genomehubs/genomehubs-2.6.15.zip
genomehubs-genomehubs-e0153bd
.bumpversion.cfg
1.4 kB
.coveragerc
239 Bytes
.github
workflows
package-genomehubs-archive.yml
1.8 kB
package-genomehubs-develop.yml
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package-genomehubs.yml
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test-genomehubs.yml
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.gitignore
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.pre-commit-config.yaml
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.travis.yml
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AUTHORS
267 Bytes
AUTHORS.rst
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CHANGELOG.rst
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CONTRIBUTING.rst
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LICENSE
1.1 kB
MANIFEST.in
392 Bytes
README.rst
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_conftest.py
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bump_version.sh
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ci
bootstrap.py
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requirements.txt
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templates
.travis.yml
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conda-recipe
meta.yaml
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docs
authors.rst
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changelog.rst
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conf.py
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contributing.rst
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index.rst
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installation.rst
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readme.rst
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reference
index.rst
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requirements.txt
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spelling_wordlist.txt
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usage.rst
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examples
file_import.json
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quick_file_import.json
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logo.svg
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package-api.sh
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package-lock.json
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package-ui.sh
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package.json
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package.sh
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pip_install_latest.sh
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pyproject.toml
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requirements.txt
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run_ui_tests.py
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scripts
conda_build.sh
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lint_code.sh
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pre-commit.sh
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run_tests.sh
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test_only.sh
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tox_build.sh
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setup.cfg
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setup.py
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src
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Dockerfile
699 Bytes
api
.env
604 Bytes
Dockerfile
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goat
.env
204 Bytes
Dockerfile
591 Bytes
ui
.env
326 Bytes
Dockerfile
566 Bytes
genomehubs
__init__.py
212 Bytes
__main__.py
93 Bytes
config
dist.config.yaml
1.1 kB
genomehubs.py
1.5 kB
lib
__init__.py
26 Bytes
analysis.py
389 Bytes
attributes.py
5.0 kB
btk.py
3.9 kB
busco.py
4.9 kB
config.py
6.4 kB
directory.py
3.2 kB
es_functions.py
13.6 kB
feature.py
327 Bytes
files.py
16.9 kB
fill.py
34.3 kB
gbif.py
3.2 kB
geo.py
775 Bytes
hub.py
35.8 kB
index.py
22.5 kB
init.py
11.6 kB
ncbi.py
11.9 kB
parse.py
7.9 kB
run.py
527 Bytes
sample.py
7.3 kB
search.py
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taxon.py
37.9 kB
taxonomy.py
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test.py
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validate.py
3.5 kB
version.py
73 Bytes
wikidata.py
8.1 kB
window.py
1.9 kB
templates
ATTR_busco.types.yaml
741 Bytes
ATTR_feature.types.yaml
2.9 kB
ATTR_window_stats.types.yaml
1.1 kB
analysis.json
4.5 kB
assembly.json
15.5 kB
assembly.types.yaml
7.0 kB
attributes.json
2.5 kB
btk.types.yaml
4.2 kB
busco.types.yaml
1.1 kB
busco_feature.types.yaml
1.5 kB
feature.json
9.9 kB
file.json
3.4 kB
identifiers.json
1.2 kB
organelle.types.yaml
2.7 kB
sample.json
10.7 kB
sample.types.yaml
3.4 kB
scripts
analysis_lookup.json
499 Bytes
analysis_suggest.json
499 Bytes
assembly_lookup.json
1.2 kB
assembly_suggest.json
1.4 kB
attribute_types_by_group.json
168 Bytes
attribute_value_by_primary_id.json
858 Bytes
attribute_values_by_taxon.json
2.5 kB
attributes_by_keyword_value.json
360 Bytes
attributes_identifiers_by_keyword_value.json
224 Bytes
attributes_names_by_keyword_value.json
360 Bytes
file_lookup.json
499 Bytes
file_suggest.json
499 Bytes
max_nested_value.json
307 Bytes
max_nested_value_by_key_value.json
490 Bytes
max_nested_value_by_type.json
882 Bytes
max_nested_value_by_type_by_lineage.json
1.2 kB
search_by_ancestral_taxon.json
855 Bytes
search_by_taxon.json
500 Bytes
taxon_attributes_by_root_depth.json
993 Bytes
taxon_attributes_by_taxon_id.json
279 Bytes
taxon_by_any_name.json
1.0 kB
taxon_by_any_name_by_lineage.json
1.7 kB
taxon_by_lineage.json
1.2 kB
taxon_by_name.json
585 Bytes
taxon_by_specific_name.json
828 Bytes
taxon_lookup.json
1.3 kB
taxon_lookup_by_lineage.json
1.8 kB
taxon_missing_attribute_by_ancestor_id.json
1.7 kB
taxon_name_sayt_attribute.json
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taxon_names.json
281 Bytes
taxon_names_by_root.json
499 Bytes
taxon_suggest.json
1.4 kB
taxonomy_node_by_taxon_id.json
382 Bytes
value_by_type_by_lineage.json
994 Bytes
taxon.json
18.2 kB
taxon.types.yaml
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taxonomy.json
3.1 kB
wikidata.names.yaml
355 Bytes
window_full.types.yaml
1.1 kB
window_stats.types.yaml
1.3 kB
genomehubs-api
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678 Bytes
.gitignore
32 Bytes
AUTHORS
259 Bytes
LICENSE
1.1 kB
README.md
482 Bytes
package-lock.json
233.2 kB
package.json
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package.sh
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src
api
v2
functions
aInB.js
96 Bytes
addCondition.js
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attrTypes.js
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cache.js
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checkDocResponse.js
482 Bytes
checkResponse.js
761 Bytes
combineQueries.js
497 Bytes
config.js
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connection.js
148 Bytes
fetchIndices.js
591 Bytes
fetchTaxonomies.js
648 Bytes
formatCsv.js
3.8 kB
formatJson.js
138 Bytes
generateQuery.js
15.9 kB
getRecordsById.js
3.0 kB
getRecordsByTaxon.js
3.2 kB
getResultCount.js
568 Bytes
getResults.js
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indexName.js
813 Bytes
logger.js
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lookupAlternateIds.js
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memcached.js
373 Bytes
operations.js
254 Bytes
parseFields.js
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processDoc.js
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processHits.js
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progress.js
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qs.js
3.0 kB
redis.js
344 Bytes
setExclusions.js
557 Bytes
setRanks.js
275 Bytes
subsets.js
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summaries.js
78 Bytes
queries
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396 Bytes
aggregateRanks.js
383 Bytes
aggregateRawValueSources.js
2.0 kB
aggregateRawValuesByTaxon.js
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histogramAgg.js
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queryFragments
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excludeSources.js
2.3 kB
filterAssemblies.js
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filterAttributes.js
7.0 kB
filterIdentifiers.js
689 Bytes
filterProperties.js
744 Bytes
filterSamples.js
1.8 kB
filterTaxId.js
277 Bytes
filterTaxa.js
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limitDepth.js
265 Bytes
matchAttributes.js
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matchNames.js
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matchRanks.js
1.2 kB
restrictToRank.js
169 Bytes
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530 Bytes
setAggregationSource.js
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setIncludes.js
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setSortOrder.js
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saytQuery.js
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suggestQuery.js
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reports
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71 Bytes
getBounds.js
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getCatLabels.js
880 Bytes
histogram.js
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incrementDate.js
161 Bytes
incrementFloat.js
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map.js
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oxford.js
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precision.js
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queryParams.js
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scaleBuckets.js
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scales.js
201 Bytes
setAggs.js
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setScale.js
465 Bytes
setTerms.js
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tree.js
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valueTypes.js
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routes
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490 Bytes
download.js
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indices.js
424 Bytes
lookup.js
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progress.js
772 Bytes
record.js
480 Bytes
report.js
27.2 kB
resultFields.js
965 Bytes
search.js
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summary.js
2.3 kB
taxonomies.js
436 Bytes
api-v2.yaml
45.4 kB
app.js
4.1 kB
genomehubs-ui
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482 Bytes
.eslintrc.json
250 Bytes
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37 Bytes
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54 Bytes
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AUTHORS
259 Bytes
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463 Bytes
LICENSE
1.1 kB
README.md
42 Bytes
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1.2 MB
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4.2 kB
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57 Bytes
src
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favicon-16x16.png
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manifest.json
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mstile-150x150.png
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index.html
685 Bytes
static
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api.md
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explore.md
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landing.md
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record.md
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sources.md
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tabs.md
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views
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AttributeTableRow.jsx
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Tabs.jsx
807 Bytes
TabsFixed.jsx
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ZoomComponent.jsx
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ZoomControl.jsx
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_colors.scss
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img
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bbsrc-logo.png
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browse.png
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darwin-tree.png
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tutorial.png
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functions
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charWidth.js
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formatter.js
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sortByFrequency.js
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stringLength.js
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dispatchGeography.jsx
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514 Bytes
dispatchLookup.jsx
840 Bytes
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dispatchReport.jsx
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withExpansion.scss
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397 Bytes
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useVisible.jsx
640 Bytes
useWindowDimensions.jsx
632 Bytes
index.jsx
758 Bytes
querySync.jsx
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reducers
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api.js
587 Bytes
archive.js
254 Bytes
autocomplete.js
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color
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batlowS.js
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paired12.js
463 Bytes
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file.js
2.9 kB
geography.js
734 Bytes
history.js
168 Bytes
location.js
5.7 kB
lookup.js
1.0 kB
map.js
43 Bytes
message.js
604 Bytes
pages.js
1.0 kB
record.js
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report.js
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root.js
1.6 kB
routes.js
517 Bytes
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selectorCreators.js
499 Bytes
taxonomy.js
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types.js
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selectors
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checkProgress.js
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file.js
1.2 kB
pages.js
1.3 kB
record.js
590 Bytes
report.js
28.3 kB
routes.js
434 Bytes
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taxonomy.js
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tree.js
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types.js
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store.jsx
437 Bytes
config
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webpack.config.js
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packaged-ui
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package.json
678 Bytes
package.sh
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src
app.js
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tests
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19 Bytes
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infile
17 Bytes
infile.gz
44 Bytes
integration_tests
config
config.yaml
440 Bytes
data
assembly-data
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ncbi_datasets_eukaryota.types.yaml
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ncbi_datasets_tests
9612-has-assembly.yaml
502 Bytes
GCA_905319855.2-has-unique-entries.yaml
321 Bytes
refseq_organelles.tsv.gz
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refseq_organelles.types.yaml
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assembly-data-taxon
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ncbi_datasets_eukaryota_taxon.types.yaml
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btk.tsv
902 Bytes
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btk.types.yaml
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btk_tests
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502 Bytes
GCA_905319855.2-has-unique-entries.yaml
321 Bytes
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CAJNRB02.busco.metazoa_odb10.full_table.tsv
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CAJNRB02.window_stats.tsv
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FILE_window_stats.types.yaml
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nigon
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ASM1342590v1.window_stats.tsv
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ATTR_busco.types.yaml
720 Bytes
ATTR_feature.types.yaml
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ATTR_nigon.types.yaml
353 Bytes
ATTR_window_stats.types.yaml
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FILE_CAAHFE01.nigon.types.yaml
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FILE_CAAHFE01.window_stats.types.yaml
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ATTR_genome_size.types.yaml
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ATTR_karyotype.types.yaml
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DTOL_Plant_Genome_Size_Estimates.tsv
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70 Bytes
FILE_ACC_DB_Download_2021-07-12.types.yaml
562 Bytes
FILE_DTOL_Plant_Genome_Size_Estimates.types.yaml
409 Bytes
FILE_DTOL_assembly_informatics_status_kmer_draft.types.yaml
471 Bytes
FILE_genome_size_genomesize_2021-07-12.types.yaml
938 Bytes
FILE_kewplantcvalues_tblCoreFields.types.yaml
735 Bytes
genomesize_2021-07-12.tsv
2.4 kB
genomesizedotcom_tests
1431472-has-no-values.yaml
741 Bytes
9627-has-values.yaml
397 Bytes
kewplantcvalues_tblCoreFields.csv.gz
23.3 kB
names
ACC_DB_Download_2021-07-12.csv
416.4 kB
DTOL_Plant_Genome_Size_Estimates.tsv
22.5 kB
Nematoda_species_karyotype_records_2021-07-12.tsv
6.1 kB
amphib-2021-02-24.csv
58.1 kB
apidae-2021-07-07.csv
6.0 kB
data-of-chromosome-number-in-birds-v2-0-2021_clean.csv
34.4 kB
genomesize_2021-07-12.tsv
192.4 kB
kewplantcvalues_tblCoreFields.csv.gz
122.4 kB
lep_karyotypes_de_vos.tsv
57.2 kB
polyneopteraDB-2021-08-17.tsv
11.6 kB
www_zbi_ee_fungal_genomesize_20210319.tsv
42.1 kB
lineages
lineage_tests
33554-has-odb10lineage.yaml
335 Bytes
taxon_id_odb10_lineage.tsv
2.4 kB
taxon_id_odb10_lineage.types.yaml
2.3 kB
ott3.3
ncbitaxid_ottid_ottsynonym.names.yaml
165 Bytes
ncbitaxid_ottid_ottsynonym.tsv.gz
142.0 kB
regional_lists
ATTR_regional_list.types.yaml
306 Bytes
BOU_The_British_List_2020-11-23.tsv
55.1 kB
FILE_BOU_The_British_List_2020-11-23.types.yaml
1.5 kB
FILE_Irish_Rare_Birds_Committee_2020-11-23.Cleaned.expanded.types.yaml
528 Bytes
FILE_ireland_bats_2020-11-24.types.yaml
348 Bytes
FILE_ireland_cetacea_2020-11-24.types.yaml
398 Bytes
FILE_uk_bats_2020-11-24.types.yaml
400 Bytes
FILE_uk_cetacea_2020-11-24.types.yaml
388 Bytes
Irish_Rare_Birds_Committee_2020-11-23.Cleaned.expanded.tsv
25.5 kB
ireland_bats_2020-11-24.tsv
740 Bytes
ireland_cetacea_2020-11-24.tsv
1.2 kB
names
BOU_The_British_List_2020-11-23.tsv
21.1 kB
Irish_Rare_Birds_Committee_2020-11-23.Cleaned.expanded.tsv
16.8 kB
ireland_bats_2020-11-24.tsv
416 Bytes
ireland_cetacea_2020-11-24.tsv
639 Bytes
uk_bats_2020-11-24.tsv
654 Bytes
uk_cetacea_2020-11-24.tsv
980 Bytes
uk_bats_2020-11-24.tsv
950 Bytes
uk_cetacea_2020-11-24.tsv
2.7 kB
status_lists
ATTR_status_lists.types.yaml
653 Bytes
ATTR_target_lists.types.yaml
1.5 kB
CBP_expanded_2022-02-15.tsv
3.5 kB
DTOL_Chordata_20210817_expanded.tsv
72 Bytes
DTOL_Plants_20210817_expanded.tsv
4.7 kB
DTOL_uksi_longlist.csv
12.6 MB
EBPN_expanded_2022-02-10.tsv
11.3 kB
ENDEMIXIT_expanded_2022-02-07.tsv
822 Bytes
FILE_CBP_expanded.types.yaml
1.1 kB
FILE_DTOL_Chordata_20210817_expanded.types.yaml
408 Bytes
FILE_DTOL_Plants_20210817_expanded.types.yaml
413 Bytes
FILE_DTOL_sts.types.yaml
898 Bytes
FILE_DTOL_uksi_longlist.types.yaml
447 Bytes
FILE_EBP_Nor_long_list.types.yaml
1.1 kB
FILE_ENDEMIXIT_expanded.types.yaml
919 Bytes
FILE_erga_pilot_species_list.types.yaml
758 Bytes
FILE_vgp_table_tracker.types.yaml
1.0 kB
erga_expanded_2022-02-14.tsv
262 Bytes
names
ASG_pilot_long_list.tsv
13.6 kB
CBP_expanded_2022-02-07.tsv
1.3 kB
CBP_expanded_2022-02-15.tsv
1.2 kB
DTOL_Arthropoda_20210817_expanded.tsv
23.2 kB
DTOL_Arthropoda_dtol_all_20210817_expanded.tsv
1.2 MB
DTOL_Bryophytes_20210817_expanded.tsv
40.5 kB
DTOL_Chordata_20210817_expanded.tsv
18.3 kB
DTOL_Fungi_20210817_expanded.tsv
110.6 kB
DTOL_Other_Metazoa_20210817_expanded.tsv
29.6 kB
DTOL_Plants_20210817_expanded.tsv
55.5 kB
DTOL_Protists_20210817_expanded.tsv
7.9 kB
DTOL_uksi_longlist.csv
2.6 MB
nhm_2022-02-15_6852.tsv
74.9 kB
vgp_table_tracker_2022-02-14.tsv
9.4 kB
sts_2022-02-15_3036.tsv
7.3 kB
vgp_table_tracker_2022-02-14.tsv
264 Bytes
tolids
names
tolids.tsv.gz
25.1 kB
tests
drSpiMult-exists.yaml
318 Bytes
tolids.names.yaml
443 Bytes
tolids.tsv.gz
43.8 kB
uk_legislation
1_Council_Directive_92_43_EEC_1992_ANNEX_IIb_Plants.tsv
59.9 kB
1_Council_Directive_92_43_EEC_1992_ANNEX_IVa_Animals.tsv
26.6 kB
1_Council_Directive_92_43_EEC_1992_ANNEX_IVb_Plants.tsv
4.5 kB
2_The_Conservation_of_Habitats_and_Species_Regulations_2017_Schedule_2_Animals.tsv
4.7 kB
3_The_Conservation_of_Habitats_and_Species_Regulations_2017_Schedule_5_Plants.tsv
592 Bytes
4_The_Conservation_of_Offshore_Marine_Habitats_and_Species_Regulations_2017_Schedule_1.tsv
2.9 kB
5_Wildlife_and_Countryside_Act_1981_SCH1_Birds.tsv
4.5 kB
6_Wildlife_and_Countryside_Act_1981_Sch_5_Animals.tsv
12.6 kB
7_IrishStatuteBook_Wildlife_Act_1976_3rd_Schedule_birds.tsv
28.7 kB
8_IrishStatuteBook_Wildlife_Act_1976_5th_Schedule_Animal.tsv
2.7 kB
9_Protection_of_Badgers_Act_1992.tsv
103 Bytes
ATTR_legislation.types.yaml
2.0 kB
FILE_1_Council_Directive_92_43_EEC_1992_ANNEX_IIb_Plants.types.yaml
715 Bytes
FILE_1_Council_Directive_92_43_EEC_1992_ANNEX_IVa_Animals.types.yaml
749 Bytes
FILE_1_Council_Directive_92_43_EEC_1992_ANNEX_IVb_Plants.types.yaml
678 Bytes
FILE_2_The_Conservation_of_Habitats_and_Species_Regulations_2017_Schedule_2_Animals.types.yaml
717 Bytes
FILE_3_The_Conservation_of_Habitats_and_Species_Regulations_2017_Schedule_5_Plants.types.yaml
596 Bytes
FILE_4_The_Conservation_of_Offshore_Marine_Habitats_and_Species_Regulations_2017_Schedule_1.types.yaml
644 Bytes
FILE_5_Wildlife_and_Countryside_Act_1981_SCH1_Birds.types.yaml
604 Bytes
FILE_6_Wildlife_and_Countryside_Act_1981_Sch_5_Animals.types.yaml
599 Bytes
FILE_7_IrishStatuteBook_Wildlife_Act_1976_3rd_Schedule_birds.types.yaml
722 Bytes
FILE_8_IrishStatuteBook_Wildlife_Act_1976_5th_Schedule_Animal.types.yaml
622 Bytes
FILE_9_Protection_of_Badgers_Act_1992.types.yaml
424 Bytes
names
1_Council_Directive_92_43_EEC_1992_ANNEX_IIb_Plants.tsv
15.9 kB
1_Council_Directive_92_43_EEC_1992_ANNEX_IVa_Animals.tsv
11.7 kB
1_Council_Directive_92_43_EEC_1992_ANNEX_IVb_Plants.tsv
1.9 kB
2_The_Conservation_of_Habitats_and_Species_Regulations_2017_Schedule_2_Animals.tsv
2.2 kB
3_The_Conservation_of_Habitats_and_Species_Regulations_2017_Schedule_5_Plants.tsv
331 Bytes
4_The_Conservation_of_Offshore_Marine_Habitats_and_Species_Regulations_2017_Schedule_1.tsv
1.2 kB
5_Wildlife_and_Countryside_Act_1981_SCH1_Birds.tsv
3.0 kB
6_Wildlife_and_Countryside_Act_1981_Sch_5_Animals.tsv
5.3 kB
7_IrishStatuteBook_Wildlife_Act_1976_3rd_Schedule_birds.tsv
16.8 kB
8_IrishStatuteBook_Wildlife_Act_1976_5th_Schedule_Animal.tsv
1.6 kB
9_Protection_of_Badgers_Act_1992.tsv
47 Bytes
ena-taxonomy.extra.jsonl
125.4 kB
scripts
load_lep_test_data.sh
1.3 kB
load_test_data.sh
3.3 kB
taxdump
ncbi
names.dmp
515.7 kB
nodes.dmp
256.4 kB
templates
api
json
max()-invalid-attribute.yaml
213 Bytes
max()-valid-attribute.yaml
146 Bytes
ncbi-analysis-search-returns-results.yaml
286 Bytes
ncbi-taxon-count-tax_name(mCanLup).yaml
251 Bytes
ncbi-taxon-count-tax_tree(Canis-lupus)-excludeAncestral-assembly_span.yaml
357 Bytes
ncbi-taxon-count-tax_tree(Canis-lupus)-max(assembly_span).yaml
336 Bytes
ncbi-taxon-count-tax_tree(Canis-lupus).yaml
319 Bytes
ncbi-taxon-record-9612.yaml
909 Bytes
ncbi-taxon-report-hist-by-assembly_date.yaml
462 Bytes
ui
conftest.py
871 Bytes
requirements.txt
42 Bytes
test_landing.py
1.8 kB
unit_tests
test_config.py
2.4 kB
test_genomehubs_cli.py
1.1 kB
test_init_cli.py
1.1 kB
tox.ini
2.1 kB