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* Rename Bioreplicate columns, remove BioReplicatesMetadata table * Submit experiment form on pressing the "add" button * Submit experiment form, persist, then show next one * Fixes * Placeholder "Duplicate" button * Extract code from experiment subform into a shared utility * Reorganize step 2 to use ajax subforms and add validation * Use ajaxSubform for step4 forms * Implement "Duplicate" button * Duplicate compartments and communities * Duplicate experiment form * Minor fix * Handle nested bioreplicate form * Basic perturbation form * Introduce client-side Page() abstraction * Visual adjustments of subforms * Remove spacing from level 2 subforms * Reorganize step 6 to remove study form * Move data spreadsheet out of legacy, do some renaming * Generate data spreadsheet * Working client-side data upload * Working submission (no measurements) * Minor improvement for clarity * Perturbations and their form * Save perturbations to the database * WIP measurement creation * Insert measurements with compartments * Fix bug Need to commit before creating measurements, since subjects are referred to by id. * Fix charts * Fix exports * Test technique creation * Fix certain error messages * Fixes to tooltip js library * Validation of the "download template" button * Validate spreadsheet data * Show error if there's no data file * Fix subform counter * Fixes to upload form * Change some bioreplicate and compartment fields * Fix issues with submissions with old data * Add support for ODS spreadsheets * Slightly lighter boxes * Revert vendored js change * Hack to work around bug * Additional documentation note * Delete most of streamlit, keep data scripts Thank you streamlit code, you served us well. At this point, the core logic is likely too incompatible with this code, so we should clean it up. The data scripts should be ported to python background jobs at some point. * Delete temporary data snapshots Now that we have a reasonable upload form, we should be able to import via the excel spreadsheets. This format of the data is incompatible with bioreplicates + compartments anyway. * Remove legacy code * No need for a tempdir * Linter fixes * Use sqlalchemy types consistently * Use Page() for javascript loading * Fix some Page() bugs * Fix issue with gaps in time points * Minor clarification * Read a secret key to initialize the production environment * Script to create data backup * Delete measurements, add warning * Delete `get_general_info`, replace usage * Delete unused tables * Remove moment.js, replace with server-side time tag * Minor import move * Remove and gitignore Vim stuff * Remove legacy SQL scripts * Revert "Remove legacy SQL scripts" This reverts commit 94e242d. The code for populating metabolites might actually be necessary. * Remove only unnecessary SQL scripts * Remove duplicated scripts * Restore email-sending example * Fix a variety of flask-admin issues * Add projects to admin * Create a bootstrap script for initial studies That way, we can reset the studies onto an empty database. * Render measurement table of contents * WIP Extract MeasurementContext * Clear bugs with form uploading and rendering * Render measurements by iterating over contexts * Add auto-incrementing primary key to Taxa * Also delete measurements in the down migration * Fix merge conflict * Taxon-related fixes * Progress on single study form instead of per-experiment forms * Working basic chart * Scope charts to compartment * Restructure chart, leave only one for the page * List of measurement contexts, cleanup * Make sidebar smaller * Fix call of get_subject * Working checkboxes * Adjust legend positioning, add label * Reorganize partial templates * Set SVG color to a soft black * Better chart visuals * Add time units, log-transform, collect measurement units * Placeholder units * Unit conversion function * Visual fixes * Add primary key to metabolites, add average mass * Unit conversion * Log labels, unit visibility * Remove unnecessary line * Fix font * Fix bug with submission names * Fix export page * Unit selection dropdowns * Visual improvements * Fix upload form javascript * Add "compare" button * Text update * Rename calculation tables/models `CalculationTechnique` is renamed to `ModelingRequest` `Calculation` is renamed to `ModelingResult` * Fix tests * Progress on adapting modeling forms * Working model chart * Working comparison page * Add contextual information to comparison page * Minor fixes * Hacky "permalink" feature * Slightly less hacky permalink * Remove unused method * Generate average measurements * Test average bioreplicate creation * Minor fix * Don't create measurement context if no values * UI for Log view on modeling chart (doesn't work yet) * Unroll bioreplicate dropdown Too few subjects per bioreplicate, comparison requires a lot of dropdown-juggling. Each experiment is likely to have a small number of bioreplicates, so just showing them all in groups is probably going to be easier. * Sort averages on top, show tooltips on headers * Render technique name on chart if units are missing * Show x axis in exponential format * Minor tweaks * Visual fixes to model chart * Log-transform model charts * More robust modeling requests * UI fixes to models, WIP R changes * Remove focus style override * Reorganize technique dropdown to make it easier to use * Work-in-progress modeling status indicators * More modeling interface fixes * Remove calculated averages from export CSV * Add model CSV download * Use jsonlite to serialize json Still kind of terrible, just in a different way. * Add input parameters to models * Study show page * Limit x axis on compare view * Test fixes * Add logistic model * Visual improvements to study show page * Minor refactoring * Add the R summary output to the model results * Export input parameters * Restructure application by MVC lines * No need for explicit SECRET_KEY setup * Add orcid javascript widget * Show study uploader (for now, hardcoded) and dates * Change fitting methods and initial h0 estimation I really should estimate h0 better, but for now, the "CG" algorithm seems to converge more reliably. * CSS tweaks * Homepage for experiments * Fix bug with std scaling * White "select all/none" buttons * Add units to the comparison view * Label changes * Add script to reset test database * Remove orcid javascript, implement backend flow instead * Create users on login * Allow logout, show username, add users to admin * Load env vars * Minor tweaks * Add backdoor page for development * Fix admin bug with timezones * Add user relationships * Add owner relationship to studies and projects * Pluralize Study and Project tables, making table names consistent * Fix issues * Fix env var * Fix issue with variable naming * Submission relationship fixes * Require login for submission page * Minor cleanup * Protect the admin for admin users * Mount mysql volume to maintain data * Create backups in the var/ directory * Add debug toolbar for testing purposes * Extract filters to app/view/filters * Replace image headings with real headings * Pin setuptools dependency * Rename "new strains" to "custom strains" * Fix tests * Admin extension and fixes * Reorganize help pages * Show an icon on all external links * Remove strain and metabolite pages (for now) * Fix search * Add missing CFU conversion * Cleanup * Fix study reuse functionality * Fix test * Basic page test * Another page test, fixes * Add secret key for testing * Avoid loading .env in test mode Otherwise we might end up with development env vars locally that don't work in CI tests. * Don't open connection and load user for /static requests * Optimizations using "selectinload" and caching * Don't show compartments if there is only one * Search fixes * Help page contents * Cache help pages, allow searching through them * Extract link helpers * Javascript fixes * Use ajax subform js for techniques, remove vessel, timepoint inputs * Move timepoints to experiments, drop vessel info * Fix tests, bootstrap data * Fade-in and fade-out effects * Reorganize technique forms * Add help links to the upload process * Remove debug statement * Sanitize search function * Remove sqlparse-related logic, not needed * Remove references to "carbonSource" * Cleanup * Update comment * Help search fixes * Add prod-server script for easier deployment * Documentation: uploading, analysis * Test that only published studies are searchable * Fix help search * Documentation about the submission process * Remove technique table, some misleading values * Search documentation * Add links to the help documentation * Fixes * Minor fix * Fix for number incrementing * Help and about fixes * Fill in submission first, only save on validation * Technique units are optional * Add community-level plate counts, AUC for metabolites * Fix inoculum volume units * External link * Remove style guidelines They don't apply to the current codebase * Update README update autoapi_dirs fix quotes
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