| 1896c2d | Austin Leong | 05 April 2021, 18:10:10 UTC | Drug Target Search Graph development preview (expect to revert) | 05 April 2021, 18:21:47 UTC |
| 664bfdd | Austin Leong | 05 April 2021, 17:33:59 UTC | Update requirements.txt | 05 April 2021, 17:33:59 UTC |
| 3016062 | Austin Leong | 23 November 2020, 17:07:27 UTC | Commented out warning to match production server | 23 November 2020, 17:07:27 UTC |
| 2ca20d0 | Austin Leong | 23 November 2020, 16:34:10 UTC | Version bump: Django (2.2.17) and cryptography (3.2.1), among others | 23 November 2020, 16:34:10 UTC |
| a29c05d | Austin Leong | 09 November 2020, 17:06:30 UTC | Hide Extended Annotations column by default | 09 November 2020, 17:59:06 UTC |
| f1f5a48 | Austin Leong | 09 November 2020, 13:52:26 UTC | Download compound data via AJAX available for ChEMBL and PubChem. Currently the ChEMBL compound detail page and Structural Similarity Search page use this feature. | 09 November 2020, 16:58:43 UTC |
| 8cb8235 | Austin Leong | 02 November 2020, 17:55:35 UTC | Merge branch 'dl_ajax' into ts_anno | 02 November 2020, 17:55:35 UTC |
| adbf50f | Austin Leong | 28 September 2020, 17:39:38 UTC | Extended annotation savepoint | 02 November 2020, 17:52:48 UTC |
| d64a9fd | Austin Leong | 25 September 2020, 03:03:06 UTC | snapshot | 25 September 2020, 03:03:06 UTC |
| 1cdbf81 | khoran | 21 September 2020, 16:45:49 UTC | Merge remote-tracking branch 'origin/master' | 21 September 2020, 16:45:49 UTC |
| 5d29e7f | khoran | 21 September 2020, 16:45:33 UTC | improved error messages for addCompounds. added addH option to ChemmineR properties tool | 21 September 2020, 16:45:33 UTC |
| 86bfdc2 | Austin Leong | 09 September 2020, 13:14:58 UTC | Upgraded Django and Pillow in requirements.txt | 09 September 2020, 13:14:58 UTC |
| e03ca51 | Austin Leong | 09 September 2020, 13:01:17 UTC | Merge branch 'develop' into master | 09 September 2020, 13:01:17 UTC |
| 95616a4 | Austin Leong | 29 August 2020, 02:24:24 UTC | PubChem downloads now use the XML asynchronous API. | 09 September 2020, 12:55:59 UTC |
| 9ae33d8 | khoran | 31 August 2020, 16:24:40 UTC | enable URLs like targetsearch/ID1,ID2,... | 31 August 2020, 16:24:40 UTC |
| e4ee2d7 | Austin Leong | 29 August 2020, 01:21:06 UTC | Added favicon | 29 August 2020, 01:21:06 UTC |
| 642b5cd | khoran | 26 August 2020, 19:54:35 UTC | added detail entity id disambiguation page | 26 August 2020, 19:54:35 UTC |
| a265771 | khoran | 26 August 2020, 17:03:55 UTC | remove usless print messages from drugbank module | 26 August 2020, 17:03:55 UTC |
| 4a396d1 | khoran | 26 August 2020, 16:44:40 UTC | db change, migration required. altered max-length of name field from 256 to 1024 | 26 August 2020, 16:44:40 UTC |
| 9bd09d1 | khoran | 17 August 2020, 17:30:12 UTC | added compound summary info for detail page. removed chembl embedded block | 17 August 2020, 17:30:12 UTC |
| 9c2a826 | khoran | 17 August 2020, 16:12:56 UTC | Merge remote-tracking branch 'origin/develop' into develop | 17 August 2020, 16:12:56 UTC |
| 7915080 | Austin Leong | 05 August 2020, 18:55:27 UTC | Added a "Download CID List" button to Structural Similarity Search This is mainly a stop-gap solution to an issue raised by Fxotics on GitHub, but hopefully can be useful as a general feature. | 05 August 2020, 19:03:24 UTC |
| ed91b7f | Austin Leong | 05 August 2020, 15:13:23 UTC | Merge branch 'develop' | 05 August 2020, 15:13:23 UTC |
| eb8e5b1 | Austin Leong | 31 July 2020, 04:11:30 UTC | Refactored Drug-Target Search code to be more modular and shareable Fixes several issues related to incomplete DOM initialization and separation of JS code | 05 August 2020, 15:08:51 UTC |
| 150728f | Austin Leong | 28 July 2020, 16:48:21 UTC | Merge branch 'develop' | 28 July 2020, 16:48:21 UTC |
| 72a0a76 | khoran | 27 July 2020, 22:43:19 UTC | Merge remote-tracking branch 'origin/master' | 27 July 2020, 22:43:19 UTC |
| 1bb5688 | khoran | 27 July 2020, 22:42:54 UTC | updated eiR and chembl update script | 27 July 2020, 22:42:54 UTC |
| 0956c43 | Austin Leong | 27 July 2020, 19:06:03 UTC | Changed URL for documentation site in top toolbar. | 27 July 2020, 19:06:03 UTC |
| 8460107 | Austin Leong | 27 July 2020, 18:43:04 UTC | Updated requirements.txt | 27 July 2020, 18:43:04 UTC |
| ac66468 | Austin Leong | 27 July 2020, 18:05:11 UTC | Added setting switch to toggle paralog-cache in targetsearch | 27 July 2020, 18:15:11 UTC |
| 999a38a | Austin Leong | 27 July 2020, 17:27:32 UTC | Update help URLs to point to new documentation. | 27 July 2020, 17:35:59 UTC |
| 9e6c9a4 | Austin Leong | 27 July 2020, 14:08:22 UTC | Merge branch 'master' into develop | 27 July 2020, 14:08:22 UTC |
| 68d1d23 | khoran | 21 July 2020, 23:34:31 UTC | display number of compounds in corner of each page | 21 July 2020, 23:34:31 UTC |
| e71cf38 | khoran | 21 July 2020, 21:20:40 UTC | finished landing page | 21 July 2020, 21:20:40 UTC |
| 99516b9 | Austin Leong | 20 July 2020, 19:45:48 UTC | Merge branch 'dt_help' into develop | 20 July 2020, 19:45:48 UTC |
| 8371801 | Austin Leong | 06 July 2020, 14:51:32 UTC | Additional info and help buttons in Drug-Target Search | 20 July 2020, 19:11:41 UTC |
| f32fc44 | Austin Leong | 20 July 2020, 18:34:02 UTC | Added '@guest_allowed' to newTS to resolve Job retrieval error. | 20 July 2020, 18:40:02 UTC |
| 2d5c298 | Austin Leong | 20 July 2020, 18:03:57 UTC | Merge branch 'master' into develop | 20 July 2020, 18:03:57 UTC |
| 7844fb1 | khoran | 06 July 2020, 17:50:14 UTC | refactor ts_table a bit. create an initial detail page. | 06 July 2020, 21:07:46 UTC |
| 7c9dd9a | Austin Leong | 15 June 2020, 17:25:18 UTC | Additional paralog info in tooltip. | 06 July 2020, 13:13:11 UTC |
| bc81ddc | khoran | 30 June 2020, 16:12:08 UTC | duplicate clean up feature done | 30 June 2020, 16:12:08 UTC |
| 11106bb | Austin Leong | 01 June 2020, 15:10:07 UTC | Added sample compounds to Drug-Target search interfaces | 15 June 2020, 17:06:22 UTC |
| b6415c1 | khoran | 10 June 2020, 22:29:54 UTC | addded option to skip duplicate compounds during upload | 10 June 2020, 22:30:54 UTC |
| e952377 | khoran | 03 June 2020, 16:24:19 UTC | compound query tracking feature | 03 June 2020, 16:24:19 UTC |
| 6ad017d | Austin Leong | 15 May 2020, 02:36:37 UTC | Added switch to remove Google Analytics during development. | 01 June 2020, 14:11:33 UTC |
| 0fb03cd | Austin Leong | 14 May 2020, 23:04:23 UTC | Disabled caching of paralog results. | 14 May 2020, 23:04:23 UTC |
| a6ec863 | Austin Leong | 14 May 2020, 22:35:40 UTC | Initial paralog search feature for Drug-Target Search (for testing) | 14 May 2020, 22:35:40 UTC |
| db09424 | khoran | 14 May 2020, 19:34:58 UTC | removed some debug output from chemblSearch.py tool script | 14 May 2020, 19:34:58 UTC |
| 4ac3126 | khoran | 14 May 2020, 17:34:30 UTC | fixed broken png url | 14 May 2020, 17:34:30 UTC |
| 696e104 | khoran | 06 May 2020, 16:00:05 UTC | Merge branch 'paralogs' into develop | 06 May 2020, 16:00:05 UTC |
| c3c2fd5 | khoran | 06 May 2020, 15:58:54 UTC | added getParalogs function | 06 May 2020, 15:58:54 UTC |
| feea05c | Austin Leong | 27 April 2020, 22:07:35 UTC | Fix issue with deleting compounds and add/remove tags. | 27 April 2020, 22:12:16 UTC |
| 16eab91 | Austin Leong | 13 April 2020, 01:03:06 UTC | Last fix for selection mode, I promise... | 13 April 2020, 01:12:32 UTC |
| bc0db02 | Austin Leong | 03 April 2020, 17:07:20 UTC | Changed Drug-Target Search select style, for real this time... | 03 April 2020, 17:07:20 UTC |
| 6ccd239 | Austin Leong | 03 April 2020, 17:03:21 UTC | Default select mode in Drug-Target Search now 'Desktop'. Tooltip init. This matches the behavior of the workbench. | 03 April 2020, 17:03:21 UTC |
| 0bf7104 | Austin Leong | 03 April 2020, 16:41:47 UTC | Added back 'filename' parameters to compounddb/urls.py | 03 April 2020, 16:54:09 UTC |
| bfc88e9 | Austin Leong | 21 March 2020, 01:04:59 UTC | Updates to settings_sample.py for new middleware, IFrame settings. | 21 March 2020, 01:04:59 UTC |
| bede605 | Austin Leong | 07 March 2020, 02:53:00 UTC | Applied compound image changes to workbench and detail page. Also... - Unified SVG rendering code under compounddb/ - Rendered SVGs should now be properly cached on the client - Upgraded FontAwesome to 5.12.1 to resolve a missing icon - Started work on changing legacy url() routes to path() - Created a simple middleware to allow overriding HTTP headers - Opportunistic code cleanup as usual... | 19 March 2020, 07:13:28 UTC |
| ce97be9 | Austin Leong | 03 March 2020, 02:01:10 UTC | Implemented SVG compound image output. Drug-Target Search PNG to SVG. | 05 March 2020, 02:10:35 UTC |
| c3cfab3 | Austin Leong | 26 February 2020, 02:25:49 UTC | Added a precheck routine for Target Search compound import. The precheck routine checks for compounds that do not have structure information in the ChEMBL database, as well as for compounds that are already in the user's workbench. If we discover other conditions that could cause an import to fail, we can easily add further restrictions. Also, chembl_helpers.py has been renamed to simply helpers.py to better reflect its current purpose, and for consistency with the new helpers.py in myCompounds. In targetsearch/helpers.py, get_chembl_sdfs() and get_chembl_smiles() will now cast chemblIds into a tuple, so we can now pass in lists, sets, etc. as is. Hopefully this doesn't create problems down the road... | 28 February 2020, 01:22:21 UTC |
| 4f0b34b | Austin Leong | 22 February 2020, 01:55:33 UTC | Rearranged table buttons. Added tooltip explanations. | 25 February 2020, 02:48:23 UTC |
| 8314945 | Austin Leong | 21 February 2020, 03:46:52 UTC | Compound structures can now be viewed from Target Search | 22 February 2020, 01:17:28 UTC |
| 0dcb95f | Austin Leong | 14 February 2020, 23:56:16 UTC | Added initial chemblPNG stuff to targetsearch | 20 February 2020, 23:29:32 UTC |
| eced04c | Austin Leong | 14 February 2020, 02:20:38 UTC | Rewrote drug-indication table code The previous code stored drug-indication tables as bare HTML code in a JS variable, which can get quite inefficient. Further, every table for each compound was rendered on page load. Now, the table data is stored in JSON format, which saves significant space, and might yield some flexibility benefits down the road. Also, the DataTable is now rendered on-demand and destroyed when the modal window is dismissed. | 14 February 2020, 05:35:02 UTC |
| f62d70b | Austin Leong | 14 February 2020, 01:42:36 UTC | Pointless targetsearch code cleanup Mostly stray whitespace, but also some commented code. It's an itch that just needs to be scratched... | 14 February 2020, 01:42:36 UTC |
| ae98414 | Austin Leong | 13 February 2020, 02:51:07 UTC | Tweaked compound and target autocomplete behavior Previously, targetNameAutocomplete would manually put results beginning with the user query ahead of those where the query appears in the middle. This work is completely redundant since Selectize seems to do just that. Search terms in targetNameAutocomplete can now span the description and organism fields. compoundNameAutocomplete and targetNameAutocomplete now sort results. Even though Selectize will disturb the sorting, pre-sorting the results seems to "chunk" together results with lexical proximity, despite whatever Selectize does. It also doesn't seem to affect query time much. On the HTML side, the user now needs to enter at least 3 characters before an autocomplete query is sent. | 13 February 2020, 02:51:07 UTC |
| 5cc2c0e | Austin Leong | 12 February 2020, 21:48:23 UTC | Remove unimplemented row-selection buttons before bumping master | 12 February 2020, 21:48:23 UTC |
| 9739e91 | Austin Leong | 12 February 2020, 20:53:24 UTC | Autocomplete for target names | 12 February 2020, 20:53:24 UTC |
| 9e4ce9b | Austin Leong | 06 February 2020, 22:31:38 UTC | Add IDs to search boxes via row selection feature. Users can now select rows and send the compound/target IDs to the corresponding search box with a button similar to the workbench compound submission process. Also I disabled duplicate CID handling. IDs need to be exact to be useful in most contexts. Later on I'll put in a feature to merge duplicate records. | 06 February 2020, 22:31:38 UTC |
| f27f09a | Austin Leong | 05 February 2020, 05:05:17 UTC | Compound names are now handled when imported from TargetSearch. Apparently Tyler intended name imports to be handled by an SDF tag named 'PUBCHEM_IUPAC_NAME'. This will still work, but the handler will now accept the tag 'NAME' as well. This way, an imported SDF file can hold both a proper IUPAC name and a common name. get_chembl_sdfs now embeds the NAME tag into the SDF so it is picked up by handlers further down. | 05 February 2020, 05:05:17 UTC |
| 5a1e558 | Austin Leong | 05 February 2020, 01:08:26 UTC | Templatized/functionized duplicate Annotation/Activity table stuff. | 05 February 2020, 01:15:37 UTC |
| 3ffda58 | Austin Leong | 01 February 2020, 04:07:01 UTC | Apply deferred redrawing to toggleTableColumns Minor change that was "lost" when I moved development from AWS to my local machine. | 01 February 2020, 04:07:01 UTC |
| 4f4c7fb | Austin Leong | 01 February 2020, 03:49:44 UTC | Upload compounds to Workbench from Target Search This commit contains a limited implementation of (see title). Currently it's only applied to the Annotation table. I'll likely templatize the Annotation and Activity tables in the near future, since new_ts.html is getting insanely long at this point, and there's quite a lot of stuff that can be deduplicated. | 01 February 2020, 03:49:44 UTC |
| 6fdf6ac | Austin Leong | 01 February 2020, 03:43:13 UTC | Remaining files related to installation script overhaul. bootstrap.sh has only been tested in parts, rather than from beginning-to-end in one run. It's a pretty long process, so I plan to test it when setting up another development instance. That being said it should provide enough guidance to reach a complete installation. The sample settings files now assume that Python packages are installed in a virtual environment (venv). Existing installations shouldn't be affected, provided they don't overwrite their old settings. Finally, this commit will modify runQuery() in targetsearch/chembl_helpers.py to expect database credentials from chemminetools/settings.py . If this information is absent, queries to the local ChEMBL database will fail. | 01 February 2020, 03:43:13 UTC |
| 2a1caac | Austin Leong | 22 January 2020, 04:15:27 UTC | A bunch of small changes I made while doing a local deployment. Proper documentation/scripts to follow... | 22 January 2020, 04:15:27 UTC |
| 873a348 | Austin Leong | 22 January 2020, 02:31:22 UTC | Changed Python shebang lines. Removed Python2 compat. Changed the shebang lines for Python scripts under tools/tool_scripts to '/usr/bin/env python' so the scripts pick up the virtualenv. For those files modified, I also went ahead and removed unnecessary __future__ imports. | 22 January 2020, 02:31:22 UTC |
| 7856795 | Austin Leong | 22 January 2020, 02:16:16 UTC | Some (hopefully all) missing migration scripts. | 22 January 2020, 02:16:16 UTC |
| 1bfeb12 | Austin Leong | 09 January 2020, 07:30:14 UTC | Columns can now be suppressed during CSV output with the "export" setting. Also rewrote column manipulation functions with more descriptive names and to take advantage of the new targetSearch namespace variable. | 09 January 2020, 07:34:35 UTC |
| c80b0ba | Austin Leong | 08 January 2020, 23:45:17 UTC | Removed old child-row code. | 08 January 2020, 23:45:17 UTC |
| 90314d9 | Austin Leong | 07 January 2020, 00:05:49 UTC | Minor tweaks to "Query ID" feature, column select. | 07 January 2020, 00:05:49 UTC |
| c50e63c | Austin Leong | 16 December 2019, 21:48:05 UTC | Updated UCR URLs, SysV init to Systemd in installation scripts. | 16 December 2019, 21:48:05 UTC |
| 52d11c4 | Austin Leong | 12 December 2019, 15:38:44 UTC | Merge branch 'master' into develop | 12 December 2019, 15:38:44 UTC |
| b9a1601 | Austin Leong | 12 December 2019, 15:31:44 UTC | Fixed TargetSearch main page error. | 12 December 2019, 15:31:44 UTC |
| f0a84fa | Austin Leong | 12 December 2019, 14:38:50 UTC | Merge branch 'master' into develop | 12 December 2019, 14:38:50 UTC |
| 4acd714 | Austin Leong | 12 December 2019, 14:06:02 UTC | Quick fix to show ChEMBL ID in DrugInd table headers and filename. | 12 December 2019, 14:06:02 UTC |
| e7c0cb5 | khoran | 11 December 2019, 22:57:55 UTC | fixes after merging query id mapping feature in | 11 December 2019, 22:57:55 UTC |
| ee38488 | khoran | 11 December 2019, 22:35:29 UTC | Merge remote-tracking branch 'origin/develop' into develop | 11 December 2019, 22:35:29 UTC |
| e3b76e0 | khoran | 11 December 2019, 22:21:57 UTC | add optional result column to target results that shows un-mapped ids | 11 December 2019, 22:21:57 UTC |
| 2ec300c | Austin Leong | 10 December 2019, 06:05:42 UTC | Omnibus commit: DrugInd tables; Search classes now OOP... Drug Indication tables moved from child rows to modal windows. DrugInd tables now have DataTable functionality. Restructured all the *Search classes to inherit from a common SearchBase class. Brought back the MeSH summary string, along with a similar one for EFO. Renamed *_list.json to *_info.json to better reflect current purpose. | 10 December 2019, 06:05:42 UTC |
| cb50b58 | Austin Leong | 02 December 2019, 20:51:07 UTC | Removed targetsearch lockdown Also changed menu name to "Drug-Target Search" | 02 December 2019, 20:51:07 UTC |
| cbab8a6 | Austin Leong | 02 December 2019, 20:44:01 UTC | Merge remote-tracking branch 'refs/remotes/origin/develop' into develop | 02 December 2019, 20:44:01 UTC |
| 840d77f | khoran | 27 November 2019, 21:46:25 UTC | added autocomplete for compound names in targetsearch | 27 November 2019, 21:46:25 UTC |
| 66c00d0 | khoran | 27 November 2019, 18:30:17 UTC | batch queries to support more than 1000 given identfiers | 27 November 2019, 18:30:17 UTC |
| 386a784 | Austin Leong | 25 November 2019, 23:04:27 UTC | Merge remote-tracking branch 'refs/remotes/origin/develop' into develop | 25 November 2019, 23:04:27 UTC |
| 8435c6f | Austin Leong | 25 November 2019, 23:01:38 UTC | Separate drug indication table, first attempt | 25 November 2019, 23:01:38 UTC |
| a0bf33f | khoran | 20 November 2019, 22:25:04 UTC | added target protein db translation feature to targetsearch page | 20 November 2019, 22:25:04 UTC |
| f9a3001 | khoran | 20 November 2019, 18:06:37 UTC | Merge remote-tracking branch 'origin/develop' into develop | 20 November 2019, 18:06:37 UTC |
| ceac4fe | khoran | 20 November 2019, 18:06:13 UTC | make column selection box look nicer | 20 November 2019, 18:06:13 UTC |
| 7c6e6db | Austin Leong | 18 November 2019, 22:55:30 UTC | Minor tweaks and correction to upgrade notes. | 18 November 2019, 22:55:30 UTC |
| 944cb99 | khoran | 11 November 2019, 19:00:14 UTC | updated settings_sample.py for new django version | 11 November 2019, 19:00:14 UTC |
