Specify 6.7.02 Changes (readme.txt)
28 March 2019
General Release Notes
- With the release of Specify 6.7.02 we are recommending that Specify 6 sites change their installed Java software package from Oracle Java SE 8, to Amazon Corretto 8. Oracle has changed its licensing policy for Java SE 8 as of January 31, 2019; it is no longer available for free for non-personal use. Specify 6 is compatible with the new Amazon Corretto implementation of the Java runtime environment. Amazon has committed to provide long-term support of Corretto including security patches at no cost. A guidance document is available on the Consortium's web site about this change. Specify users are encouraged to first contact institutional systems support department to determine if there is an organizational plan to respond to the change in Oracle's Java license terms.
- We recommend that Specify 6 Windows installations use a 64-bit Specify version for better performance, if workstations are running a 64-bit version of Windows. Oracle Java 8 SE, and its replacement Corretto 8, must also be a 64-bit version to operate with 64-bit Specify. We have noticed that 32-bit versions of Specify 6 for Windows occasionally stutter on startup. No other 32-bit specific bugs of Specify 6 are known.
Tables Added to Database Schema (name, relationship, purpose/requestor)
- Collecting Trip Attachment, linked M:1 to Collecting Trip. This was added to allow association of one or more files to a Collecting Trip record. Requested by SAIAB.
- Collecting Trip Attribute, linked 1:1 to Collecting Trip. This was added to provide fields for more detail about Collecting Trip(s). Requested by SAIAB for marine video sampling.
- Collecting Trip Authorization. This is a join table between the Collecting Trip (CT) and Permit tables, enabling a M:M relationship between CT and Permit. One CT record can have more than one Permit record, and one Permit may have more than one associated CT.
- Collecting Event Authorization, This is a join table between Collecting Event and Permit, creating a M:M relationship between those two tables. One CE may have more than one Permit, and one Permit record may have more than one associated CE. (In the Specify data model, CT is 1:M with CE.) Requested by Barcelona and South Africa.
- Collection Object Property (COP), M:1 relationship to Collection Object. COP has fields for describing custom properties of Collection Objects such as measurements. Note: Specify will continue to use the Collection Object Attribute table in a 1:1 relationship with Collection Object to provide additional customizable fields for describing Collection Objects. COP adds an additional mechanism for custom attributes for Collection Objects, but in a M:1 relationship to Collection Object--similarly for Preparation and the new Preparation Property table noted below. These new tables are intended for uses not supported by the existing Collection Object Attribute and Preparation Attribute tables and their 1:1 relationships. The two Property tables will support the Darwin Core Measurement or Fact extension. See the field list below. The Consortium will publish usage guidance on the new COP and Preparation Property tables on its web site in early 2019. Requested by the Florida MNH and Barcelona NHM.
- Preparation Property, M:1 to Preparation. This table was added to enable custom fields for description detail about Preparations in a M:1 relationship. Similar data support functions as for #5 but for Preparation attributes.
- Voucher Relationship, 1:M to Collection Object. This new table contains fields to facilitate the export of tissue and DNA sample identifiers to GGBN to comply with the GGBN standard format. See: https://wiki.ggbn.org/ggbn/Mandatory_and_recommended_fields_for_sharing_data_with_GGBN#The_voucher_identifiers_2. Requested by the University of Kansas.
New Relationships Between Tables (Trailing numbers refer to Specify GitHub issues (https://github.com/specify/specify6/issues/###)
- Conservation Description table now has a M:1 relationship to Preparation table, allowing the documentation of Conservation details for particular preparations. Requested by Barcelona, KU Paleo and Nebraska Paleo. 178
- A second link between Preparation and Storage Tree for 'Permanent Location' enables documenting permanent and current locations of a Preparation. Requested by Barcelona. 177
- Permit now has M:1 relationships with both Collecting Event Authorization and Collecting Trip Authorization. Requested by South Africa. 210
Data Fields Added
- Collection Object table fields added: Agent1, Date1, and Inventory Date Precision.
- Preparation table fields added: AlternateStorage (link to Storage Tree), ConservDescription, Date1, Date1Precision, Date2, Date2Precision, Date3, Date3Precision, Date4, Date4Precision, PreparationProperties (link to new table, see above), Text6, Text7, Text8, and Text9.
- Collection Object Attribute table fields added: Date1, Date1Precision, and Agent1.
- Collecting Trip table fields added: Agent1, Agent2, CollectingTripAttachments (link to Attachment), CollectingTripAttribute (link to new table, see above), CollectingTripAuthorizations (link to new table, see above), Date1, Date1Precision, Date2Precision, Text5, Text6, Text7, Text8, and Text9. 209
- Reference Work table fields added: DOI and URI. 207
- Exsiccata table fields added: Remarks and Schedae. Univ. of Michigan request. 205
- DNA Sequence table fields added: SequenceDate, ExtractionDate, Extractor (link to Agent). 231
- Material Sample table field added: Extractor (link to Agent). 231
- Collection Object Property (new table) fields:
Preparation Property (new table) fields: same as for table Collection Object Property above.
Attachment table field: AttachmentStorageConfig to support the use of more than one attachment or asset server. Requested by Denmark developer.
- Customizable fields: Agent1–10 (int11, Specify Agent IDs), Date1–10, Integer1–20 (smallint), Integer21-30 (int), Text1-15 (Varchar50), Text16-30 (varchar100), Text31-40 (text), Yes/no1-20 (boolean), Number1-20 (float), Number21-30 (double), Remarks (memo4096).
- Fields used by Specify: CollectionMemberID, CreatedByAgent, ModifiedByAgent, TimestampCreated, TimestampModified, Version, GUID
User Interface Schema Changes
- The Inventory Date field in the Collection Object Table can now be configured as a partial date field to accommodate incomplete dates. 196
- Specify plug-ins can now be displayed or hidden using "true/false" commands in the UI schema xml file. 184
- Specify user interface schema files with non-ASCII characters exported from Specify now display correctly upon re-import due to the use of UTF-8 encoding. 183
Darwin Core Exporter Schema Changes
- Organism Quantity and Organism Quantity Type fields have been added to Darwin Core export schema XSD file. 202
WorkBench (Upload) Schema Changes
- DNA sequence data can now be uploaded to the DNA Sequence Table via the WorkBench. 175, 217
- The WorkBench can now be configured to upload Locality Name Alias data to the Locality table. 180
- Until now, users without permission to add data could still do so through drop down pick lists. Now only users with "add" permission can add new records in that way. Rancho Santa Ana BG reported this bug. 228
- Upon startup, when using a proxy server, Specify slowed dramatically when it checked for special messages. We created a preference to allow disabling of the special message check. Brisbane reported this bug. 226
- Permits can now be searched by Permit Type, Issued By Last Name, and various Permit date fields, in addition to Permit Number. 215
- Delay in the Query Builder resulting from clicking on 'Members' in the Agent table has been fixed. 193
- When creating new queries, repeated switching back and forth between two or more base table choices in the upper left window no longer results in a pattern of increasing performance delays. 191
- An error stemming from using the ampersand "&" character in table formatters has been fixed. The ampersand characters are required to conform with GGBN voucher identifier standards. Previously if an ampersand was used, an error occurred when the Specify Schema Configuration tool was opened. 185
- Preparation table fields that have been formatted in the UI schema configuration tool can now be auto-incremented when multiple preparations are added or in grid view. 157, 179
- If "Save and New" is checked, it will continue to be in effect until unchecked regardless of whether Collection Object records have been closed and reopened. 169
- The Apache httpclient library now works correctly. Resolving a proxy server issue for Brisbane. 159
- Fields with partial dates can now be queried by day, month, or year. 156
- Data can be exported to Symbiota when fields are included in Specify export mappings as criteria for record selection, but which are marked not to be displayed or exported. 147
- When sending records to Symbiota databases, the timestamp indicating the last time the export cache was updated is now evaluated correctly to avoid unnecessary record updates to the cache. Reported by Rancho Santa Ana. 146
- When uploading Collection Object records via the WorkBench, catalog numbers are now correctly highlighted as invalid if they already exist in the database. 142
- Paleo Context Name can be used to find Paleo Context records using the query combo box or the magnifying glass search even if there is no Chronostratigraphy associated. 154, 155, 149
- WorkBench Upload Settings window no longer pops up behind the Match Existing Records window in the WorkBench. 141
- Accurate counts of update progress are now displayed in the Data Exporter when more than 100,000 records need to be updated and some records have been deleted. 140
- Series data entry no longer creates catalog number offset errors in certain situations when a previously entered series does not reach its maximum value of 500 records. 139
- Queries that return counts no longer display the message: "Query returned no results." after the Count window is closed. 130
- When saved queries with 'Series' or 'Distinct' checkboxes checked are opened and run in the Batch Editor, the checked parameters are ignored, and the BE queries run as if they are not checked. Queries like this in BE no longer fail silently because 'Series' and 'Distinct' are not allowed. 128, 129
- WorkBench DataSets cannot be opened if fields from the original mapping are not in the current machine's WorkBench configuration files. Previously Specify would throw unuseful errors. 236
- When a new Specify 6 software and schema update is available and the software is updated by the user but not the schema, thus making the software and database schema versions incompatible, Specify will shutdown at startup. 237
- In field searches using the magnifying glass icon, when a specified search term is used but finds no hits, that term is now correctly removed from subsequent searches in that field. 251
- The Batch Edit system no longer creates a needless RecordSet when edits are not saved. 262
- Importing Images into a WorkBench now correctly creates a row for each attachment with an existing mapping or with a newly created mapping. 267
- Adding a Container to a Query no longer causes Specify's performance to degrade. 269
- All ranks of a Taxon Tree can now be 'un-enforced" except for 'Life'. This is to accommodate collections where higher level taxonomy may not be completely defined, commonly with paleo collections. 201
- Specify is now compatible with Amazon Corretto 8 and Oracle Java SE 11. Most current installations of Specify 6 use Oracle Java SE 8 but this version of the Java runtime environment as of January 2019 is no longer available at no cost from Oracle. Existing Specify 6 installations should move to Amazon's version of Java, Corretto 8. See the general note above, and for more detail the Amazon Corretto announcement on the Consortium web site. 165
- The names of exported queries remain the same when re-imported across users within the same database. Numbers are no longer appended to query names when queries are shared in this way. 152
- Weblinks are now exported as URLs to the Specify Web Portal where they can be used to connect to targets. They will be active links in the next release, but can be right-clicked to open in 6.7.02. 144
- Batch Edit permissions can now be set for all user levels. Users must also have WorkBench Upload and Query Builder permissions to work with the Batch Editor. 137
- Default permissions for different user levels have been updated to account for added data tables and preferences. 127
- The logic of the 'Show Loans' button on the Preparations form has expanded to include associated gifts or exchange transactions for a Preparation, in addition to displaying its loans. The existing 'Show Loans' button can be manually edited to read 'Show Interactions', contact Consortium staff if you would like assistance. Also a message now appears when there are no interactions (loans, exchanges, or gifts) associated with a Preparation. 203, 218
- Query Builder fields were lengthened to allow for more text in Query fields. 229
- The new 'Show Interactions' button shows all associated loans, not just open, unresolved loans. 254
- WorkBench DataSets can now be transferred to other users within a Collection, if they have WorkBench access permissions. Requested by U. Michigan.