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).

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

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

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

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)

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

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

Merge 1.9 changes into Head

Merge METACAT_1_8_1 to cvs head.

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

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....

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.

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

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.

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

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

Some small bug fixes...

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

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.

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.

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)

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

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.

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...

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

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

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.

made changes so that organization name for the site or project is entered before
any other creater.

fixed a bug in reloading of kewords from an eml file for edit-datapackage form.

Minor changes to allow the registry to work in the knb skin, mainly in
how to treat the 'site' field. Now it is a free-text organization
field in the KNB skin. Need to test, install this on ecoinfo and link it
into the KNB web pages.

Added subroutine for replacing characters that might create problem in HTML.
Specifically written for "being used in any text field. This create a
problem in confirmData template, when you specify input name value pair with value
having a " in it.

Made changes so that & and other characters dont mess up the url that is passed to metacat.