SciCrunch/sparc-curation issues and pull requests

#120 - objects parent_id list duplicates dataset

Issue - State: open - Opened by tgbugs 4 months ago

#119 - dataset template workflow cannot preserve rich text cells

Issue - State: open - Opened by tgbugs 5 months ago - 1 comment
Labels: dataset-template

#118 - remote dataset updated no longer tracks file changes

Issue - State: open - Opened by tgbugs 8 months ago - 2 comments

#117 - add preliminary dataset dictionary approach

Issue - State: closed - Opened by tgbugs 12 months ago
Labels: dataset-template

#115 - if protocols are provided in subjects/samples sheets related identifiers protocol is not required

Issue - State: open - Opened by tgbugs 12 months ago

#114 - sds 3.0 add dataset description level relation type that works like also in dataset for subjects

Issue - State: closed - Opened by tgbugs about 1 year ago
Labels: dataset-template

#113 - curation viewer figure out how to indicate that a dataset is still downloading

Issue - State: open - Opened by tgbugs about 1 year ago

#112 - single dataset pipelines automate update of published index

Issue - State: open - Opened by tgbugs about 1 year ago - 3 comments

#111 - Offline Message from Maryann Martone: Why are none of these terms annotated e

Issue - State: closed - Opened by SciCrunch-Synapse about 1 year ago - 1 comment
Labels: Zendesk

#110 - update meta species field to regularize structure

Issue - State: open - Opened by tgbugs over 1 year ago

#109 - sds 3.0 make sure we have a place for license

Issue - State: closed - Opened by tgbugs over 1 year ago
Labels: dataset-template

#108 - sds 3.0 add aux folder

Issue - State: closed - Opened by tgbugs over 1 year ago
Labels: dataset-template

#107 - discover sourceDatasetId is not unique, needs organizationId as well

Issue - State: closed - Opened by tgbugs over 1 year ago

#106 - need a curator notes file of some kind

Issue - State: closed - Opened by tgbugs over 1 year ago - 2 comments
Labels: dataset-template

#105 - dataset template 3.0.0 freeze first row or first column

Issue - State: closed - Opened by tgbugs over 1 year ago
Labels: dataset-template

#104 - Add files via upload - Split_Excel_Sheet.ipynb

Pull Request - State: closed - Opened by Yugine09 over 1 year ago

#103 - template 3.0.0 ensure relevant submission metadata and field alignment organs sheet have a home in metadata files

Issue - State: closed - Opened by tgbugs over 1 year ago
Labels: dataset-template

#102 - Create split_excel_sheet.py

Pull Request - State: closed - Opened by SPra03 over 1 year ago - 3 comments

#101 - Offline Message from Maryann Martone: There are a whole bunch of terms here t

Issue - State: open - Opened by SciCrunch-Synapse over 1 year ago
Labels: Zendesk

#100 - sds 3.0.0 file name restrictions

Issue - State: open - Opened by tgbugs over 1 year ago

#99 - template 3.0.0 make it possible to specify modality in manifest instead of as folder

Issue - State: closed - Opened by tgbugs over 1 year ago
Labels: dataset-template

#98 - template 3.0.0 possibly add prot- folder for protocol type

Issue - State: open - Opened by tgbugs almost 2 years ago - 1 comment

#97 - align/normalize wasDerivedFrom (and related) columns from manifests when they refer to other dataset ids

Issue - State: closed - Opened by tgbugs about 2 years ago - 2 comments
Labels: dataset-template

#96 - dataset description processing doesn't detect orcid/affil swap

Issue - State: open - Opened by tgbugs about 2 years ago

#95 - Non-existent link in documentation

Issue - State: closed - Opened by dbrnz about 2 years ago - 1 comment

#94 - Please provide a link to a sample Cypher query for getting species information about connectivity models

Issue - State: closed - Opened by dbrnz about 2 years ago - 12 comments

#93 - Please provide links to sample Cypher queries for getting SCKAN version information

Issue - State: closed - Opened by dbrnz about 2 years ago - 2 comments

#92 - Link to example query to get model version is broken

Issue - State: closed - Opened by dbrnz about 2 years ago - 4 comments

#91 - stale doi issue -> sparcron needs to add logic to check discover for publication events

Issue - State: open - Opened by tgbugs about 2 years ago - 2 comments

#90 - dataset template 3.0.0 needs to include metadata-only column for specimens

Issue - State: closed - Opened by tgbugs about 2 years ago - 2 comments
Labels: dataset-template

#89 - improvements to the dataset structure validator for 1.2.3 trasition

Issue - State: closed - Opened by tgbugs about 2 years ago

#88 - Connectivity for Ardell path 12 is missing from production SCKAN

Issue - State: closed - Opened by dbrnz over 2 years ago - 3 comments

#87 - schema not producing errors for malformed dates in the input schema, only ir

Issue - State: open - Opened by tgbugs over 2 years ago

#86 - dataset template 3.0.0 needs to differentiate sites from performances and samples

Issue - State: closed - Opened by tgbugs over 2 years ago - 1 comment
Labels: dataset-template

#85 - Update overview.org

Pull Request - State: closed - Opened by stappan over 2 years ago - 1 comment

#84 - dataset template 2.0.1 needs to restore description

Issue - State: closed - Opened by tgbugs almost 3 years ago
Labels: dataset-template

#83 - folder names with dots in them are truncated

Issue - State: closed - Opened by tgbugs almost 3 years ago - 1 comment

#82 - embed rdfs:label in curation export ttl

Issue - State: closed - Opened by tgbugs almost 3 years ago - 1 comment

#81 - Paxinos spinal cord atlas import

Issue - State: closed - Opened by SciCrunch-Synapse over 3 years ago - 1 comment
Labels: Zendesk

#80 - sympathetic ganglion children

Issue - State: closed - Opened by SciCrunch-Synapse over 3 years ago - 1 comment
Labels: Zendesk

#79 - collections with period `.` in name drop everything after the `.`

Issue - State: closed - Opened by tgbugs over 3 years ago - 1 comment

#78 - Additional method for installing emacs on Windows

Pull Request - State: closed - Opened by megasanjay over 3 years ago - 2 comments

#77 - total connectivity query

Issue - State: open - Opened by tgbugs over 3 years ago - 2 comments

#76 - Curation Export: Unpublished dataset showed as published

Issue - State: closed - Opened by deepali-2018 over 3 years ago - 2 comments
Labels: invalid

#75 - segmentation -> image mapping

Issue - State: open - Opened by tgbugs over 3 years ago - 2 comments

#74 - New terms to distinguish additional URLs in a dataset

Issue - State: open - Opened by agarny over 3 years ago - 5 comments

#73 - explore loading and converting ephys files using neo

Issue - State: open - Opened by tgbugs almost 4 years ago

#72 - git commit hash not in curation export prov?

Issue - State: open - Opened by tgbugs almost 4 years ago

#71 - query update for sparc

Pull Request - State: closed - Opened by tmsincomb almost 4 years ago - 1 comment

#70 - resolve formulas in manifest and metadata files

Issue - State: open - Opened by tgbugs almost 4 years ago

#69 - first pass

Pull Request - State: closed - Opened by tmsincomb almost 4 years ago - 1 comment

#68 - "U01" awards are valid SPARC awards code is not recognizing

Issue - State: closed - Opened by ankap2 almost 4 years ago - 1 comment

#67 - extend additional links to related identifiers for dataset description file

Issue - State: closed - Opened by tgbugs about 4 years ago
Labels: dataset-template

#66 - log a curation error if protocols.io identifier does not have a doi

Issue - State: open - Opened by tgbugs over 4 years ago

#65 - common source for sparc mappings

Issue - State: open - Opened by tgbugs over 4 years ago

#64 - term set workflow

Issue - State: open - Opened by tgbugs over 4 years ago

#63 - modelling for models

Issue - State: open - Opened by tgbugs over 4 years ago - 2 comments
Labels: MIS

#62 - regularize manifest structure

Issue - State: closed - Opened by tgbugs over 4 years ago - 1 comment
Labels: dataset-template

#61 - create a schema for computational datasets with slightly different requirements

Issue - State: open - Opened by tgbugs over 4 years ago

#60 - add model_id parameter to ApiNATOMY queries

Issue - State: open - Opened by tgbugs over 4 years ago
Labels: ApiNATOMY

#59 - elements in the objects cache can become corrupted

Issue - State: closed - Opened by tgbugs over 4 years ago - 1 comment

#58 - align animalSubjectIsOfSpecies to NCBITaxon

Issue - State: closed - Opened by tgbugs over 4 years ago - 1 comment

#57 - add a command to check all permissions configurations

Issue - State: open - Opened by tgbugs over 4 years ago

#56 - spc --help ...HELP on Windows!!

Issue - State: open - Opened by MCSZ over 4 years ago - 2 comments

#55 - separate data tests from unit tests

Issue - State: open - Opened by tgbugs over 4 years ago

#54 - Organ information in metadata is blank for all datasets

Issue - State: closed - Opened by jgrethe over 4 years ago - 10 comments
Labels: bug

#53 - how to deal with integer subject and sample ids?

Issue - State: open - Opened by tgbugs over 4 years ago - 5 comments

#52 - Need Updated List of RRID's used for in the SPARC datasets (ASAP plz)

Issue - State: closed - Opened by gabimpine over 4 years ago

#51 - always use idlib.Pio.uri_api_int as the identifier for protocols if it is available

Issue - State: closed - Opened by tgbugs over 4 years ago - 4 comments

#50 - Switch from using .operations/objects to store remote blobs to a folder in ~/.cache/sparcur/.

Issue - State: closed - Opened by tgbugs over 4 years ago - 1 comment

#49 - ApiNATOMY queries for flatmaps

Issue - State: closed - Opened by tgbugs over 4 years ago - 1 comment
Labels: ApiNATOMY

#48 - convert ttl export pipeline to use json-ld intermediate

Issue - State: open - Opened by tgbugs over 4 years ago - 1 comment

#47 - protbot

Issue - State: closed - Opened by tgbugs over 4 years ago - 1 comment

#46 - lifters and sheets sourced metadata should come from protocol curation workflow

Issue - State: open - Opened by tgbugs over 4 years ago

#45 - curation-export.ttl documentation

Issue - State: closed - Opened by tgbugs over 4 years ago - 1 comment

#44 - mis-accounting

Issue - State: open - Opened by tgbugs over 4 years ago - 1 comment

#43 - file level metadata export integration

Issue - State: open - Opened by tgbugs over 4 years ago - 1 comment

#42 - protcur export integration

Issue - State: open - Opened by tgbugs over 4 years ago

#41 - MIS2.0 release

Issue - State: closed - Opened by tgbugs over 4 years ago - 1 comment

#40 - Gspread Integration

Issue - State: closed - Opened by tmsincomb over 4 years ago - 2 comments
Labels: enhancement

#39 - Adding a Sheet Column

Issue - State: closed - Opened by tmsincomb over 4 years ago - 4 comments
Labels: enhancement

#38 - streamline ApiNATOMY xlsx -> SciGraph pipeline so that it does not need human intervation

Issue - State: closed - Opened by tgbugs over 4 years ago - 1 comment
Labels: ApiNATOMY

#37 - Sparc Protcur GoogleSheet update

Pull Request - State: open - Opened by tmsincomb over 4 years ago

#36 - sporadic failure to fetch files results in files of zero size

Issue - State: open - Opened by tgbugs over 4 years ago

#35 - extract author ordering from dataset_description

Issue - State: closed - Opened by tgbugs over 4 years ago - 1 comment

#34 - strategies for preventing column removal

Issue - State: open - Opened by tgbugs over 4 years ago
Labels: dataset-template

#33 - exclude large apinatomy files from release

Issue - State: closed - Opened by tgbugs over 4 years ago - 1 comment

#32 - some rrid synonyms are blobs not strings

Issue - State: open - Opened by tgbugs over 4 years ago

#31 - Dataset-template 1.2.3

Issue - State: open - Opened by memartone over 4 years ago
Labels: dataset-template

#30 - all organ parts query addition

Pull Request - State: closed - Opened by tmsincomb almost 5 years ago - 2 comments

#29 - banned files

Issue - State: open - Opened by tgbugs almost 5 years ago - 2 comments
Labels: dataset-template

#28 - pipelines breaking network sandbox e.g. PipelineExtras.added

Issue - State: open - Opened by tgbugs almost 5 years ago

#27 - scaffold ingest issue

Issue - State: open - Opened by tgbugs almost 5 years ago - 4 comments

#26 - sparql queries

Pull Request - State: closed - Opened by tmsincomb almost 5 years ago

#25 - curation export releases tracking

Issue - State: open - Opened by tgbugs almost 5 years ago - 297 comments

#24 - https://api.blackfynn.io/datasets/N:dataset:fd07322c-ac30-488f-a6db-f5ff52c69e1b

Issue - State: closed - Opened by memartone almost 5 years ago - 1 comment

GitHub / SciCrunch/sparc-curation issues and pull requests