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Restore pose column in metadata.csv #664

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merged 162 commits into from
Sep 13, 2024
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7f4ac78
build(deps): bump django from 3.2.24 to 3.2.25
dependabot[bot] Mar 18, 2024
fd9fd08
stashing
kaliif Mar 22, 2024
816145c
Target loader now accepts experiments marked as 'manual'
kaliif Mar 26, 2024
2bd0d06
Merge pull request #567 from xchem/m2ms-1282-rcsb-pdb
kaliif Mar 26, 2024
4cbe000
build(deps): bump pillow from 10.2.0 to 10.3.0
dependabot[bot] Apr 3, 2024
57346b4
Attempt to reduce pop-up "flicker" (1403) (#569)
alanbchristie Apr 5, 2024
208df48
feat: endpoint to download first reference pdb from assemblies.yaml
kaliif Apr 9, 2024
fe61db2
stashing
kaliif Apr 10, 2024
6afddf9
stashing
kaliif Apr 10, 2024
8eaf124
fix: removed code mentioned in previous commit
kaliif Apr 10, 2024
d4706f1
Merge pull request #571 from xchem/m2ms-1373-first-assembly
kaliif Apr 10, 2024
ad37b45
basic functionality
kaliif Apr 10, 2024
94b177a
stashing
kaliif Apr 11, 2024
fefe343
build(deps): bump idna from 3.6 to 3.7
dependabot[bot] Apr 11, 2024
5ae1dd4
stashing
kaliif Apr 12, 2024
bf56876
Added 'hidden' property to viewer.Tag model
kaliif Apr 12, 2024
b6399d9
Merge pull request #573 from xchem/m2ms-1389-tags
kaliif Apr 17, 2024
41fb8ff
Better user/proposal cache (#576)
alanbchristie Apr 18, 2024
890c7a1
stashing
kaliif Apr 24, 2024
b1d8bd5
feat: added compound_code to pose serializer
kaliif Apr 24, 2024
b5c3dc9
fix: deeper nesting level to site observaton in meta_aligner.yaml
kaliif Apr 25, 2024
9da3b35
fix: renamed panddas_event_files to ligand_binding_events in meta_al
kaliif Apr 25, 2024
2b4854a
fix: static resources are now loaded again
kaliif Apr 25, 2024
9e54c7a
fix: fixed nginx config
kaliif Apr 25, 2024
eb49ed4
Merge pull request #578 from xchem/fix_static_res_not_loaded
kaliif Apr 25, 2024
1cd6320
Revert "Fix static ressources not being loaded"
kaliif Apr 26, 2024
27db93e
Merge pull request #579 from xchem/revert-578-fix_static_res_not_loaded
kaliif Apr 26, 2024
6813102
stashing
kaliif Apr 29, 2024
5e04ecb
fix: more robust update method
kaliif Apr 30, 2024
ee1ed54
feat: added pose tags
kaliif Apr 30, 2024
5dae9f0
stashing
kaliif May 1, 2024
8de2dfa
feat: fully functional versioned data
kaliif May 2, 2024
597e1d7
fix: removed some dead code
kaliif May 2, 2024
c8669ea
Merge branch 'staging' into m2ms-1311-observation-levels
kaliif May 2, 2024
dd48d31
Merge pull request #580 from xchem/m2ms-1311-observation-levels
kaliif May 2, 2024
5bbe6ce
stashing
kaliif May 3, 2024
e795865
build(deps): bump tqdm from 4.66.1 to 4.66.3
dependabot[bot] May 3, 2024
b783d8a
feat: only non-superseded sites available from the api
kaliif May 7, 2024
a52d8de
Merge pull request #583 from xchem/m2ms-1311-observation-levels
Waztom May 7, 2024
d7ab5b7
Merge pull request #564 from xchem/dependabot/pip/django-3.2.25
kaliif May 7, 2024
6c76dba
build(deps-dev): bump black from 23.12.0 to 24.3.0
dependabot[bot] May 7, 2024
b6239a0
Merge branch 'staging' into m2ms-1392-poses-backend
kaliif May 7, 2024
6bb6ebf
chore: merged conflicting migrations from issue 1311 branch
kaliif May 7, 2024
b5f034a
fix: pose instance attributes updating successfully
kaliif May 8, 2024
1d8f73d
fix: better check for already uploaded data
kaliif May 9, 2024
2107026
Merge pull request #568 from xchem/dependabot/pip/pillow-10.3.0
kaliif May 9, 2024
78849ba
Merge pull request #572 from xchem/dependabot/pip/idna-3.7
kaliif May 9, 2024
48bf8d0
Merge pull request #585 from xchem/fix_upload_fail_message
kaliif May 9, 2024
18a5fcd
Merge pull request #584 from xchem/dependabot/pip/black-24.3.0
kaliif May 10, 2024
493b2fd
Merge pull request #581 from xchem/dependabot/pip/tqdm-4.66.3
kaliif May 10, 2024
faa04e1
Merge branch 'staging' into m2ms-1392-poses-backend
kaliif May 15, 2024
b6e77e9
Merge pull request #586 from xchem/m2ms-1392-poses-backend
kaliif May 15, 2024
f54694b
fix: merge conflicting migrations
kaliif May 16, 2024
4a4c045
Merge pull request #587 from xchem/m2ms-1392-poses-backend
kaliif May 16, 2024
12c8653
Adds basic metrics (#588)
alanbchristie May 20, 2024
ed9f0fd
Attempt to add prometheus to DB (#589)
alanbchristie May 20, 2024
a2b6a5a
feat: service state queries to backend
kaliif May 21, 2024
818d833
feat: service state queries to backend
kaliif May 22, 2024
9142eb5
Add custom (security) metrics (#593)
alanbchristie May 22, 2024
5ba881d
feat: service state queries to backend
kaliif May 22, 2024
d117daf
fix: Fixed connection retry metric (#594)
alanbchristie May 22, 2024
85d3eb0
feat: service state queries to backend
kaliif May 22, 2024
513d9f7
fix: missing migration and pylint ignore
kaliif May 22, 2024
b01b096
Merge branch 'staging' into m2ms-1205-separating-services
kaliif May 22, 2024
cab7efa
fix: remove auto-generating pose tags
kaliif May 22, 2024
9d6a21b
Merge pull request #595 from xchem/m2ms-1205-separating-services
kaliif May 22, 2024
c909329
Merge pull request #596 from xchem/m2ms-1392-remove-pose-tags
kaliif May 22, 2024
b08240f
fix: Fix for tunnel connection failure metrics (#597)
alanbchristie May 23, 2024
df41b50
fix: Adjust metrics (tunnels and cache) (#598)
alanbchristie May 23, 2024
039ac60
fix: service test functions now scheduled correctly
kaliif May 23, 2024
2940874
Merge pull request #599 from xchem/m2ms-1205-separating-services
kaliif May 23, 2024
0f950d2
fix: changed canon site autogenerated tag name
kaliif May 23, 2024
69dd49e
Merge pull request #600 from xchem/m2ms-1358-change-tagname
kaliif May 24, 2024
b7a4f55
docs: Updated grafana dashboard
May 24, 2024
d173f1b
feat: filename attribute to RHS download serializer
kaliif May 29, 2024
3485e2e
Merge pull request #601 from xchem/m2ms-1393-download-file-name
kaliif May 29, 2024
e2d58ea
fix: update observation's longcode template
kaliif May 29, 2024
920049f
Merge pull request #602 from xchem/fix_broken_download_names
kaliif May 29, 2024
aa8cc22
Adjust logging for cache debug (#603)
alanbchristie May 30, 2024
392d1bf
Fix connection failure logic (#604)
alanbchristie May 30, 2024
47cef8c
Reduced security logging (#605)
alanbchristie May 30, 2024
e27d672
feat: add management commands to save and restore curated tags
kaliif May 31, 2024
e05f056
Merge pull request #606 from xchem/save_curated_tags
kaliif May 31, 2024
a7b5a9d
feat: incremental RHS upload (issue 1394)
kaliif Jun 13, 2024
bb6d964
feat: incremental RHS uploads
kaliif Jun 14, 2024
87597eb
fix: set ConformerSites and CrystalformSites tags to hidden by default
kaliif Jun 17, 2024
275445e
Merge pull request #608 from xchem/m2ms-1460-tag-improvements-be
kaliif Jun 17, 2024
4cba2d8
fix: code cleanup for merge
kaliif Jun 24, 2024
b778ab0
Merge branch 'm2ms-1394-incermental-RHS-upload' into staging
kaliif Jun 24, 2024
db18354
Merge pull request #610 from xchem/m2ms-1394-incermental-RHS-upload
kaliif Jun 24, 2024
8da1620
fix: updated crystalform site tag generation scheme
kaliif Jun 24, 2024
18e568c
Initial 'security' changes - Target PATCH now "locked down" (#612)
alanbchristie Jun 25, 2024
11f6777
fix: update tag generation scheme
kaliif Jun 25, 2024
806b76c
Merge pull request #613 from xchem/m2ms-1466-tags
kaliif Jun 25, 2024
9b4a959
fix: remove version field from ComputedMolecule
kaliif Jul 10, 2024
1dc9040
fix: forgot to stage migration file..
kaliif Jul 10, 2024
e70d37a
fix: fix querysets in target_loader.py
kaliif Jul 10, 2024
bd65a59
fix: add warning to logs about overwriting ComputedMolecule metadata
kaliif Jul 10, 2024
d5c1555
Merge pull request #617 from xchem/fix_target_loader_querysets
kaliif Jul 10, 2024
3a540d0
Merge pull request #618 from xchem/m2ms-1394-incermental-RHS-upload
kaliif Jul 10, 2024
489767a
fix: add additional ccp4 files to download (issue 1448)
kaliif Jul 12, 2024
2275b00
Merge pull request #622 from xchem/m2ms-1448-extra-ccp
kaliif Jul 12, 2024
eb17541
fix: updates to tag generation
kaliif Jul 29, 2024
e6878e6
feat: added centroid_res field to CanonSite model
kaliif Jul 29, 2024
9751f5c
feat: added new fields to metadata.csv
kaliif Jul 29, 2024
f055121
feat: added tag aliases to metadata.csv
kaliif Jul 30, 2024
4345c1b
Copies Target proposals to new (RHS) Compounds (#629)
alanbchristie Aug 6, 2024
2ec2594
Merge branch 'staging' into m2ms-1482-metadata
kaliif Aug 8, 2024
2821be6
Merge pull request #630 from xchem/m2ms-1482-metadata
kaliif Aug 8, 2024
6fad98c
fix: Fix typo accessing Target projects (#632)
alanbchristie Aug 13, 2024
97a56a5
fix: Add support for target_warning_message context variable (#634)
alanbchristie Aug 27, 2024
7a5b4a8
API authentication and security changes (#635)
alanbchristie Aug 27, 2024
5f5e876
fix: Adds variable to context
Aug 27, 2024
e0ab265
fix: Fix variable order
Aug 27, 2024
76481ad
Merge pull request #636 from xchem/m2ms-1489-view
kaliif Aug 27, 2024
427cfdc
style: Add note and display template and its context (#637)
alanbchristie Aug 29, 2024
1de69ee
fix: fixed tag loading management command
kaliif Aug 29, 2024
3a01e25
Merge pull request #638 from xchem/fix_tag_loader_mgmnt_cmd
kaliif Aug 29, 2024
8bbfbf5
fix: fixed tag loader management command some more
kaliif Aug 29, 2024
e6d83c9
Merge pull request #639 from xchem/fix_tag_loader_mgmnt_cmd
kaliif Aug 29, 2024
6adec86
feat: Add support for RESTRICTED_TAS_USERS (#640)
alanbchristie Aug 30, 2024
61a6790
Better handling of project path AttributeError (#641)
alanbchristie Aug 30, 2024
a28d5e2
fix: Protect permissions from bad objects (#642)
alanbchristie Sep 2, 2024
6675729
fix: Fix merge issue (#643)
alanbchristie Sep 2, 2024
bfbc302
Relaxes authentication for SessionProject (#644)
alanbchristie Sep 3, 2024
96d47a8
refactor: Now displays object class name (#645)
alanbchristie Sep 3, 2024
e99c7d7
Add additional context to the API error (#646)
alanbchristie Sep 3, 2024
e823247
stashing
kaliif Sep 3, 2024
37a8fcd
Relaxed auth for SessionActionsView & SnapshotActionsView (#647)
alanbchristie Sep 3, 2024
0702740
fix: fix subsequent upload file path overwriting bug (1492)
kaliif Sep 3, 2024
da94db0
fix: Relax auth on SessionProjectTag & SiteObservationTag (#648)
alanbchristie Sep 3, 2024
7e07d5a
fix: Can now download public RHS without being logged int (#649)
alanbchristie Sep 3, 2024
85c0ae2
feat: updated LHS downloads to new data schema
kaliif Sep 3, 2024
6568ea1
Merge branch 'staging' into m2ms-1492-upload2
kaliif Sep 3, 2024
819b659
Merge pull request #650 from xchem/m2ms-1492-upload2
kaliif Sep 3, 2024
3bb91b1
fix: log compound names when alignment is not found (issue 1495)
kaliif Sep 4, 2024
388f968
Merge pull request #651 from xchem/m2ms-1495-RHS-upload
kaliif Sep 4, 2024
0daf690
stashing
kaliif Sep 4, 2024
21c9ed7
Merge pull request #652 from xchem/m2ms-1496-tags
kaliif Sep 4, 2024
f00db39
fix: sort canon sites by number of site observations
kaliif Sep 4, 2024
1648028
Merge pull request #653 from xchem/m2ms-1498-tag-sorting
kaliif Sep 4, 2024
81ff613
stashing
kaliif Sep 5, 2024
7db40c4
fix: fixed issue 1504, missing yaml files
kaliif Sep 5, 2024
52fecaf
fix: shortened crystalform sites tags
kaliif Sep 5, 2024
a49db62
feat: added code prefix to experiment model
kaliif Sep 5, 2024
852db67
Merge pull request #654 from xchem/m2ms-1496-tags
kaliif Sep 5, 2024
7a8d982
feat: updated both short- and longcode
kaliif Sep 6, 2024
ed6bb69
fix: fixed tagging issues
kaliif Sep 6, 2024
7f31bb5
fix: fixed remaining tag issues
kaliif Sep 6, 2024
f6d6b6d
Merge pull request #655 from xchem/m2ms-1499-shortcode
kaliif Sep 6, 2024
99118e4
Merge branch 'staging' into m2ms-1492-upload2
kaliif Sep 6, 2024
72eada3
fix: the return of the ribbon
kaliif Sep 6, 2024
f7a1ced
Merge pull request #656 from xchem/m2ms-1492-upload2
kaliif Sep 6, 2024
0c3e7a6
chore: Merge out from production
Sep 9, 2024
6c62ecc
stashing
kaliif Sep 10, 2024
51eb5b8
fix: a bug in target loader's create_objects func
kaliif Sep 11, 2024
65de5c0
Merge pull request #660 from xchem/fix_target_loader_object_proc
kaliif Sep 11, 2024
f96703d
Merge branch 'staging' into m2ms-1508-tag-format
kaliif Sep 11, 2024
13b0da4
feat: changed tag name format
kaliif Sep 11, 2024
a7c5345
Merge pull request #661 from xchem/m2ms-1508-tag-format
kaliif Sep 11, 2024
33ad5bd
fix: restore pose column to metadata.csv (#663)
kaliif Sep 13, 2024
d74a36d
Merge branch 'production' into staging
alanbchristie Sep 13, 2024
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3 changes: 3 additions & 0 deletions viewer/download_structures.py
Original file line number Diff line number Diff line change
Expand Up @@ -482,6 +482,9 @@ def _metadata_file_zip(ziparchive, target, site_observations):
header.append(f'{category.category} upload name')
annotations[upload_tag] = UploadTagSubquery(category.category)

values.append('pose__display_name')
header.append('Pose')

pattern = re.compile(r'\W+') # non-alphanumeric characters
for tag in SiteObservationTag.objects.filter(
category__in=TagCategory.objects.filter(category__in=CURATED_TAG_CATEGORIES),
Expand Down