Metacat

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

Following changes:
1. Fixed a bug in checking of contact email address field
2. Added functions to display the result of accept, reject and revise actions
3. Added variable to control if the document creator should be the skin admin
4. a common function to check if the present user is a moderator

Added new variables to the script which creates templates for new skins

Some small bug fixes...

New functions in the dataset registry to support moderation feature needed for ESA

Modified the login method in the perl metacat client so that status of the user logging is also returned
Earlier if login info was not valid, 0 was returned. And 1 is sent back if login info was valid.

Now, if valid then following values are returned to indicate user status...

Removed unused subroutines that were for testing.

Adding the control-services.pl utility for failover montitoring. From
the README:

This program is designed to run as a script under the Hobbit system
monitoring program (http://hobbitmon.sourceforge.net/). When Hobbit is
configured properly, this script will be called to make changes to the...

If skin cfg specified access rights to be included for a certain set of users and groups, then those are entered in the access permissions given.

Fix for bug 2220. And check the cfg file if the eml documents generated should be publically readable or not.

Added a function to strip out the whitespace that was around the bounding
coordinates retrieved from metacat, and also now writing the full set of
bounding coordiantes (east,west,south,north).

bug fix so that error is displayed if station or reserve is not selected

Added code to enter publication date into the dataset.

Fix for 2214. Allow 0 in coordinates now.

Fix for bug 2215. Error message is displayed if project name is not selected in the nceas skin.

Fixed a typo.

Changed the headers.

Filed used my the Metacat Spatial Option. Generally these files represent
the portion of the spatial option that harvests spatial elements from a
Metacat, and stores the elements as a shapefile on the file system. This
option, at this point, is pretty much independent of the metacat application....

The template for displaying the error is not executed when passwords are not same. Hence the user doesnt know what the error was. Fixed this.

Adding perl script for changing ldap password for an account.

Modified the code so that lastid file is created in a skin when lastid file is not found.
Commented out the code which uses AdminDB module and uncommented the test function.

Replaced Usage Constraints with Usage Rights and Data Originator with Dataset Owner.

(Commit done by Saurabh Garg for Veronique)

Changes made in the css for the skins.

Fixed some bugs from previous commits. Veronique changes the text of error messages. Added a new stage to distinguish errors because of logins.

Added new actions so that error message is not shown the first time resetPassword and changePasswords are called. Also fixed a bug where $cfg was not being passed to genericHeader.tmpl

Changed the code which handles Associated Party, Keywords and Taxonomic Information.

Fix for bug# 1344

Added code to fix bug 1323. % sign is replaced by its http equivalent now

Added code to fix bug# 1344. Response template is called when cancel delete is pressed.

Integrating ldapweb.cgi & create-ldap-account.pl into metacat CVS tree.

Fixed bug #1551 by adding a conditional statement.

Made changes to fix bug# 1310. Now while parsing old documents, the script checks for ACLs also.

Fixed a bug in creation of EML documents when coordinates from the site_list have to be used.

Modifications to the registry to support the new ESA skin. Factored out some of
the configuration-specific code into properties that are set in the various
cfg files in the skins. New properties in the cfg files are lsite, usite,
showSiteList, showWgList, showOrganization. These now need to be set in every skin...

Changed path for eml xsd stylesheet

Made change in the registry so that new documents produced are of eml-2.0.1 standard.
Also made changes in create-registry folder

Adding a new perl script. Running this script creates a new skin.

Fixed bug# 1309. Also put a regex check on ending year and beginning year.

Made changes to fix bug # 1365.

Made changes to fix bug# 1303 and 1367.(Both are related)
Following variables can now be specifieD from the cfg file to control behaviour of the skin: hasKeyword, hasMethod, hasSpatial, hasTaxonomic and hasTemporal. Following two also can be used: spatialRequired and temporalRequired

Made changes to fix bug# 1303 and 1367.(Both are related) - corresponding changes need to be made in tmpl file and testing needs to be done before bugs can be closed.

Made changes to fix 1301. Works fine with eml2 - need to check if works with emlbeta6.

Made changes to control whether a skin wants to use keywords or not. Keywords probably will be used by all skins alsways. But similar changes can be made for Geographic Coverage or Temporal COverage to control whether a particular section of the insert data template needs to be shown or not. This can be controlled from .cfg file. For example, in nceas.cfg is you define hasKeyword = false, none of the templates will show the keyword part. (Unless, you are using NCEAS skin and you try to modify a document which already has keywords.)

Removed beta6 specific code which is no longer being used.

Removed repetition of code. Also fixed the link to the modified file submitted from responseTemplate

Perl script for transfering documents from one metacat to another metacat. list_of_docids contains list of names of the documents that will be transfered.

Fixed a bug which doesn't occur everytime. The bug occurs when lastid in (cfg).lastid is not unique. i.e. there is already a document in the server which has same docid. The earlier algorithm was:

while(not unique){
get accession number;
update accession number written in document; (BUG)...

Added extra parameters (cfg & docid) to be passed on to generic response screen.