jalview

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Merge branch 'releases/Release_2_11_1_Branch'

JAL-3940 errant heading in release notes..

Merge branch 'patch/r2_11_1_branch_JAL-3703_closing_files' into releases/Release_2_11_1_Branch

I know the problems you had with close() - you mentioned in the comments on the issue. However, you might have noticed that FileParse.close() is not called from many places, so changing its behavio...

I know the problems you had with close() - you mentioned in the comments on the issue. However, you might have noticed that FileParse.close() is not called from many places, so changing its behaviour wouldn't have too many side effects.

The intended pattern for FileParse.close() was:

ParserThing pt;
try {
pt = new <? assignable to FileParse>(data spec..)
.. do whatever needed to trigger parsing
.. then check pt's error/warning status and report any problems.
} catch (IOException ..) {
.. handle read or parse errors 
}
finally {
if (pt!=null) {
pt.close();
} // catch and report any IOErrors if desired
}
I tried this first, but FileParse.close() deliberately leaves the FileParse in an error state, which caused problems later (I don't remember the specifics). I could not work out why the FileParse.c...

I tried this first, but FileParse.close() deliberately leaves the FileParse in an error state, which caused problems later (I don't remember the specifics). I could not work out why the FileParse.close() was designed to do this but suspect changing this methos so it's (in general) not left in an error state will cause bigger problems. Also, since Jalview is used to having dataIn for the lifetime of the alignment, I wasn't sure if nulling the object would cause unforeseen errors (in e.g. filename etc).

Maybe it would be best to overload FileParse.close() to pass in an error value/message, then it would essentially be calling FileParse.closeDataIn() instead of FileParse.dataIn.close()

Agree with the finally {} – forgot that (not been a java programmer for quite long enough!). Presumably that should go in FileParse and not AlignFile too.

JAL-3703 patch Windows save file test for 2.11.1 codebase

Merge branch 'patch/r2_11_1_branch_JAL-3703_closing_files' into releases/Release_2_11_1_Branch

JAL-3940 fix issues in release notes

JAL-3940 bump version and update release notes - release set for Tuesday 18th January 2022

JAL-3940 update release notes for JAL-3702,JAL-3935 in 2.11.1.7 release

Ideally, any low level file ops should happen in the base class (FileParse) rather than here. AlignFile should call the FileParse.close() method rather than directly manipulate dataIn, which is man...

Ideally, any low level file ops should happen in the base class (FileParse) rather than here. AlignFile should call the FileParse.close() method rather than directly manipulate dataIn, which is managed by FileParse. Note that FileParse.close() nulls the dataIn reference so the stream can be garbage collected properly.

It's also good practice to try to close() in a finally {} clause, catching and reporting exceptions if needed... this is actually what the FileParse.close() method's design was intended for, since the caller should have already checked 'error' and 'errormessage' for parsing problems. Exceptions/Errors on close are not fatal for file import.

file close error will trash import of project

file close error will trash import of project

close filehandles straight after parse, without setting an error
close filehandles straight after parse, without setting an error
JAL-3703 Test that fails in Windows only, and only when the file handle isn't relinquished

    • -0
    • +93
    /test/jalview/io/WindowsFileLoadAndSaveTest.java
JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

close filehandles straight after parse, without setting an error

Conflicts:

src/jalview/project/Jalview2XML.java

(locale aware PDBID string compare)

JAL-3937 update releases.html

JAL-3937 enable AIA download of intermediate certificates when needed

JAL-3934 update whats new

Merge branch 'task/JAL-3934_update_log4j_again' into releases/Release_2_11_1_Branch

JAL-3934 trigger patch release for log4j version bump

JAL-3934 updated log4j from 2.16.0 to 2.17.0

    • binary
    /j11lib/log4j-1.2-api-2.17.0.jar
    • binary
    /j11lib/log4j-api-2.17.0.jar
    • binary
    /j11lib/log4j-core-2.17.0.jar
    • binary
    /j11lib/log4j-slf4j18-impl-2.16.0.jar
    • binary
    /j11lib/log4j-slf4j18-impl-2.17.0.jar
    • binary
    /j8lib/log4j-1.2-api-2.17.0.jar
    • binary
    /j8lib/log4j-api-2.17.0.jar
    • binary
    /j8lib/log4j-core-2.17.0.jar
    • binary
    /j8lib/log4j-slf4j18-impl-2.16.0.jar
    • binary
    /j8lib/log4j-slf4j18-impl-2.17.0.jar
Merge branch 'releases/Release_2_11_1_Branch'

JAL-3842 remove replacement tokens in html text - not properly resolved in this release branch

JAL-3842 patch what’s new text

JAL-3842 release 2.11.1.5 release notes

Merge branch 'critical/JAL-3933_log4shell_mitigation' into releases/Release_2_11_1_Branch

JAL-3933 updated THIRDPARTYLIBS