[pull] develop from solgenomics:master#29
Open
pull[bot] wants to merge 116 commits intoBreeding-Insight:developfrom
Open
[pull] develop from solgenomics:master#29pull[bot] wants to merge 116 commits intoBreeding-Insight:developfrom
pull[bot] wants to merge 116 commits intoBreeding-Insight:developfrom
Conversation
…r detection tool; upgrade fieldmap to d3 v4; add back missing generic message function; show non-numeric traits and raw trait data on trait detail page; other improvements.
…e BTI logo in footer.
…h, the genotyping plate loading script, seed transaction loading and management, and new reporting pages.
…eing one present.
…sted in alphabetical order, and planting date has been made optional again. The multiple trial fieldmap view now overlays phenotypic data correctly on all the trials. Fixed population requirement for stock loading script. BrAPI observations query fixed to not use materialized views. In the Cview repo, includes fixes for Cview IL map.
…n the accession detail page. Fixes issue with entrypoint.sh and how database are loaded automatically.
…olgenomics repo (not GMOD).
…lInfo for germplasm; require genotype protocol and warn of too large datasets for wizard genotype download; add script that downloads accessions for seedlot names.
…m trial using plot names; add new R libraries.
…ool; add dihaploid_induction as a new cross_type; fix issue with BrAPI observation values of 0; fix genotype download issue without protocol; fix download from project detail page; other improvements.
…pe dihaploid_induction; fix blast db related script; allow synonyms in accession upload to be replaced or appended; add new rtb logo; allow download of cached vcf files that were uploaded; other improvements.
…t data when creating seedlots from trial; add related stocks to vector page to see transformed accessions.
…ebugging alert in fieldbook file generator; improve related stocks section for vectors; add dumping script for ontologies to .obo files; fix issue with raw data phenotype section; plot order download: include correct name (harvest or planting order); create a file-based annotation search page.
…notyping page issues; additions to annotation page from file; allow protocol edits; show empty plots on geofieldmap and view only mode; implement marker validation for markersets; update certain brapi calls to 2.1 version; add new stability tool; add breeding_program type for breeding program folder.
…it input on Fieldbook); include entry number in trial download; add entry numbers to label designer; improve population related function on accession detail page; limit stock property autocomplete to 100 in stock search to prevent page crashes in large databases; flexible headers and entry numbers in single and multi trial upload; tweak GPCP tool for non-dioecious plants; run test on ubuntu-latest.
…ldbook files based on observation unit ids in addition to observation unit names.
…with observation units; tweak phenotype upload - do not apply checks to values that are undef, emtpy string, . or NA; fix tissue_sample count; add subplot data dimension to the wizard.
…ector detail pages; adds ability to run multiple image analyses on one image with the Image Analysis tool; allows searching with stock_id in stock search and wizard and display stock ids in result pages; adds libreoffice document format support for uploads; fixes an issue with authentication in the brapi observation call; improves loading speed of image section on trial detail pages; adds a list comparison tool.
…eenhouse design even after the trial has been created; adds a tool to view all the accessions and the genotyping protocols they were genotyped with in a table format; adds a list comparison tool with downloadable diffs between lists; fixes an issue with changing accessions in a trial using a file upload; adds the ability to scan barcodes in images containing observation unit information, with options to associate the image automatically with that observation unit; do not check the trait constraints for trait values that are not defined; adds a vector viewer on the vector construct detail pages; improve label writer features - display dimensions in either S.I. units or inches, adds options to left align or center align label texts, fixes an issue with barcode fuzzyness by moving internal barcode image creation from jpg to png; adds .ods file format support for all uploads; fixes an issue with authentication in the observation brapi call; adds ability to run image analysis for analyses that detect mulitple sub-objects and report multiple values, creates a new tissue sample for each sub-image; speeds up image section on trial detail page; adds a feature that stores marker names associated with each marker in a genotyping protocol, can assign specific names for markers in an alias column; adds improved logging for pca tool; fixes how the wizard download handles tempfiles; fixes a bug in the spatial correction tool.
…etter deal with web downloads.
…es in-silico PCR tool; fix an issue with the vector viewer css import; return ids in the same order as the names in the accession transform utility; add the new CASS logo; fix an issue with start and end date in the phenotype download; enable COMP trait variable uploads; fix an issue with CXGN::Jobs; in label designer tool, store the selected units (cm or inches) so that it is retrieved correctly when it is opened later; other improvements to label designer.
…es on trial detail page; adds a trend line to repetitive measurement graph with linear regression; fixes an issue with genotyping download; adds the ability to create new accessions from other accessions, plots, plants or tissue_samples; adds BrAPI NIRS endpoints.
…ot information on the accession detail page; fixes issues with the motif finder tool.
…adds support for Synonym Search Tool auth client; fixes aspects of the find genotypes by accession feature and allow filtering by genotyping projects; adds study create date to additional info for BrAPI call (needs to be added to the spec!).
…ue with trial downloads when crosses are used in the trial instead of accessions; fixes an issue with coordinates of plants within a plot in the greenhouse trial type; optimizes the loading of the field view on the trial detail page by speeding up the respective brapi call; adds more options to the trial layout download; prepare breedbase for compatibility with snpsnapp app.
…new Perl modules to local-lib for the upcoming SSO feature; tweaks dbpatch system for improved script integration.
…sue with the new treatment backend dbpatch; revises a section about images to the manual; removes the requirement for an organism to be associated with a vector construct; allows fieldbook uploads in xlsx format; fixes image previous on accession detail pages; fixes icons in unsupported browser alert; adds an eggplant genome section.
… no longer used contact phone number; fixes links to trials on subplot, plot, plant, etc. pages; adds a captcha like check for creating new user accounts; fixes phenotypes not found on analysis page; fixes the manual for which a directory had accidentally been removed.
…ly trait_ontology type traits in the wizard; adds subplots as a source observation unit type for creating genotyping plates.
…f transgenes in transgenic lines; adds new BrAPI calls for expression high dimensionality phenotypes; adds Coordinate and Intercross apps as authorized clients in BrAPI; adds new NIRS devices; removes stockprop materialized view from vectors search; removes stockprop materialized view from stock search; adds an improved upload for field layout data with better support for popular spreadsheet formats; fixes a bug that removed completely empty phenotype rows from the phenotype download and adds test for that; allows the seedlot inventory upload to use count, in addition to weight of seeds; adds a tool to manage macropropagation; adds new metadata to image detail page, such as associated trials, accessions, plots, etc, in a new data table; adds a scatterplot to the correlation heatmap tool; fixes an issue with the derived traits feature.
…orarily deactivates vectorviewer.
…h Google and other OAuth providers; adds back a link to compose traits page; adds a message to LabelDesigner that labels have to printed from a PDF viewer (not from browser).
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
6 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
See Commits and Changes for more details.
Created by
pull[bot] (v2.0.0-alpha.4)
Can you help keep this open source service alive? 💖 Please sponsor : )