Metacat

Merge 1.9.2 changes back into the trunk

Fix two issues: Remove State from 'Data Set Contact' section of confirmation form (part of #3922), and make sure when editing a document that email addresses are picked up appropriately (capitalization).

Update the filename reference

Get the latest revision from metacat when a modify call docid does not have a revision number.

remove extra open paren

When comparing lat and long ranges, make sure the values have content first. Perl values with no content = 0.

fix file name reference for skin configuration file

Add Content_type line so debug prints

Further fixes to handle mixed-file uploads:
- set the fileCount object based on upCount existing files
- use ucount only if it exists; remove debugging'
- the entry form javascript now correctly tracks the file numbers, and can be relied on instead of using upCount...

Display helpful error message when user lacks permissions to edit a document, supress the 'use Morpho' message (closes Bug #3928)

Three small fixes:
- 'salutation' was misspelled and wasn't picked up correctly in document modificiation
- keyword handling wasn't setting the thesaurus correctly
- check against the full list of moderators for the ACL validation

Adding back fix for editing documents with multiple keywords, closing #3929

Include hack for UCNRS organization properties.

- build up username using base if username isn't fully qualified (e.g. cn=Manager,dc=ecoinformatics,dc=org)
- additional debugging statements for changePassword

- fix error reporting for failed password reset request
- automatically generate necessary LDAP parameters from our defaults,
included in auth.base and unaffiliated properties. This won't work for
skins such as UCNRS with a different base, which still need to be ...

- reformat header
- add debugging for getLdapEntry searches
- add 'filter' parameter for organizations

Provide improved contextUrl, provide proper URL in password reset message body

Handle all places where ldap may be null

enclose more references to ldap and mesg in the if (ldap) statement.

made mesg var global to function.

left off ;

Do not try to use non-existant ldap object if ldap server is down.

Add a short sleep when moderator accepts document so system can update. This will make sure correct documents get returned to moderators list.

Changing the ChangePassword method to fix password reset broke the password change functionality. Moved the fix (add dc to username) into the handleResetPassword function.

Fix typo after the error message

Include the dc in the user name when connecting to ldap to change password.

Handle non-responsive LDAP referrals without killing the script, but still require the main LDAP to be up.

Add cgiPrefix to the template variables.

Add a few more debugging messages to LDAPweb to help find timeout issues

A slew of fixes in the process of fixing bug #3679:
- omit port number from the contextUrl if running on 80, looks bad in exposed URLs
- explicitly pass the metacat object to newAccessionNumber, the global definition of the object had introduced a difficult to track bug...

- move moderatorComments into //additionalMetadata/metadata/ as per EML 2.1 (Bug #3679)
- overlay skin-specific email properties on system-level properties (email hostname)

Fix problem with failing authentication for creating new accounts. (Bug #3725)

minor change to help nick test irccat

Enable debugging for LDAPweb.

DRY out login request code

Ensure that file permission is always set. If unset, it'll cause the EML document to be invalid.

Complete implementation of otherEntity editing and deletion, syncronizing changes to EML document. Now all elements which are created by the form can also be edited (Bug #3319). Also prevented associated party duplication on modification.

only shift once; fix typo in writeFile

Fix issue with missing AdminDB parameters causing the registry script to fail (Bug #3741)

standardize registry debug messages with 'Registry:' prefix

Further fixes for allowing editing with otherEntity objects, completed deserialization and copying of file metadata from existing data objects (Bug #3319). Still needs more work.

fix typo preventing guide pages from showing (Bug #3726)

Don't die if the xml-debug file can't be written to the temporary directory. Instead, write a warning. Include the directions for making the temporary dir writable to the apache user in documentation.

Include error checking for required distribution elements, which must be non-empty strings in EML 2.1 (bug #3721).

Update properties usage to be correct, use proper LDAP URL, move template function higher up to prevent prototyped subroutine definition issues.

Update moderators element to current token, fix undefined variable in ESA logic.

Add script for converting documents with docnames into the filename stored within the objectName field of the EML. This, along with changes in the 1.9 release should eliminate incorrect filenames (Bug #2566).

Number of ESA-related fixes:
- fix review panel to reference valid URL using cgiPrefix
- update ESA document creation to use XSLT methods instead of split()
- add code for ESA access rules fix (to be used in 1.9.1)
- use moderators in metacat.properties (postpone skin-based configuration till 1.9.1)...

Further ESA fixes: More 2.1.0 compliance, fix security issue

updated handleModAccept to be EML 2.1.0 compliant, streamlined document generation to use EML creation functions.

Update accessElement to accept a value for publicly readable

Add wrapper function for transforming XML documents to current EML, change ESA skin to use newAssessionNumber, parse EML document with query instead of split()

Add incrementRevision function to replace duplicated code

CODE FORMATTING ONLY: Fix all the inconsistencies I found within the script to follow the standards used within 80% of the code: No tabs, 'if (eval) {' operator spacing, four spaces indentation, replace exit(0) with exit().

add start of otherEntity processing for registry edits

Editing documents should check for ACL elements under //access now instead of //dataset/access

Transform EML 2.0.x documents to 2.1.0 which are found when editing with the registry, using an XSLT transformation.

Remove EML2 beta6 document conversion support, the files required for conversion have been deprecated from Metacat.

Update STMML to the newest version as per EML 2.1.0

Dump copy of EML document being uploaded when debug mode is enabled.

Partial fix for #3496, making the registry create EML 2.1.0 documents. The documents are internally valid 2.1.0 (they run against the validator correctly) but aren't inserting into Metacat correctly as of yet.

Further rework on ldapweb.cgi for 1.9 compatibility. Finished changes needed to have skinnable presentation for ldapweb.cgi, and reworked the organization logic to be compatible with our current method of storing the data (organization.* within metacat.properties).

Number of fixes, including removing all lastid code and replacing with a single function which always queries remotely instead of relying on lookups, solving #3019. Fixed parsing of spatial coordinates for site-based skins, removed dependency on AppConfig as we're fully using .properties files at this point.

Source the lib directory in the metacat application. This is the new location of Metacat.pm

Further improvements to the registry to properly support the new properties. Removed all variables previously passed around between forms which should always be available canonically from the skin.properties file and replaced with refences to properties value for the skin being used. Removed some cruft from both files, fixed mior issues mentioned in bug #3487.

Allow script to be run from command line, more token changes including all path changes for URLs and directories.

Consolidation of property names in register-dataset.cgi; returned runConfiguration to default true

initial doc id list from original conversion

script used to update keywords for existing kruger documents when upgrade to new SANParks/SAEON skin. committing before additional work to update the package ids for these files (incorrectly set to the wrong rev number)

Merge 1.9 changes into Head

Merge METACAT_1_8_1 to cvs head.

Fixes to record sies of ecogrid files, and to flag html files.

Modified the normalize subroutine - don't use 26 (url encoding) to replace x%x

Skeleton for data insertion script. Also added documentation to Metacat
library.

MOdified query passing, and default cache location.

Initial script for downloading and caching data entities associated
with an EML document that is stored in Metacat.

Workaround for a bizzare submission issue stemming from the debug sub. Modified the NCEAS project list to be robust and rely on the presence of the AdminDB module and a working connection to the DB for listing projects.

Updated the ResponsibleParty object creation to be more robust. Now handles N MetadataProvider elements as expected.

refactored <access> and <allow> element creation. Added logic to give both owner and skin admin privilages to access uploaded data objects.

Cleaned up regexes used in register-dataset.cgi to support arbitrary numbers of elements for keywords. Cleaned up regexes for state selection, to omit default values. Added debug as a GET parameter, so a page can be debugged by appending `&debug=1'. Committed latest changes to file processing, to allow files to be deleted after returning to the entry page from confirmation or processing errors. Seperated out entryForm.js from entryForm.tmpl to simplify debugging.

Added submission of data files to the registry. New parameter 'hasUpload' can be set on a per-skin basis to enable the uploading of data objects to be associated with a metadata document. NCEAS skin is using this by default, to be changed in the future for other skins....

Added upload method. Modified sendData to respect form encodings and POST files.

Getting project list from nceas admin db.

fixed bug that input form coudn't be shown.

Fixed bug that docid has no seperator in email.

Remove the rule that the access allow rule should equals three.

Replace die statement in the script

Change the behavior if the ldap server is down. Now main server is down, a html will be sent back. If it is referral, it will ignore it.

added function to get list of projects for NCEAS from a given project list

dded TLS support to the ldapweb.cgi script, cleaned up some TempToolkit
template processing so that the results display CSS properly, and some minor
formatting issues. The TLS support should probably be enabled only if the
server supports it, which can be queried with supported_extensions, but for...

variable for showing instructions

added code to give access to moderator group on the review document

Added template for getting the review

Made changes so that the user is prompted to login before entering a dataset

Added functionality for storing comments and displaying them. Also added functionality for reading the eml document.

hardcoded the organization as unaffiliated

bugfixes in previous code and added functionality to store reviews on various documents...

Added setaccess method

This is a basic commandline client for resolving LSIDs. It is meant as
a quick and dirty testing utility. It requires the SOAP::Lite,
SOAP::MIME, and MIME::Entity CPAN modules. Run without arguments, it
uses a default LSID and endpoint to resolve. WIth the lsid and endpoint...

modified mod_revise so that Revision Requested is added to the document in additionalMetadata/moderatorComment which can be used by the skin in searching for documents which havnt been requested for revision