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ft_master/proto_v10_import #72

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a87357d
Merge remote-tracking branch 'origin/proto_dev' into proto_master
sveinugu Oct 23, 2017
1da3cee
Morj: Removing some HyperBrowser code from ProTo. Clean up ProTo cont…
morj-uio Aug 9, 2016
b4e6378
Cleanup
sveinugu Jan 5, 2018
889f66f
Small ProTo edits and fixes
morj-uio Nov 7, 2016
faa9f97
ProTo: Add common functions, plus small bugfix
sveinugu Nov 7, 2016
ad7e735
Added thousands separator in ProTo
sveinugu Nov 7, 2016
1d4b103
Refactored HtmlCore in ProTo
sveinugu Nov 16, 2016
b500ddb
ProTo: Refactored HtmlCore. Added TextCore. Moved Advanced table crea…
sveinugu Nov 16, 2016
39cac19
ProTo: UniCode fix in dataset decoding
morj-uio Nov 16, 2016
9fea498
ProTo: Fix missing reference
sveinugu Nov 16, 2016
e5faee9
ProTo: Moved dataset security code into separate file. Added output_p…
morj-uio Nov 23, 2016
aa93c0c
ProTo: Small refactorings
sveinugu Nov 23, 2016
83e912f
ProTo: Removed HB code from StaticFile
morj-uio Nov 24, 2016
f85fa51
ProTo: Forgot to add the Security module some commits ago
morj-uio Nov 24, 2016
ba4231d
ProTo: Moved config parsing to GalaxyConfigParser. Made sure dynamic …
sveinugu Nov 24, 2016
7977518
ProTo: Fixed bug in GalaxyConfigParser in startup.
sveinugu Nov 24, 2016
e2f0d3e
ProTo: Small bug
sveinugu Nov 24, 2016
c695d6c
ProTo: Removed unneeded config
sveinugu Nov 24, 2016
3b1153f
ProTo: Fix load file to history bug
morj-uio Nov 24, 2016
e231c70
ProTo: Updated config parsing with type handling
sveinugu Nov 29, 2016
d90407f
ProTo: Added extra database flushes to hopefully reduce database errors.
morj-uio Nov 29, 2016
6ad23d1
ProTo: Handle empty histories. Move some methods to HyperBrowser. Cle…
morj-uio Nov 29, 2016
b793ae5
ProTo: Attempted fix of the database exceptions that appeared after f…
morj-uio Dec 7, 2016
eeb7541
ProTo: Fixing UniCode support, removing all type checks explicitly to…
sveinugu Dec 6, 2016
d5ffa53
Misc bugfixes and cleanup
morj-uio Dec 6, 2016
40b05f5
ProTo: Small code cleanups
morj-uio Dec 7, 2016
12343ab
ProTo: support for checkbox paragraph id for CSS
morj-uio Dec 21, 2016
2fd00c4
ProTo: Checkbox bugfix
sveinugu Dec 21, 2016
fe7ff46
ProTo: Added getOutputName to GeneralGuiTool, defining the title of t…
morj-uio Dec 21, 2016
e1a4032
ProTo: Added secure encoding to cached choices (in hidden field) to c…
morj-uio Dec 21, 2016
16ab031
ProTo: Misc. fixed to support ProTo - HyperBrowser divide. Increased …
sveinugu Dec 21, 2016
b5325fc
ProTo: Added support in Explore and Install tools for excluding subto…
sveinugu Dec 21, 2016
ff90fd9
ProTo: Created proto.less -> proto.css for ProTo related CSS changes
sveinugu Dec 21, 2016
8e2b91f
ProTo: Fixed bug in list of uninstalled tools. Refactored install too…
sveinugu Dec 22, 2016
27d9187
ProTo: Added support for history output naming in load to history URL…
sveinugu Dec 22, 2016
34f43f5
ProTo: fixed import bugs (in particular that proto.config is imported…
sveinugu Dec 22, 2016
d400561
ProTo: changed tool ids into underscore. Made tool_type selectable.
sveinugu Dec 22, 2016
e4b3a48
ProTo: refactored run_tool method in ProTo controller to support for …
sveinugu Feb 23, 2017
3e96797
ProTo: Correct list elements
sveinugu Dec 23, 2016
d7b1023
ProTo: Fix to also show all subtools of uninstalled multitools
sveinugu Jan 6, 2017
8e3ceb3
ProTo: Added "upload file" tool link methods
sveinugu Jan 6, 2017
091a7c6
ProTo: FIxed bug in job rerun in older browser versions (e.g. Opera 1…
sveinugu Jan 9, 2017
f83111d
Fixed bug with sorting of collapsed tables.
sveinugu Jan 11, 2017
7cd4e61
ProTo: "Load to history" file paths are now relative to the Galaxy ba…
sveinugu Jan 12, 2017
b94ef44
ProTo: Moved FileImport tool from HyperBrowser code. Updated to only …
sveinugu Jan 12, 2017
768eaad
Detailed path checks are no longer needed for security. Removed the c…
sveinugu Jan 12, 2017
4deedbc
ProTo: Added support for StaticImage overloading
sveinugu Jan 12, 2017
367aeca
Added R library dependencies. Added automatic dependency installation
sveinugu Jan 14, 2017
ffd8c7a
ProTo: Added Proto tool shelf config
sveinugu Jan 15, 2017
1429d84
ProTo: Small fixes. Changed to unicode casting some places
sveinugu Jan 15, 2017
eb17840
ProTo: Prepare for usage and error logging in HyperBrowser
sveinugu Jan 15, 2017
eae5728
ProTo: Fixed super() calls. Removed cache fail error printing
sveinugu Jan 15, 2017
c527b73
ProTo: Better handling of unicode values
sveinugu Jan 15, 2017
54d5e60
Merged with feature branch "hb_feature/text_table_output"
sveinugu Jan 18, 2017
99ec78b
Removed HyperBrowser import
sveinugu Jan 6, 2018
9d3357e
ProTo: Moved Proto development tools into separate modules. Other rel…
sveinugu Feb 16, 2017
f02e10f
ProTo: removed logging
sveinugu Feb 23, 2017
e9dcd4a
ProTo: Unfinished update of core dev tools. Added directory listing a…
sveinugu Feb 23, 2017
2059ac7
ProTo: Finished support for package selection via subdirectories in G…
sveinugu Feb 23, 2017
67f8277
ProTo: Updated help text. Improved directory naming validation. Incre…
sveinugu Feb 23, 2017
922988e
ProTo: Removed tool type selection box. Cleanup
sveinugu Feb 23, 2017
9ca12c0
ProTo: small refactorings needed for HB subclassing
sveinugu Feb 24, 2017
9f136b7
ProTo: Made tool root configurable
sveinugu Feb 24, 2017
3c75ebe
ProTo: refactored to allow HyperBrowser subclassing. Improved input v…
sveinugu Feb 24, 2017
50b9fd9
ProTo: Refactored ProtoToolRegister in order to handle equal classnam…
sveinugu Feb 24, 2017
3aa0ec3
ProTo: Full refactor of ProtoToolRegister. Added tool for hiding modu…
sveinugu Mar 3, 2017
96d8e49
ProTo: Added tool to debug exceptions in import of ProTo tools.
sveinugu Mar 3, 2017
9200b21
ProTo: Added and edited tool descriptions
sveinugu Mar 3, 2017
3282d83
ProTo: Reverted import in ToolTemplate. Relative import path to suppo…
sveinugu Mar 3, 2017
cf01824
ProTo: Fixed imports
sveinugu Mar 3, 2017
eadbe06
Now also excludes HB tool templates
sveinugu Mar 3, 2017
59dd0c6
ProTo: except_classes -> installed_classes. Fixed logic for filling o…
sveinugu Mar 3, 2017
8410615
ProTo: rename tools
sveinugu Mar 3, 2017
d5295e4
Added initial "hidden nontool modules" config file
sveinugu Mar 3, 2017
23c2a50
ProTo: Removed GPL Copyright messages from code files
sveinugu Apr 8, 2017
a5d7493
Fixed bug in loading old HB analysis tool
sveinugu Apr 12, 2017
f7b9deb
ProTo: Added standard excluded 'files' directory to gitignore
sveinugu May 7, 2017
dbe827d
ProTo: now does not print names instead of label='' in various box ty…
sveinugu May 19, 2017
a9790f9
ProTo: Now sorts directory structure lists
sveinugu May 19, 2017
92b088f
ProTo: Fixed rpy2 version dependency
sveinugu Nov 3, 2017
98540d7
ProTo: Added html_title config. Pull request?
sveinugu Nov 29, 2016
64c30a4
Removed HyperBrowser-specific modules
sveinugu Jan 7, 2018
06189e8
Added and reformatted license information for The Genomic HyperBrowse…
sveinugu Apr 12, 2017
23d237f
Removed HyperBrowser licenses and license info
sveinugu Jan 7, 2018
e4374d6
Moved FileImport hidden tool to ProTo
sveinugu Jan 12, 2017
d87a4bf
Added new tools to tool_conf.xml sample files.
sveinugu Mar 3, 2017
e095142
Changed linebreaks to LF
sveinugu Jan 7, 2018
0f0eefc
Added syncthins ignores
sveinugu Jan 14, 2018
ed98c48
Rebuild of client using node.js v9.4.0 and npm v5.6.0
sveinugu Jan 14, 2018
1537a17
Bugfix
sveinugu Jan 14, 2018
4729030
Ran webpack using Node.js v9.4.0 and npm v5.6.0
sveinugu Jan 18, 2018
115bcc7
Added link to standard Galaxy favicon.png to allow for subdirectory o…
sveinugu Jan 18, 2018
801a7ac
Removed remaining HyperBrowser imports and mentions
sveinugu Jan 18, 2018
e74e329
Moved some more styles from HyperBrowser
sveinugu Jan 19, 2018
2d03540
Added 'customhtml' datatype
sveinugu Jan 19, 2018
92f24a5
Added documentation of check box GUI element
sveinugu Jan 19, 2018
d43996c
Added 1st Galaxy ProTo test tool: Basic GUI elements
sveinugu Jan 19, 2018
952bbff
Removed Conda check to force virtualenv creation
sveinugu Jan 19, 2018
122dfba
Removed bootstrap import again
sveinugu Jan 19, 2018
29fc2f7
Renamed. Made text areas non-dynamic (will not reload page when edited)
sveinugu Jan 19, 2018
0bd3866
Added Galaxy ProTo GUI test tool #2, for dynamic content
sveinugu Jan 19, 2018
bb94ec6
Reordered tools
sveinugu Jan 19, 2018
141980a
Added hidden element
sveinugu Jan 20, 2018
31aee03
Various HTML and style updates. Added new proto_base.css for HTML fil…
sveinugu Jan 26, 2018
2cb05d2
Updated FileImport.py to newest ToolTemplate. Fixed importing of HTML…
sveinugu Jan 26, 2018
4497096
Added label to getLoadToHistoryLink in StaticFile
sveinugu Jan 26, 2018
6a0f4e4
Fixed import path of GeneralGuiTool and some cleanup
sveinugu Jan 26, 2018
dad9422
Added file suffix convenience functions
sveinugu Jan 26, 2018
4eb4f4c
Added Galaxy ProTo test tool #3, testing various input/output-related…
sveinugu Jan 26, 2018
ed4526c
Added UniCode support to ProTo Gui test tool #3. Fixed file suffix ha…
sveinugu Jan 26, 2018
0040c05
Fix bug when reset boxes are hidden. Might have unforeseen consequences
sveinugu Jan 26, 2018
f43e087
Fix language
sveinugu Jan 26, 2018
d97c253
Added logging of some exceptions in generictool.py
sveinugu Jan 27, 2018
8fb6429
Misc cleanup
sveinugu Jan 27, 2018
7b99c76
Added Galaxy ProTo GUI test tools #4-6
sveinugu Jan 27, 2018
885c586
Turn off debug mode
sveinugu Jan 27, 2018
ca1709e
Made tool public
sveinugu Jan 27, 2018
b343076
Added testing of isPublic() and isDebugMode()
sveinugu Jan 27, 2018
dec6458
Merge pull request #13 from elixir-no-nels/proto_hb_backport
sveinugu Jan 27, 2018
3e4bf26
Release v1.0 of Galaxy ProTo. Updated README with version information.
sveinugu Jan 30, 2018
0b91e7d
Revert incorrect and probably unneeded hack
morj-uio Nov 15, 2016
f64047d
Small update
sveinugu Jan 30, 2018
e314b30
Updated client
sveinugu Jan 31, 2018
c0090c3
Merged ProTo v1.0 back into HB. Various fixes. Added Galaxy ProTo GUI…
sveinugu Jan 31, 2018
f4df045
Release v1.0.1 of Galaxy ProTo
sveinugu Jan 31, 2018
7446eaa
Merge remote-tracking branch 'proto/proto_master' into ft_master/prot…
sveinugu Jan 31, 2018
97511d2
Merge remote-tracking branch 'public/hb_master' into ft_master/proto_…
sveinugu May 24, 2018
1f6d880
Addedn Proto GUI test tools to tool_conf.dev.xml.sample
sveinugu May 24, 2018
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Added UniCode support to ProTo Gui test tool #3. Fixed file suffix ha…
…ndling
sveinugu committed Jan 26, 2018

Verified

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commit ed4526cf033eb80b5a7777b2f041906ea46c0686
12 changes: 8 additions & 4 deletions lib/proto/tools/guitest/ProtoGuiTestTool3.py
Original file line number Diff line number Diff line change
@@ -265,8 +265,10 @@ def _createEmbeddedFile(cls, datasetInfo, inFileName, outFileName):

inFileSuffix = extractFileSuffixFromDatasetInfo(datasetInfo)
inDatasetName = extractNameFromDatasetInfo(datasetInfo)
if not inDatasetName.endswith('.' + inFileSuffix):
inDatasetName = '.'.join([inDatasetName, inFileSuffix])

embeddedBaseFileName = '.'.join([cls._cleanUpName(inDatasetName), inFileSuffix])
embeddedBaseFileName = cls._cleanUpName(inDatasetName)

embeddedFile = GalaxyRunSpecificFile(['embedded', embeddedBaseFileName], outFileName)
shutil.copy(inFileName, embeddedFile.getDiskPath(ensurePath=True))
@@ -284,7 +286,8 @@ def _generateHtmlContent(cls, datasetInfo, embeddedFile, inFileName):
core.header('File contents')
core.fieldsetBegin('Ten first lines of file: ' +
extractNameFromDatasetInfo(datasetInfo))
core.preformatted(''.join([cgi.escape(inFile.readline()) for _ in range(10)]))
core.preformatted(''.join([cgi.escape(inFile.readline()).decode('utf-8', 'ignore')
for _ in range(10)]))
core.fieldsetEnd()

core.header('Direct URL to file')
@@ -298,11 +301,12 @@ def _generateHtmlContent(cls, datasetInfo, embeddedFile, inFileName):

core.end()

return str(core)
return unicode(core)

@classmethod
def _writeHtmlContent(cls, htmlContent, outFileName):
with open(outFileName, 'w') as outFile:
import io
with io.open(outFileName, 'w', encoding='utf-8') as outFile:
outFile.write(htmlContent)

@classmethod