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update
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monicacecilia committed Aug 3, 2017
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4 changes: 2 additions & 2 deletions ChangeLog.md
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Expand Up @@ -10,8 +10,10 @@ Features
- Restrictions are now in place to prevent users from modifying or deleting annotations that they did not create. [#1260](https://github.com/GMOD/Apollo/issues/1260)
- Updated settings for the ability to filter by organism when applying metadata. For instance, admin may now apply canned comments, keys and values, only to a subset of organisms in their server. As well, statuses can be retrieved per type of genomic element, per organism, etc. [#1676](https://github.com/GMOD/Apollo/pull/1676)
- Admins can now build public URLs to hyperlink directly to a specific genomic element. [#1482](https://github.com/GMOD/Apollo/pull/1482)
- It is now possible to set _Statuses_ as well as adding or editing _Canned elements_ using our Web Service (REST) API. [#1538](https://github.com/GMOD/Apollo/pull/1538)
- In the absence of ```Name``` attribute in GFF3 file, Apollo uses ```ID``` attribute to name the annotation in JSON. [#1639](https://github.com/GMOD/Apollo/pull/1639)
- A number of other improvements to performance have been made, such as fetching preferences from session. [#1604](https://github.com/GMOD/Apollo/pull/1604)
- Added documentation for a Web Service wrapper for Python, PHP, etc. See [Web Services API documentation](http://genomearchitect.readthedocs.io/en/latest/Web_services.html).

Bugfixes

Expand All @@ -20,11 +22,9 @@ Bugfixes
- Added warning to Production pre-requisites: if using gradle and gradlew, admins should define ```JAVA_HOME``` to avoid build fails. See documentation [here](http://genomearchitect.readthedocs.io/en/latest/Setup.html#production-pre-requisites).
- Fixed sorting bug on the dropdown list of organisms. [#1497](https://github.com/GMOD/Apollo/issues/1497)
- Fixed a bug in which the absence of an organism created downstream issues such as errors listing groups of users in Annotator panel. (Feature for admins). [#1504](https://github.com/GMOD/Apollo/pull/1504)
- It is now possible to set _Statuses_ as well as adding or editing _Canned elements_ using our Web Service (REST) API. [#1538](https://github.com/GMOD/Apollo/pull/1538)
- Fixed a bug in which creating a user via Web Service API generated an error message. [#1510](https://github.com/GMOD/Apollo/pull/1510)
- Fixed import script ```add_transcripts_from_gff3_to_annotations.pl``` to introduce correct handling of sequence alterations and read-through stop codons. [#1524](https://github.com/GMOD/Apollo/pull/1524)
- Fixed bug that now allows leading start non-M codons in organisms with non-standard code to be translated as Methionine (M). [#1544](https://github.com/GMOD/Apollo/issues/1544)
- Added documentation for a Web Service wrapper for Python, PHP, etc. See [Web Services API documentation](http://genomearchitect.readthedocs.io/en/latest/Web_services.html).
- Updated GWT code to fix a bug that prevented Apollo from generating URLs appropriately - pipes were not being encoded. [#1606](https://github.com/GMOD/Apollo/pull/1606)
- Fixed bug in the calculation of open reading frames for the negative strand for the purpose of coloring each exon according to the CDS. Exported sequences had been - and remain - correctly generated. [#1629](https://github.com/GMOD/Apollo/issues/1629)
- Fixed bug that delayed propagation of updates when boundaries for an annotation's parent element were changed. [#1631](https://github.com/GMOD/Apollo/issues/1631)
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