Metacat

fixes for creating SM for legacy docs

fixing generateSystemMetadata

updated replicate to only use GET requests. added notes for tomorrows standup

use the detected document encoding when getting the outputstream writer from the response
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2495

fixed bug with http/https port

adding additional debugging info

undoing last commit

added additional debugging info

adding war version replacement token

fix for member variables but in the request wrapper

adding war version to node response

implemented health api

use debug level for request encoding message

new class

implemented ping

added url decoding to the filter

use detected document encoding or Metacat's default encoding (UTF-8)

use UTF-8 encoding when getting bytes from the DB and converting them into a string.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2495

only call response.getWriter() when we are about to send text/xml to the client, otherwise we end of calling both getWriter() and getOutputStream() - resulting in an illegal state.

use detected XML encoding when reading/writing files
use UTF-8 as default when performing queries in the DB (assume DB is using UTF-8)
remove as many PrintWriters (uses system default character encoding only) as possible and construct OutputStreamWriters where explicit encoding can be given....

fixed a bug with trailing slashes

fix for paths with semi-colons or other 'reserved' characters in them for D1 rest services

added semi-colon id test

fixed bug where comparisons didn't work because of my change this morning

made this method more robust

fixed bug in new code

fixed bug where permission would get set to -1 for no good reason

typo - "dataset/pubDate"

add pubDate to return fields

add support for EML 2.1.1

fix the setaccess() method so that it accepts strings not numbers (i.e. "read" not "4")

added response type

allow public access to log information when docid is given. IP and principal are not returned unless an administrator makes the request.

added the root registry node response

changed d1 url to knb/d1/....

organized code for inputstream handling

fixed date problem

add a timer to delete the temp file

removed dependency on InputStreamToOutputStream so that exceptions will be passed correctly.

return the identifier object instead of nothing

made delete serialize the identifier

got getChecksum working. working on delete now. all tests in d1clienttest now pass

changes for new d1 schemas

implemented crud.delete

changed date format a bit to get the parser to like it

implemented describeObject

Bug fix for #5241: OAI-PMH: ListRecords verb returns content containing XML processing instructions.

implemented crud.describe

adding getChecksum method

added milliseconds back onto date format

remove temp files after multipart read

got the streaming mime multipart working

still working on mmp stream parsing

working on integrating streaming mmp into resourceHandler

more work on streaming mmp support

getting closer to a non-memory bound solution for mime multipart de/encoding

fixed a couple bugs with dates and fixed a major bug where metacat was reading the entire document from the database everytime a DocumentImpl instance was created even though it didn't need to

changes for dataone .5 schema updates

updated all exception codes to match spec

fixed task 729

fixed a bunch of small errors, did some reformatting, and fixed a bug that I thought was fixed last week

fixed redmine task 864. Metacat will now download an http:// referenced schema when a reference is put in the xml_catalog table.

fixing redmine task 738

fixing trac bug 828

profiler code for metacat

exception to throw when the sax parse should stop

changed log labels per trac 843

fixed bug 818

updated the metacatpopulator to use the d1 eml parser to create system metadata in a smarter fashion.

better log message

more debugging for objectInfo problem

checking for a null objectformat

checking for a null objectformat

checking for a null objectformat

backtracking

add some error output

add some error output

added a check for bad data into listObjects

commented out a println

updated DB scripts for D1 schemas

changed improper use of getFS() to a /. getFS() should never be used with a URL since it will return \ on windows which is not a valid separator in a URL.

moved the dataone types to the metacat.properties file

updated for new dataone jars

changes to work with new dataone jars

include MetacatHandlerPlugin interface so that other projects [semtools] can extend the actions handled by Metcat without editing the codebase directly. The SemtoolsPlugin is the prototype for this and can be registered using the Metacat admin interface. Note that the plugin implementation class and supporting jars must be included in the webapp in order for the request to be handled correctly (the semtools build is injecting these as part of it's build process).

added explicit 200 codes to ResourceHandler

added better logging and http code setting

fixed bug where the query cache was not getting reset by a REST insert/query combo.

[merged from 1.9.3 branch] security fix: never unregister the "public" user session

re-added some code inadvertently removed

merged with version from 1.9.3 branch to fix bug with character encodings

added a todo

new todos from code review with roger

added TODOs and cleaned up the code a bit

do not read from the inputstream before passing it off to the SAXParser

fixed mime multipart problems so that roger can try to use the d1client

fixed error where insert/update errors were not getting caught as exceptions

fixed bug with logger where localid didn't get appended when inserting a data file

reformatting logs for robert

added another logging statement