Ecosyste.ms: Issues

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GitHub / omicidx/omicidx-parsers issues and pull requests

#30 - Look for missing `element.clear()`s to avoid memory leaks

Issue - State: open - Opened by seandavi almost 2 years ago
Labels: bug

#29 - Bump certifi from 2021.10.8 to 2022.12.7

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#28 - Error with empty contact_web_link in omicidx.geo.parser

Issue - State: open - Opened by seandavi about 2 years ago
Labels: bug

#27 - Bump numpy from 1.21.1 to 1.22.0

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#26 - Bump httpx from 0.22.0 to 0.23.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#25 - Bump mkdocs from 1.2.2 to 1.2.3

Pull Request - State: open - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#24 - Bump ujson from 4.2.0 to 5.1.0

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#23 - License?

Issue - State: open - Opened by mukund109 about 4 years ago - 1 comment

#22 - Pull in ontology tables for easy attribute mapping

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

#21 - add UMLS tables for metamap enrichment

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

#20 - GSE24417 is a "reanalysis" series. No samples or platform entries are available

Issue - State: open - Opened by seandavi almost 5 years ago
Labels: bug

#19 - Tag aligned reads as aligned

Issue - State: open - Opened by seandavi almost 5 years ago - 1 comment
Labels: enhancement

#18 - Enhance biosample metadata during parsing and building

Issue - State: open - Opened by seandavi almost 5 years ago
Labels: enhancement

#17 - refactor elasticsearch stuff from omicidx to omicidx-builder

Issue - State: closed - Opened by seandavi about 5 years ago
Labels: enhancement

#16 - Mismatches between bigquery SRA schema descriptions and pydantic models

Issue - State: closed - Opened by seandavi about 5 years ago
Labels: bug

#15 - add pydantic model for biosample

Issue - State: open - Opened by seandavi about 5 years ago

#14 - Refactor biosample.py to biosample/parser.py

Issue - State: open - Opened by seandavi about 5 years ago

#13 - Migrate bigquery and es schema data to omicidx-builder

Issue - State: closed - Opened by seandavi about 5 years ago
Labels: enhancement

#12 - Normalize return types in geo parser

Issue - State: open - Opened by seandavi about 5 years ago

#11 - Tests for geo parser

Issue - State: closed - Opened by seandavi about 5 years ago
Labels: enhancement

#10 - GSE24314 lists SRX values as "relations".

Issue - State: open - Opened by seandavi about 5 years ago
Labels: bug

#9 - Refactor `sra_parsers.py` to `sra/parser.py`

Issue - State: closed - Opened by seandavi about 5 years ago
Labels: enhancement

#8 - Refactor `geometa.py` to `geo/parser.py`

Issue - State: closed - Opened by seandavi about 5 years ago
Labels: enhancement

#7 - Migrate geo command-line parsing to omicidx-builder

Issue - State: open - Opened by seandavi about 5 years ago
Labels: enhancement

#6 - SRA project accessions can be ERP or SRP

Issue - State: closed - Opened by seandavi about 5 years ago

#5 - Some GEO channel characteristics are not key/value pairs

Issue - State: closed - Opened by seandavi about 5 years ago

#4 - Web addresses in GEO contact entries do not always include http

Issue - State: closed - Opened by seandavi about 5 years ago - 1 comment

#3 - add command-line for elasticsearch indexing

Issue - State: closed - Opened by seandavi about 5 years ago - 1 comment

#2 - Parse experiment_links to get experiment pubmeds

Issue - State: closed - Opened by seandavi over 6 years ago - 1 comment

#1 - A few EXPERIMENT_PACKAGES have no STUDY, only STUDY_REF

Issue - State: closed - Opened by seandavi over 6 years ago - 1 comment