16 research outputs found
CRI iAtlas: an interactive portal for immuno-oncology research.
The Cancer Research Institute (CRI) iAtlas is an interactive web platform for data exploration and discovery in the context of tumors and their interactions with the immune microenvironment. iAtlas allows researchers to study immune response characterizations and patterns for individual tumor types, tumor subtypes, and immune subtypes. iAtlas supports computation and visualization of correlations and statistics among features related to the tumor microenvironment, cell composition, immune expression signatures, tumor mutation burden, cancer driver mutations, adaptive cell clonality, patient survival, expression of key immunomodulators, and tumor infiltrating lymphocyte (TIL) spatial maps. iAtlas was launched to accompany the release of the TCGA PanCancer Atlas and has since been expanded to include new capabilities such as (1) user-defined loading of sample cohorts, (2) a tool for classifying expression data into immune subtypes, and (3) integration of TIL mapping from digital pathology images. We expect that the CRI iAtlas will accelerate discovery and improve patient outcomes by providing researchers access to standardized immunogenomics data to better understand the tumor immune microenvironment and its impact on patient responses to immunotherapy
Meta-Analysis of the Alzheimer\u27s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models.
We present a consensus atlas of the human brain transcriptome in Alzheimer\u27s disease (AD), based on meta-analysis of differential gene expression in 2,114 postmortem samples. We discover 30 brain coexpression modules from seven regions as the major source of AD transcriptional perturbations. We next examine overlap with 251 brain differentially expressed gene sets from mouse models of AD and other neurodegenerative disorders. Human-mouse overlaps highlight responses to amyloid versus tau pathology and reveal age- and sex-dependent expression signatures for disease progression. Human coexpression modules enriched for neuronal and/or microglial genes broadly overlap with mouse models of AD, Huntington\u27s disease, amyotrophic lateral sclerosis, and aging. Other human coexpression modules, including those implicated in proteostasis, are not activated in AD models but rather following other, unexpected genetic manipulations. Our results comprise a cross-species resource, highlighting transcriptional networks altered by human brain pathophysiology and identifying correspondences with mouse models for AD preclinical studies
Sage-Bionetworks/schematic: v23.9.2
What's Changed
implement GE list rule by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/655
Develop initial rule pairs by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/802
Cross Manifest Validation: Value Level Comparisons and Reworked Warning Messages by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/751
Develop schema viz tool tests by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/659
make sorting case insensitive by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/830
Develop fix submit keyerror by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/831
updating the release documentation by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/817
Develop an endpoint to return data types of columns in a manifest by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/815
Develop rule combination by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/766
BugFix: Import dataType from CLI as list not string by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/836
BugFix: Manifest Import - Mask null cells as empty strings instead of NaNs by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/837
BugFix: list like behavior by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/840
Check type of 'url' entry when raising errors by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/844
Fix example data model list validation rule and update "list" in ManifestGenerator to handle both list strict and list like by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/847
add warning to validate_manifest endpoint by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/859
Develop NA string behavior by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/842
Develop blank annotation behavior by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/862
Develop Missing Entity Handling by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/871
rename manifest based on manifest_basename when submit to synapse by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/869
Output errors generated from jsonSchema (when submitting manifest) to the console by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/873
Develop manifest submission error handle by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/879
do not create dir if located in cwd by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/881
Update annotations unit test by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/880
Develop optional rule args by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/843
Containerizing schematic (and update dependencies as needed) by @BrunoGrandePhD in https://github.com/Sage-Bionetworks/schematic/pull/882
add endpoint find_class_specific_properties by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/890
add route get_subgraph_by_edge_type by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/891
create endpoint to return schema as a pickle file by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/892
poetry documentation by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/895
Add support for Schematic API to Dockerfile by @BrunoGrandePhD in https://github.com/Sage-Bionetworks/schematic/pull/887
Create project table manifests, move entities to new project by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/829
add concurrency to github action by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/896
HOTFIX: Mixed type column manifest table upload by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/902
update asset view table endpoint to allow returning a json by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/912
added get_node_range endpoint by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/904
added get_property_label endpoint by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/905
added node_dependencies endpoint by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/906
Allow schema.org schema to be loaded and used by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/903
add example workbook to demo cli functions by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/916
change manifest name for censored manifest when upload by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/931
Add Restriction Flag to Make Synapse Table Method by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/935
Develop Table Uploads: Replace by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/917
allow users to upload csv or json file when submitting manifest using API endpoints by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/908
allow users to upload csv or json file when validating manifest using API endpoints by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/910
Develop table schema fix replacements by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/947
Fixing parsing of table schema parameters on table replace by @milen-sage in https://github.com/Sage-Bionetworks/schematic/pull/945
Develop schema viz tool cors by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/942
Move Schema Visualization to Schematic by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/645
add default max size for columns missing this key by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/952
populate manifest as an excel spreadsheet without sending data to Google api by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/940
Skip Trashed Entities and Entities that "do not exist" by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/985
Reword conditional requirements for the attribute table by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/987
add tests related to manifest get by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/979
fix api endpoint for docker container by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/974
Remove unused libraries by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/991
Remove Manifest Table Submission Dependency on Project Scope when not Validating by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/989
HOTFIX: Extend table replacement sleep duration to ensure synapse deletion operation completes by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/999
Pass config.yml as an environment variable to docker container by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/975
update error messages in synapseStore when manifest_basename key is missing in config.yml by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/997
Added instructions for installing and using schematic and the schematic API docker containers to README by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/953
Develop pdoc by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/957
correct typo: master_basename to manifest_basename in error message by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1005
Fixed typo in conditional requirement for schema viz attribute table by adding quotes by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1003
Added tests for all API endpoints by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/995
Fixed an issue where the DCA would disconnect on manifest submission by casting UUIDs to type string by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1006
Reminded users to run synapse login --rememberMe after schematic init step in ReadMe by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1004
Added the option to populate manifest as an excel spreadsheet to avoid sending metadata to Google APIs by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/994
For schematic APIs, return excel file instead of excel file path by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/988
Emphasized that users should download the config.yml from develop branch in ReadMe by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1007
Removed validity requirement for unrequired attribute entries, allow users to specify validation rule conformity required for entries, fix DCA disconnect caused by JSON Schema validation errors by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1000
Strip hyphens from Synapse annotation keys by @milen-sage in https://github.com/Sage-Bionetworks/schematic/pull/1020
Fixed a bug where in some instances manifests would be uploaded with different display and downloadAs names by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1017
Added an API endpoint to check if a given node is required or not by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1024
added more instructions of running CLI in jupyter notebook by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1031
Added a slack bot to notify successful new releases by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1025
Turned service_account_creds.json as an environment variable and default way of authentication by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1015
Changed base docker image and removed package for security reasons by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1037
Add support for treating date entries as type datetime by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1041
Automatically updated CLI documentation on Readthedocs by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1047
Deprecated token pickle and credentials.json by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1040
Introduce tests to cover current table operations: creation and replacement by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1046
Skip api tests when rule combination tests are run by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1068
Added workflow to deploy schematic docker container in Github container registry by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1062
Remove schematic support for Python v3.7 and v3.8 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1090
Refactor table operations structure in asset store by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1069
Added input_token as a parameter for /manifest/get endpoint to fix credential issues when getting an existing manifest on AWS by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1080
Fixed getProjectManifests function in synapse storage by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1084
Develop api node display names by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1094
Create API endpoint for get_node_validation_rules by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1095
Update schematic dependencies by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1092
Raise errors for wrong schema errors by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1073
Set default of "table_manipulation" as "replace" in API endpoint when users enter None and updated tests by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1115
Update synapseClient dependency and api for manifest table uploads by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1101
set pyopenssl = "^23.0.0" by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1125
added date GE rule by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1103
Implement table upsert feature by using schematic-db by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1081
Add use_schema_label parameter to manifest submission endpoint, separate manifest submission and table upsert tests by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1129
Delete GE checkpoint after completion of GE validation by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1136
Remove try: catch: block from manifest submission command function by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1130
Save all properties that are Included in the domain of a Class by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1134
Display exceptions raised during validation with Great expectations, allow exclusion of upper bound OR lower bound for inRange rule by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1131
Update Documentation - python/package versions and POCs by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1139
Increase buffer size to a higher limit to deal with long token by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1144
lock schematic-db to version 0.0.6 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1145
use try: finally: to delete checkpoint even if running the checkpoint fails or errors out by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1155
Allowed CORS on given routes instead of all routes by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1168
Added restrict rules param to manifest/validate by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1178
Bug Fix: remedy negation of table manipulation specification by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1186
Added an endpoint to check entity type on Synapse and an endpoint to check if an entity is in the asset view by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1078
add restrict rules control to manifest validate by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1189
Added a parameter to control if GE gets used when using manifest/validate endpoint by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1177
Propagate logger level entered in from command line to other schematic submodules by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1180
Add timing of validation operations to DEBUG log by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1181
Standardize validation error format and type by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1183
Added function to calculate and clear cache by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1190
Develop add file only manifest submission option by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1175
Create example data model for single rule benchmarking by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1193
Develop api tests for benchmarking single rule validation performance by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1184
Fixed column headers problem when generating an Excel spreadsheet for getting an existing manifest by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1164
Do not index attribute visualization dataframe when converting to csv for component viz endpoint by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1196
Remove restrictions on rule number and allowed combinations by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1203
Start checking mypy and black by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1204
Add IsNA rule to validation suite | FDS-81 FDS-232 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1200
Add API endpoint to visualize attributes for a specific component by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1195
Added functionality to download a manifest by using the manifest id by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1192
Introduce workflow for API tests by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1208
Remove requirement for .synapseConfig file to use upsert feature by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1207
Parallelize operations in load_df by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1100
Id Column - fix bug preventing table updates by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1214
Id Column - fix bug where there would be two columns with uuid values by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1215
Merge AWS deployment branch to develop by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1142
Id Column - fix bug preventing upserts by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1216
Downloaded manifests to temporary folders on AWS by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1210
FDS-293 Fix column mismatch for Excel File Based Manifest Generation by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1213
Feature fds 361 pylint by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1212
Changed workflow to run poetry version 1.2.0 by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1222
remove breakpoint from command by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1224
Restrict typing-extensions package to versions before v4.6.0 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1228
Make aws group dependencies optional and restrict typing_extensions package version by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1227
Change Uuid column name to Id by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1211
Avoided publishing minor releases to Docker Hub by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1231
Remove lock on schematic_db version - FDS-287 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1232
feat: added nginx to encrypt the communication between ALB and API by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1202
Installed schematic in docker file by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1230
fix: Fixed unit test in test_manifest by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1233
Fix formatting issues when pulling data from Synapse to Excel Manifest by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1234
fix: fixed tests in test_api.py by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1225
Added test manifest by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1238
[Bug fix]: Tried install pdoc again in github action workflow pdoc.yml by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1239
Replaced synapse API calls with synapse Python client call by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1235
Feat: allowed production tag, staging tag, and manual run on existing tags to trigger building docker images for AWS deployment by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1241
Added hide-blanks parameter when submitting manifest through API by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1242
Revert "Feat: allowed production tag, staging tag, and manual run on existing tags to trigger building docker images for AWS deployment" by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1243
feat: allowed production tag, staging tag, and manual run on existing tags to trigger building docker images for AWS deployment by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1244
[Bug fix]: Fix regex in docker build workflow by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1246
Revert "[Bug fix]: Fix regex in docker build workflow" by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1248
[Bug fix]: Fix regex in docker build workflow by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1249
Feature fds 273 coniguration by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1219
Expose strict_validation option for manifest/generate endpoint by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1253
Optimize performance in table upsert backwards compatibility scenarios by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1229
Fix df_utils/load_df so it more accurately captures integers to prevent Regex Errors. by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1240
Use FAIR Data service desk for issues by @afwillia in https://github.com/Sage-Bionetworks/schematic/pull/1257
Update Black to 2023 version: 23.7.0 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1262
Update mypy to latest version by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1263
Updated cli help text for parameter json_schema by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1264
Modified Nginx parameters to fix submission issue by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1255
modify tag by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1251
BugFix: Fixed an issue where files on synapse were not being annotated correctly by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1254
[bug fix] Fixed errors when calling get_empty_manifest by @linglp in https://github.com/Sage-Bionetwork
ncihtan/data-models: v23.12.1
<h2>What's Changed</h2>
<ul>
<li>Add HTAN ID validation rules by @adamjtaylor in https://github.com/ncihtan/data-models/pull/304</li>
<li>Update CI tests and add pre-commit by @adamjtaylor in https://github.com/ncihtan/data-models/pull/287</li>
<li>Remove obselete workflow by @adamjtaylor in https://github.com/ncihtan/data-models/pull/329</li>
<li>Add DCA template JSON by @adamjtaylor in https://github.com/ncihtan/data-models/pull/330</li>
<li>Fix filename regex by @adamjtaylor in https://github.com/ncihtan/data-models/pull/327</li>
<li>Revert to basic filename regex by @adamjtaylor in https://github.com/ncihtan/data-models/pull/333</li>
<li>Return protein and metabolite to Analyte Type by @adamjtaylor in https://github.com/ncihtan/data-models/pull/336</li>
<li>Remove ORCID ID validation rule by @adamjtaylor in https://github.com/ncihtan/data-models/pull/335</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/ncihtan/data-models/compare/v23.11.1...v23.12.1</p>
Sage-Bionetworks/schematic: v23.9.3
What's Changed
BugFix: is_class_in_schema no longer errors out when a class is not in schema by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1287
BugFix: Fix error when use_annotations=True for record based metadata where there are no existing annotations by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1285
Bug Fix: Adding annotations to files with -mrt file_only parameter by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1290
Develop markers for api tests according to credentials required FDS-1026 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1289
Full Changelog: https://github.com/Sage-Bionetworks/schematic/compare/v23.9.2...v23.9.
Sage-Bionetworks/synapsePythonClient: v3.1.1
<h2>What's Changed</h2>
<ul>
<li>[SYNPY-1298] Update annotation logic by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/995</li>
<li>[SYNPY-1299] Clean up contributing.md by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/996</li>
<li>[SYNPY-1299] Update contributing.md to point to service desk by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/997</li>
<li>[SYNPY-1316] Fix for cache item names matching by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/998</li>
<li>[SYNPY-1298] flakey integration tests by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/999</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/Sage-Bionetworks/synapsePythonClient/compare/v3.1.0...v3.1.1-rc</p>
Sage-Bionetworks/synapsePythonClient: v3.1.0-rc
<h2>What's Changed</h2>
<ul>
<li>[SYNPY-49] Aggregate acl based on groups by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/979</li>
<li>[SYNPY-967] deprecated memoize and added @lru_cache by @BryanFauble, @linglp in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/983</li>
<li>SYNPY-1285: Create pipfile by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/984</li>
<li>[SYNPY-1282] Adds Type Hinting to <code>client.py</code> by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/987</li>
<li>[SYNPY-1293] Update urllib3 version dependency by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/988</li>
<li>[SYNPY-1283] Replace Broken Link URL by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/989</li>
<li>[SYNPY-1296] Config client error with api key or PAT by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/990* * [SYNPY-1283] Adds Missing Trailing Space (Broken Link Fix) by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/991</li>
<li>[SYNPY-1295] Adding to the credentials.rst doc by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/992</li>
</ul>
<h2>New Contributors</h2>
<ul>
<li>@BryanFauble made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/979</li>
<li>@BWMac made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/987</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/Sage-Bionetworks/synapsePythonClient/compare/v3.0.0...v3.1.0-rc</p>
Sage-Bionetworks/synapsePythonClient: v4.0.0-rc
<h2>Highlights</h2>
<ul>
<li><strong>Only authentication through Personal Access Token</strong>
<strong>(aka: Authentication bearer token) is supported</strong>. Review the <a href="https://python-docs.synapse.org/tutorials/authentication/">Authentication document</a> for information on setting up your usage of a Personal Access Token to authenticate with Synapse.</li>
<li><strong>Date type Annotations on Synapse entities are now timezone aware</strong>. Review our <a href="https://python-docs.synapse.org/reference/annotations/">reference documentation for Annotations</a>. The <a href="https://pypi.org/project/pytz/"><code>pytz</code> package</a> is reccomended if you regularly work with data across time zones.<ul>
<li>If you do not set the <code>tzinfo</code> field on a date or datetime instance we will use the timezone of the machine where the code is executing.</li>
<li>If you are using the <a href="https://python-docs.synapse.org/explanations/manifest_tsv/#annotations">Manifest TSV</a> for bulk actions on your projects you'll now see that [synapseutils.sync.syncFromSynapse][] will store dates as <code>YYYY-MM-DDTHH:MM:SSZ</code>. Review our documentation for an <a href="https://python-docs.synapse.org/explanations/manifest_tsv/#example-manifest-file">example manifest file</a>. Additionally, if you'd like to upload an annotation in a specific timezone please make sure that it is in <a href="https://en.wikipedia.org/wiki/ISO_8601">ISO 8601 format</a>. If you do not specify a timezone it is assumed to use the timezone of the machine where the code is executing.</li>
</ul>
</li>
<li><strong>Support for annotations with multiple values through the</strong> <a href="https://python-docs.synapse.org/explanations/manifest_tsv/#multiple-values-of-annotations-per-key"><strong>Manifest TSV</strong></a> with the usage of a comma delimited bracket wrapped list. Any manifest files wishing to take advantage of multi-value annotations need to match this format. Examples:<ul>
<li><code>["Annotation, with a comma", another annotation]</code></li>
<li><code>[1,2,3]</code></li>
<li><code>[2023-12-04T07:00:00Z,2000-01-01T07:00:00Z]</code></li>
</ul>
</li>
<li>Migration and expansion of the docs site! You'll see that the look, feel, and flow of all of the information on this site has been touched. As we move forward we hope that you'll <a href="https://sagebionetworks.jira.com/servicedesk/customer/portal/5/group/7">provide the Data Processing and Engineering team feedback on areas we can improve</a>.</li>
<li>Expansion of the available Python Tutorials can be found <a href="https://python-docs.synapse.org/tutorials/python_client/">starting here</a>.</li>
</ul>
<h2>What's Changed</h2>
<ul>
<li>Adding a label to the dockerfile to automatically label it for this repo by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1018</li>
<li>Updates Dockerfile to Correctly Install Dependencies by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1019</li>
<li>[SYNPY-1358] Correction of timestamp in annotations from manifest file by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1020</li>
<li>[SYNPY-1336] Benchmarking upload with annotations by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1021</li>
<li>[SYNPY-1321] Download benchmark results by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1024</li>
<li>[SYNPY-1360] Migrating to mkdocstrings by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1025</li>
<li>[SYNPY-1366] Add code coverage by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1029</li>
<li>[SYNPY-1362] High level best practices for project structure by @thomasyu888 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1028</li>
<li>[SYNPY-1371] Migrate to Google Style by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1033</li>
<li>[SYNPY-1302] Replace getPermission with get_acl and add new get_permissions by @danlu1 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1037</li>
<li>[SYNPY-1334] Revamp getting started docs by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1036</li>
<li>[SYNPY-1332] Pypi deployment strategy by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1038</li>
<li>[SYNPY-1370] Documentation Upgrade by @jaymedina in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1032</li>
<li>[SYNPY-1370] Minor formatting fixes by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1039</li>
<li>[SYNPY-1371] Doc fixes by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1040</li>
<li>[SYNPY-1225] Support authToken only by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1041</li>
<li>[SYNPY-1392] Remove some deprecated pieces by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1043</li>
<li>[Synpy 1369] Migrate to Google style by @danlu1 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1042</li>
<li>[SYNPY-1387] Update Structure Project doc by @danlu1 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1044</li>
<li>[SYNPY-1357] Allow multiple values in manifest TSV by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1030</li>
</ul>
<h2>New Contributors</h2>
<ul>
<li>@jaymedina made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1032</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/Sage-Bionetworks/synapsePythonClient/compare/v3.2.0...v4.0.0-rc</p>
Sage-Bionetworks/synapsePythonClient: v4.0.0-rc
<h2>Highlights</h2>
<ul>
<li><strong>Only authentication through Personal Access Token</strong>
<strong>(aka: Authentication bearer token) is supported</strong>. Review the <a href="https://python-docs.synapse.org/tutorials/authentication/">Authentication document</a> for information on setting up your usage of a Personal Access Token to authenticate with Synapse.</li>
<li><strong>Date type Annotations on Synapse entities are now timezone aware</strong>. Review our <a href="https://python-docs.synapse.org/reference/annotations/">reference documentation for Annotations</a>. The <a href="https://pypi.org/project/pytz/"><code>pytz</code> package</a> is reccomended if you regularly work with data across time zones.<ul>
<li>If you do not set the <code>tzinfo</code> field on a date or datetime instance we will use the timezone of the machine where the code is executing.</li>
<li>If you are using the <a href="https://python-docs.synapse.org/explanations/manifest_tsv/#annotations">Manifest TSV</a> for bulk actions on your projects you'll now see that [synapseutils.sync.syncFromSynapse][] will store dates as <code>YYYY-MM-DDTHH:MM:SSZ</code>. Review our documentation for an <a href="https://python-docs.synapse.org/explanations/manifest_tsv/#example-manifest-file">example manifest file</a>. Additionally, if you'd like to upload an annotation in a specific timezone please make sure that it is in <a href="https://en.wikipedia.org/wiki/ISO_8601">ISO 8601 format</a>. If you do not specify a timezone it is assumed to use the timezone of the machine where the code is executing.</li>
</ul>
</li>
<li><strong>Support for annotations with multiple values through the</strong> <a href="https://python-docs.synapse.org/explanations/manifest_tsv/#multiple-values-of-annotations-per-key"><strong>Manifest TSV</strong></a> with the usage of a comma delimited bracket wrapped list. Any manifest files wishing to take advantage of multi-value annotations need to match this format. Examples:<ul>
<li><code>["Annotation, with a comma", another annotation]</code></li>
<li><code>[1,2,3]</code></li>
<li><code>[2023-12-04T07:00:00Z,2000-01-01T07:00:00Z]</code></li>
</ul>
</li>
<li>Migration and expansion of the docs site! You'll see that the look, feel, and flow of all of the information on this site has been touched. As we move forward we hope that you'll <a href="https://sagebionetworks.jira.com/servicedesk/customer/portal/5/group/7">provide the Data Processing and Engineering team feedback on areas we can improve</a>.</li>
<li>Expansion of the available Python Tutorials can be found <a href="https://python-docs.synapse.org/tutorials/python_client/">starting here</a>.</li>
</ul>
<h2>What's Changed</h2>
<ul>
<li>Adding a label to the dockerfile to automatically label it for this repo by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1018</li>
<li>Updates Dockerfile to Correctly Install Dependencies by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1019</li>
<li>[SYNPY-1358] Correction of timestamp in annotations from manifest file by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1020</li>
<li>[SYNPY-1336] Benchmarking upload with annotations by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1021</li>
<li>[SYNPY-1321] Download benchmark results by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1024</li>
<li>[SYNPY-1360] Migrating to mkdocstrings by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1025</li>
<li>[SYNPY-1366] Add code coverage by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1029</li>
<li>[SYNPY-1362] High level best practices for project structure by @thomasyu888 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1028</li>
<li>[SYNPY-1371] Migrate to Google Style by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1033</li>
<li>[SYNPY-1302] Replace getPermission with get_acl and add new get_permissions by @danlu1 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1037</li>
<li>[SYNPY-1334] Revamp getting started docs by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1036</li>
<li>[SYNPY-1332] Pypi deployment strategy by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1038</li>
<li>[SYNPY-1370] Documentation Upgrade by @jaymedina in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1032</li>
<li>[SYNPY-1370] Minor formatting fixes by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1039</li>
<li>[SYNPY-1371] Doc fixes by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1040</li>
<li>[SYNPY-1225] Support authToken only by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1041</li>
<li>[SYNPY-1392] Remove some deprecated pieces by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1043</li>
<li>[Synpy 1369] Migrate to Google style by @danlu1 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1042</li>
<li>[SYNPY-1387] Update Structure Project doc by @danlu1 in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1044</li>
<li>[SYNPY-1357] Allow multiple values in manifest TSV by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1030</li>
</ul>
<h2>New Contributors</h2>
<ul>
<li>@jaymedina made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/1032</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/Sage-Bionetworks/synapsePythonClient/compare/v3.2.0...v4.0.0-rc</p>
Sage-Bionetworks/synapsePythonClient: v3.1.0-rc
<h2>What's Changed</h2>
<ul>
<li>[SYNPY-49] Aggregate acl based on groups by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/979</li>
<li>[SYNPY-967] deprecated memoize and added @lru_cache by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/983</li>
<li>SYNPY-1285: Create pipfile by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/984</li>
<li>[SYNPY-1282] Adds Type Hinting to <code>client.py</code> by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/987</li>
<li>[SYNPY-1293] Update urllib3 version dependency by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/988</li>
<li>[SYNPY-1283] Replace Broken Link URL by @BWMac in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/989</li>
<li>[SYNPY-1296] Config client error with api key or PAT by @BryanFauble in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/990</li>
</ul>
<h2>New Contributors</h2>
<ul>
<li>@BryanFauble made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/979</li>
<li>@BWMac made their first contribution in https://github.com/Sage-Bionetworks/synapsePythonClient/pull/987</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/Sage-Bionetworks/synapsePythonClient/compare/v3.0.0...v3.1.0-rc</p>