Update Germinate connection #435
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zoomPanCalcs.js : ZoomFilter() : if event .timeStamp is older than 1sec, drop it. In Firefox since the framework upgrade mouse-wheel zooming with split axis was rendering too slowly to keep up, leading to a multi-second backlog of events; this was not a problem in Chrome.
… tasked with installation and configuration of Pretzel Add install_and_configure.md; this includes some edited content from -hosting journal.md Add docker-compose.prod.yaml and pretzel.compose.prod.env from -hosting aws-instances/config/docker-compose/ These can be renamed without .prod, if we assume that the administrators will generally not be running multiple pretzels; (retaining .prod in this commit enabled leveraging the existing content).
Add documentation for System administrators / installers
dataset-graph.hbs : add prefix this. required after frontend framework upgrade #370. api-server-germinate.js : viewDatasetP() : Results of createRecord() are Ember Data record objects, not promises. factor code into functions linkageGroup2block(), createDataset(), blocksFinish(), shareDataset(), to enable order of creation to be changed : create dataset before blocks. Tried adding datasetId to blockAttributes, but got Uncaught Error: Assertion Failed ... is not a record instantiated by @ember-data/store, although the record was added to the (germinate) store OK, checked with store.peekRecord(dataset, dataset.id). block-adj.js : taskGetPaths() : handle undefined .lastPerformed, seen during germinate debugging (may have been caused by breakpoint causing delays).
manage-genotype.js : datasetStoreSampleNames() : use contentOf() to avoid setting .sampleNames on a proxy of dataset. vcfGenotypeSamplesDataset() : add comment that datasetStoreSampleNames() is duplicated for BrAPI, and currently it will try trim().split() on the array t. vcfGenotypeSamples() : wrap vcfGenotypeSamplesDataset() call with promiseThrottle(). headerTextP() : if isGerminate short-cut the vcfGenotypeLookup() request below because Germinate is taking ~1min for it, and there is no benefit - the header is expected to be simply samples. paths-progressive.js : vcfGenotypeLookup() : add Germinate to the BrAPI case (may have had BrAPI tag on Germinate datasets earlier). promises.js : add promiseThrottle().
axis-1d.js : buttonStateEffect() : fix check on .isDestroying, added in aa8a3ce. manage-genotype.hbs : button vcfGenotypeLookup : disabled : convert {{or (and (not ...))}} expression to vcfGenotypeLookupButtonDisabled(). The same change will apply to the other copy of this button; this allows testing both the disabled function and the . manage-genotype.js : add vcfGenotypeLookupButtonDisabled(), replacing hbs boolean expression, enabling addition of check on .vcfGenotypeLookupTask.isRunning. rename vcfGenotypeLookup() to vcfGenotypeLookupP() and wrap with added vcfGenotypeLookup() and vcfGenotypeLookupTask; this enables disabling vcfGenotypeLookup when the task is running. return promise from : vcfGenotypeLookupSelected(), vcfGenotypeLookupAllDatasets(), vcfGenotypeLookupGroup(), to enable disabling vcfGenotypeLookup until the promise completes. domElements.js : eltClassName() : also map : to _, because of Germinate feature id e.g. chr1A:1030304 in dataset 090222, causing error : circle#fc_12_1_12_chr1A:1030304 is not a valid selector. axis.js : axisFeatureCircles_eltId() : apply eltClassName() to feature.id - to handle Germinate features with chr:position as commented on previous line of commit message. ember-cli-build.js : babel : draft require of ember-concurrency/async-arrow-task-transform which will be required for ember-concurrency v4. package.json : ember-concurrency : 4.0.0 -> 3.1.1 because some dependencies (ember-bootstrap, ember-power-select) are using [email protected], and ember-concurrency error : ... the async arrow task function you've provided is not being properly compiled by Babel. ... 4. Ensure that there is only one version of ember-concurrency v2.3.0+ being used in your project (including nested dependencies). vectra-search.js : connectOpenAIApi() : in log, prefix slice with ...
…cy v4 to 3 package-lock.json : ember-concurrency : 4.0.0 -> 3.1.1, to be consistent with nested dependencies, as commented in previous commit @plantinformatics/vcf-genotype-brapi : 1.0.4 -> 1.0.7
{,frontend/}package.json : version : 3.1.0 -> 3.2.0
Merge Germinate update
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Update connection and access for the current Germinate server accessed by Pretzel.
This PR is the completion of Germinate update #423, which contains these sub-issues :
Development branch : feature/reconnectGerminate