=repository_long_description,
|
||||
|
||||
@@ -72,7 +72,7 @@ class TestRepositoryComponentReviews( ShedTwillTestCase ):
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
strings_displayed = [ 'Repository %s' % "'%s'" % repository_name,
|
||||
'Repository %s has been created' % "'%s'" % repository_name ]
|
||||
'Repository %s has been created' % "<b>%s</b>" % repository_name ]
|
||||
repository = self.get_or_create_repository( name=repository_name,
|
||||
description=repository_description,
|
||||
long_description=repository_long_description,
|
||||
|
||||
@@ -52,7 +52,7 @@ class TestRepositoryCitableURLs( ShedTwillTestCase ):
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
strings_displayed = [ 'Repository %s' % "'%s'" % repository_name,
|
||||
'Repository %s has been created' % "'%s'" % repository_name ]
|
||||
'Repository %s has been created' % "<b>%s</b>" % repository_name ]
|
||||
repository = self.get_or_create_repository( name=repository_name,
|
||||
description=repository_description,
|
||||
long_description=repository_long_description,
|
||||
|
||||
@@ -57,7 +57,7 @@ class TestToolShedBrowseUtilities( ShedTwillTestCase ):
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
strings_displayed = [ 'Repository %s' % "'%s'" % datatypes_repository_name,
|
||||
'Repository %s has been created' % "'%s'" % datatypes_repository_name ]
|
||||
'Repository %s has been created' % "<b>%s</b>" % datatypes_repository_name ]
|
||||
repository = self.get_or_create_repository( name=datatypes_repository_name,
|
||||
description=datatypes_repository_description,
|
||||
long_description=datatypes_repository_long_description,
|
||||
@@ -85,7 +85,7 @@ class TestToolShedBrowseUtilities( ShedTwillTestCase ):
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
strings_displayed = [ 'Repository %s' % "'%s'" % emboss_repository_name,
|
||||
'Repository %s has been created' % "'%s'" % emboss_repository_name ]
|
||||
'Repository %s has been created' % "<b>%s</b>" % emboss_repository_name ]
|
||||
emboss_repository = self.get_or_create_repository( name=emboss_repository_name,
|
||||
description=emboss_repository_description,
|
||||
long_description=emboss_repository_long_description,
|
||||
@@ -122,7 +122,7 @@ class TestToolShedBrowseUtilities( ShedTwillTestCase ):
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
strings_displayed = [ 'Repository %s' % "'%s'" % freebayes_repository_name,
|
||||
'Repository %s has been created' % "'%s'" % freebayes_repository_name ]
|
||||
'Repository %s has been created' % "<b>%s</b>" % freebayes_repository_name ]
|
||||
repository = self.get_or_create_repository( name=freebayes_repository_name,
|
||||
description=freebayes_repository_description,
|
||||
long_description=freebayes_repository_long_description,
|
||||
|
||||
@@ -76,7 +76,7 @@ class TestSkipToolTestFeature( ShedTwillTestCase ):
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
category = test_db_util.get_category_by_name( category_name )
|
||||
strings_displayed = [ 'Repository %s' % "'%s'" % repository_name,
|
||||
'Repository %s has been created' % "'%s'" % repository_name ]
|
||||
'Repository %s has been created' % "<b>%s</b>" % repository_name ]
|
||||
repository = self.get_or_create_repository( name=repository_name,
|
||||
description=repository_description,
|
||||
long_description=repository_long_description,
|
||||
|
||||
@@ -63,7 +63,7 @@ class TestInstallRepositoryMultipleOwners( ShedTwillTestCase ):
|
||||
self.logout()
|
||||
self.login( email=common.test_user_2_email, username=common.test_user_2_name )
|
||||
strings_displayed = [ 'Repository %s' % "'%s'" % datatypes_repository_name,
|
||||
'Repository %s has been created' % "'%s'" % datatypes_repository_name ]
|
||||
'Repository %s has been created' % "<b>%s</b>" % datatypes_repository_name ]
|
||||
repository = self.get_or_create_repository( name=datatypes_repository_name,
|
||||
description=datatypes_repository_description,
|
||||
long_description=datatypes_repository_long_description,
|
||||
@@ -105,7 +105,7 @@ class TestInstallRepositoryMultipleOwners( ShedTwillTestCase ):
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
strings_displayed = [ 'Repository %s' % "'%s'" % tool_repository_name,
|
||||
'Repository %s has been created' % "'%s'" % tool_repository_name ]
|
||||
'Repository %s has been created' % "<b>%s</b>" % tool_repository_name ]
|
||||
repository = self.get_or_create_repository( name=tool_repository_name,
|
||||
description=tool_repository_description,
|
||||
long_description=tool_repository_long_description,
|
||||
|
||||
@@ -56,6 +56,40 @@ default_galaxy_test_port_min = 9000
|
||||
default_galaxy_test_port_max = 9999
|
||||
default_galaxy_test_host = 'localhost'
|
||||
|
||||
# should this serve static resources (scripts, images, styles, etc.)
|
||||
STATIC_ENABLED = True
|
||||
|
||||
def get_static_settings():
|
||||
"""Returns dictionary of the settings necessary for a galaxy App
|
||||
to be wrapped in the static middleware.
|
||||
|
||||
This mainly consists of the filesystem locations of url-mapped
|
||||
static resources.
|
||||
"""
|
||||
cwd = os.getcwd()
|
||||
static_dir = os.path.join( cwd, 'static' )
|
||||
#TODO: these should be copied from universe_wsgi.ini
|
||||
return dict(
|
||||
#TODO: static_enabled needed here?
|
||||
static_enabled = True,
|
||||
static_cache_time = 360,
|
||||
static_dir = static_dir,
|
||||
static_images_dir = os.path.join( static_dir, 'images', '' ),
|
||||
static_favicon_dir = os.path.join( static_dir, 'favicon.ico' ),
|
||||
static_scripts_dir = os.path.join( static_dir, 'scripts', '' ),
|
||||
static_style_dir = os.path.join( static_dir, 'june_2007_style', 'blue' ),
|
||||
static_robots_txt = os.path.join( static_dir, 'robots.txt' ),
|
||||
)
|
||||
|
||||
def get_webapp_global_conf():
|
||||
"""Get the global_conf dictionary sent as the first argument to app_factory.
|
||||
"""
|
||||
# (was originally sent 'dict()') - nothing here for now except static settings
|
||||
global_conf = dict()
|
||||
if STATIC_ENABLED:
|
||||
global_conf.update( get_static_settings() )
|
||||
return global_conf
|
||||
|
||||
tool_sheds_conf_xml_template = '''<?xml version="1.0"?>
|
||||
<tool_sheds>
|
||||
<tool_shed name="Embedded tool shed for functional tests" url="http://${shed_url}:${shed_port}/"/>
|
||||
@@ -144,6 +178,9 @@ def main():
|
||||
galaxy_migrated_tool_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir )
|
||||
galaxy_tool_dependency_dir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir )
|
||||
os.environ[ 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ] = galaxy_tool_dependency_dir
|
||||
hgweb_config_dir = hgweb_config_file_path
|
||||
os.environ[ 'TEST_HG_WEB_CONFIG_DIR' ] = hgweb_config_dir
|
||||
print "Directory location for hgweb.config:", hgweb_config_dir
|
||||
if 'TOOL_SHED_TEST_DBURI' in os.environ:
|
||||
toolshed_database_connection = os.environ[ 'TOOL_SHED_TEST_DBURI' ]
|
||||
else:
|
||||
@@ -152,7 +189,29 @@ def main():
|
||||
galaxy_database_connection = os.environ[ 'GALAXY_TEST_DBURI' ]
|
||||
else:
|
||||
galaxy_database_connection = 'sqlite:///' + os.path.join( galaxy_db_path, 'universe_test.sqlite' )
|
||||
kwargs = {}
|
||||
tool_shed_global_conf = get_webapp_global_conf()
|
||||
tool_shed_global_conf[ '__file__' ] = 'tool_shed_wsgi.ini.sample'
|
||||
kwargs = dict( admin_users = 'test@bx.psu.edu',
|
||||
allow_user_creation = True,
|
||||
allow_user_deletion = True,
|
||||
database_connection = toolshed_database_connection,
|
||||
datatype_converters_config_file = 'datatype_converters_conf.xml.sample',
|
||||
file_path = shed_file_path,
|
||||
global_conf = tool_shed_global_conf,
|
||||
hgweb_config_dir = hgweb_config_dir,
|
||||
job_queue_workers = 5,
|
||||
id_secret = 'changethisinproductiontoo',
|
||||
log_destination = "stdout",
|
||||
new_file_path = new_repos_path,
|
||||
running_functional_tests = True,
|
||||
shed_tool_data_table_config = shed_tool_data_table_conf_file,
|
||||
smtp_server = 'smtp.dummy.string.tld',
|
||||
email_from = 'functional@localhost',
|
||||
template_path = 'templates',
|
||||
tool_path=tool_path,
|
||||
tool_parse_help = False,
|
||||
tool_data_table_config_path = galaxy_tool_data_table_conf_file,
|
||||
use_heartbeat = False )
|
||||
for dir in [ tool_shed_test_tmp_dir ]:
|
||||
try:
|
||||
os.makedirs( dir )
|
||||
@@ -162,11 +221,6 @@ def main():
|
||||
print "Tool shed database connection:", toolshed_database_connection
|
||||
print "Galaxy database connection:", galaxy_database_connection
|
||||
|
||||
hgweb_config_dir = hgweb_config_file_path
|
||||
os.environ[ 'TEST_HG_WEB_CONFIG_DIR' ] = hgweb_config_dir
|
||||
|
||||
print "Directory location for hgweb.config:", hgweb_config_dir
|
||||
|
||||
# Generate the tool_data_table_conf.xml file.
|
||||
file( galaxy_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template )
|
||||
# Generate the shed_tool_data_table_conf.xml file.
|
||||
@@ -174,7 +228,6 @@ def main():
|
||||
os.environ[ 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file
|
||||
# ---- Build Tool Shed Application --------------------------------------------------
|
||||
toolshedapp = None
|
||||
global_conf = { '__file__' : 'tool_shed_wsgi.ini.sample' }
|
||||
# if not toolshed_database_connection.startswith( 'sqlite://' ):
|
||||
# kwargs[ 'database_engine_option_max_overflow' ] = '20'
|
||||
if tool_dependency_dir is not None:
|
||||
@@ -183,41 +236,22 @@ def main():
|
||||
kwargs[ 'object_store' ] = 'distributed'
|
||||
kwargs[ 'distributed_object_store_config_file' ] = 'distributed_object_store_conf.xml.sample'
|
||||
|
||||
kwargs[ 'global_conf' ] = tool_shed_global_conf
|
||||
|
||||
if not toolshed_database_connection.startswith( 'sqlite://' ):
|
||||
kwargs[ 'database_engine_option_pool_size' ] = '10'
|
||||
|
||||
toolshedapp = ToolshedUniverseApplication( admin_users = 'test@bx.psu.edu',
|
||||
allow_user_creation = True,
|
||||
allow_user_deletion = True,
|
||||
database_connection = toolshed_database_connection,
|
||||
datatype_converters_config_file = 'datatype_converters_conf.xml.sample',
|
||||
file_path = shed_file_path,
|
||||
global_conf = global_conf,
|
||||
hgweb_config_dir = hgweb_config_dir,
|
||||
job_queue_workers = 5,
|
||||
id_secret = 'changethisinproductiontoo',
|
||||
log_destination = "stdout",
|
||||
new_file_path = new_repos_path,
|
||||
running_functional_tests = True,
|
||||
shed_tool_data_table_config = shed_tool_data_table_conf_file,
|
||||
smtp_server = 'smtp.dummy.string.tld',
|
||||
email_from = 'functional@localhost',
|
||||
template_path = 'templates',
|
||||
tool_path=tool_path,
|
||||
tool_parse_help = False,
|
||||
tool_data_table_config_path = galaxy_tool_data_table_conf_file,
|
||||
use_heartbeat = False,
|
||||
**kwargs )
|
||||
toolshedapp = ToolshedUniverseApplication( **kwargs )
|
||||
|
||||
log.info( "Embedded Toolshed application started" )
|
||||
|
||||
# ---- Run tool shed webserver ------------------------------------------------------
|
||||
tool_shed_server = None
|
||||
toolshedwebapp = toolshedbuildapp.app_factory( dict( database_connection=toolshed_database_connection ),
|
||||
use_translogger=False,
|
||||
static_enabled=False,
|
||||
app=toolshedapp )
|
||||
tool_shed_global_conf[ 'database_connection' ] = toolshed_database_connection
|
||||
toolshedwebapp = toolshedbuildapp.app_factory( tool_shed_global_conf,
|
||||
use_translogger=False,
|
||||
static_enabled=True,
|
||||
app=toolshedapp )
|
||||
if tool_shed_test_port is not None:
|
||||
tool_shed_server = httpserver.serve( toolshedwebapp, host=tool_shed_test_host, port=tool_shed_test_port, start_loop=False )
|
||||
else:
|
||||
@@ -268,50 +302,53 @@ def main():
|
||||
migrated_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_migrated_tool_path )
|
||||
file( galaxy_migrated_tool_conf_file, 'w' ).write( migrated_tool_conf_xml )
|
||||
os.environ[ 'GALAXY_TEST_SHED_TOOL_CONF' ] = galaxy_shed_tool_conf_file
|
||||
galaxy_global_conf = get_webapp_global_conf()
|
||||
galaxy_global_conf[ '__file__' ] = 'universe_wsgi.ini.sample'
|
||||
|
||||
kwargs = dict( allow_user_creation = True,
|
||||
allow_user_deletion = True,
|
||||
admin_users = 'test@bx.psu.edu',
|
||||
allow_library_path_paste = True,
|
||||
database_connection = galaxy_database_connection,
|
||||
datatype_converters_config_file = "datatype_converters_conf.xml.sample",
|
||||
enable_tool_shed_check = True,
|
||||
file_path = galaxy_file_path,
|
||||
global_conf = galaxy_global_conf,
|
||||
hours_between_check = 0.001,
|
||||
id_secret = 'changethisinproductiontoo',
|
||||
job_queue_workers = 5,
|
||||
log_destination = "stdout",
|
||||
migrated_tools_config = galaxy_migrated_tool_conf_file,
|
||||
new_file_path = galaxy_tempfiles,
|
||||
running_functional_tests=True,
|
||||
shed_tool_data_table_config = shed_tool_data_table_conf_file,
|
||||
shed_tool_path = galaxy_shed_tool_path,
|
||||
template_path = "templates",
|
||||
tool_data_path = tool_data_path,
|
||||
tool_dependency_dir = galaxy_tool_dependency_dir,
|
||||
tool_path = tool_path,
|
||||
tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ],
|
||||
tool_sheds_config_file = galaxy_tool_sheds_conf_file,
|
||||
tool_parse_help = False,
|
||||
tool_data_table_config_path = galaxy_tool_data_table_conf_file,
|
||||
update_integrated_tool_panel = False,
|
||||
use_heartbeat = False )
|
||||
|
||||
# ---- Build Galaxy Application --------------------------------------------------
|
||||
galaxy_global_conf = { '__file__' : 'universe_wsgi.ini.sample' }
|
||||
if not galaxy_database_connection.startswith( 'sqlite://' ):
|
||||
kwargs[ 'database_engine_option_pool_size' ] = '10'
|
||||
kwargs[ 'database_engine_option_max_overflow' ] = '20'
|
||||
galaxyapp = GalaxyUniverseApplication( allow_user_creation = True,
|
||||
allow_user_deletion = True,
|
||||
admin_users = 'test@bx.psu.edu',
|
||||
allow_library_path_paste = True,
|
||||
database_connection = galaxy_database_connection,
|
||||
datatype_converters_config_file = "datatype_converters_conf.xml.sample",
|
||||
enable_tool_shed_check = True,
|
||||
file_path = galaxy_file_path,
|
||||
global_conf = global_conf,
|
||||
hours_between_check = 0.001,
|
||||
id_secret = 'changethisinproductiontoo',
|
||||
job_queue_workers = 5,
|
||||
log_destination = "stdout",
|
||||
migrated_tools_config = galaxy_migrated_tool_conf_file,
|
||||
new_file_path = galaxy_tempfiles,
|
||||
running_functional_tests=True,
|
||||
shed_tool_data_table_config = shed_tool_data_table_conf_file,
|
||||
shed_tool_path = galaxy_shed_tool_path,
|
||||
template_path = "templates",
|
||||
tool_data_path = tool_data_path,
|
||||
tool_dependency_dir = galaxy_tool_dependency_dir,
|
||||
tool_path = tool_path,
|
||||
tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ],
|
||||
tool_sheds_config_file = galaxy_tool_sheds_conf_file,
|
||||
tool_parse_help = False,
|
||||
tool_data_table_config_path = galaxy_tool_data_table_conf_file,
|
||||
update_integrated_tool_panel = False,
|
||||
use_heartbeat = False,
|
||||
**kwargs )
|
||||
galaxyapp = GalaxyUniverseApplication( **kwargs )
|
||||
|
||||
log.info( "Embedded Galaxy application started" )
|
||||
|
||||
# ---- Run galaxy webserver ------------------------------------------------------
|
||||
galaxy_server = None
|
||||
galaxywebapp = galaxybuildapp.app_factory( dict( database_file=galaxy_database_connection ),
|
||||
use_translogger=False,
|
||||
static_enabled=False,
|
||||
app=galaxyapp )
|
||||
galaxy_global_conf[ 'database_file' ] = galaxy_database_connection
|
||||
galaxywebapp = galaxybuildapp.app_factory( galaxy_global_conf,
|
||||
use_translogger=False,
|
||||
static_enabled=True,
|
||||
app=galaxyapp )
|
||||
|
||||
if galaxy_test_port is not None:
|
||||
galaxy_server = httpserver.serve( galaxywebapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False )
|
||||
@@ -412,4 +449,8 @@ def main():
|
||||
return 1
|
||||
|
||||
if __name__ == "__main__":
|
||||
sys.exit( main() )
|
||||
try:
|
||||
sys.exit( main() )
|
||||
except Exception, e:
|
||||
log.exception( str( e ) )
|
||||
exit(1)
|
||||
|
||||
@@ -336,33 +336,4 @@
|
||||
<label text="Filtering" id="filtering" />
|
||||
<tool file="ngs_rna/filter_transcripts_via_tracking.xml" />
|
||||
</section>
|
||||
<label text="RGENETICS" id="rgenetics" />
|
||||
<section name="SNP/WGA: Data; Filters" id="rgdat">
|
||||
<label text="Data: Import and upload" id="rgimport" />
|
||||
<tool file="data_source/upload.xml"/>
|
||||
<tool file="data_source/access_libraries.xml" />
|
||||
<tool file="data_source/hapmapmart.xml" />
|
||||
<label text="Data: Filter and Clean" id="rgfilter" />
|
||||
<tool file="rgenetics/rgClean.xml"/>
|
||||
<tool file="rgenetics/rgPedSub.xml"/>
|
||||
<tool file="rgenetics/rgLDIndep.xml"/>
|
||||
<label text="Simulate" id="rgsim" />
|
||||
<tool file="rgenetics/rgfakePhe.xml"/>
|
||||
<tool file="rgenetics/rgfakePed.xml"/>
|
||||
</section>
|
||||
<section name="SNP/WGA: QC; LD; Plots" id="rgqcplot">
|
||||
<label text="QC; Eigenstrat" id="rgvisual" />
|
||||
<tool file="rgenetics/rgQC.xml"/>
|
||||
<tool file="rgenetics/rgEigPCA.xml"/>
|
||||
<label text="LD; Manhattan/QQ; GRR" id="rgld" />
|
||||
<tool file="rgenetics/rgHaploView.xml"/>
|
||||
<tool file="rgenetics/rgManQQ.xml"/>
|
||||
<tool file="rgenetics/rgGRR.xml"/>
|
||||
</section>
|
||||
<section name="SNP/WGA: Statistical Models" id="rgmodel">
|
||||
<tool file="rgenetics/rgCaCo.xml"/>
|
||||
<tool file="rgenetics/rgTDT.xml"/>
|
||||
<tool file="rgenetics/rgGLM.xml"/>
|
||||
<tool file="rgenetics/rgManQQ.xml"/>
|
||||
</section>
|
||||
</toolbox>
|
||||
|
||||
Reference in New Issue
Block a user