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Build(core): Push dev changes to main #312

Merged
merged 423 commits into from
Mar 1, 2023
Merged

Build(core): Push dev changes to main #312

merged 423 commits into from
Mar 1, 2023
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Commits on Feb 12, 2022

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  3. #109: Fix linter errors

    aswallace committed Feb 12, 2022
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Commits on Feb 14, 2022

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  3. #109: Fix linting errors

    aswallace committed Feb 14, 2022
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  4. Merge pull request #111 from Duke-MatSci/#109_Enhancement_for_explore…

    …r_home_page
    
    #109 Enhancement for explorer home page
    aswallace authored Feb 14, 2022
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Commits on Feb 17, 2022

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Commits on Feb 18, 2022

  1. #113: first draft

    kevinzunigacuellar committed Feb 18, 2022
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  3. Linting errors

    aswallace committed Feb 18, 2022
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Commits on Feb 19, 2022

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  2. Fix linting errors

    aswallace committed Feb 19, 2022
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Commits on Feb 21, 2022

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  3. #66 templated view article (#112)

    * #66 initial article commit
    
    * #66: Refactor article page, fetch article metadata
    
    Moved Article.vue, separated out into article.js to match file structure
    of other pages. Progressed on Semantic Scholar API logic.
    
    * #66: Refactor article.js
    
    * #66: Refactor Article.vue
    
    * #66: Add route for Article View
    
    Added route to explorer for the article view. Moved DOI from component
    prop to a watcher and computed property pair.
    
    * #66: Refactor article.js to move logic to services
    
    Moved article metadata retrieval logic to services. Unified all metadata
    under one object for simpler reference.
    
    * #66: First pass at article HTML view
    
    First attempt at displaying all article metadata. Also added pre-push
    linting fixes.
    
    * #66: Add loading state awareness
    
    * #66: Add article venue to retrieved fields
    
    * #66: Second pass at article view HTML
    
    Added basic loading indicator, refactored table to have better structure
    (I think)
    
    * #66: Basic CSS for article view
    
    * #66: Removed erroneous comment
    
    * #66: Fix scrolling bug
    
    Scrolling tables also scrolled their titles, but not their header rows.
    Isolated tables in their own div, maybe tables should be their own
    component...
    
    * #66: Unify dir structure, nest article page
    
    Move explorer/article/services to modules/explorer/article/services,
    clean up article now that it's nested properly (barring further change
    to nest completely under sample). Refactor extra function from fetchJSON
    into getArticleMetadata.
    
    * #66: initial Article.vue testing commit
    
    Includes mock for Semantic Scholar API calls and article.js whitespace
    linting fix.
    
    * #66: Refactored getArticleMetadata for easier mock
    
    Mocking getArticleMetadata easily required moving it into an enclosing
    object so that the manual mock could do the same, allowing it to access
    properties. The manual mock was written following along with
    [jest's manual mock](https://jestjs.io/docs/manual-mocks).
    
    The mock of the resulting getArticle also provides a stub of the
    SemanticScholar API response as of 2/2/22, for reference and testing.
    
    * #66: Write tests for Article.vue
    
    Wrote tests of DOI loading, reloading; article data loading; API
    failure. Added classes to article.html items to distinguish them and
    allow the tests to refer to them. Updated article.js to use the new
    articleMetadata.js and fixed bugs that appeared in testing.
    
    * #66: Fix linting errors
    
    * #66: Write tests for module articleMetadata.js
    
    Updated articleMetadata mock to include raw and cleaned mock data, and
    wrote tests of the fetch handler and response cleaning routines. Fixed
    issues in articleMetadata.js that came up in testing.
    
    * #66: Refactored articleMetadata.js to better track API errors
    
    Refactored .get function to remove repeated code and allow API calls to
    occur in parallel. Rewrote how internal fetch returns in order to pass
    errors (and success codes) in API call along to caller. Updated mock
    data to include mock version of success codes
    
    * #66: Updated tests to match
    
    Also added missing response codes to mock data, and fixed citation and
    reference call status not being passed through
    
    * #66: Updated Article.vue to display errors
    
    Article view now takes advantage of newly passed API errors to inform
    the user that an error has occurred. This could be expanded on
    
    * #66: Linting fixes
    
    * #66: Update test to use createWrapper
    
    Replaced localVue, shallowMount with createWrapper for consistency.
    Added test to ensure error message is displayed to user.
    
    * #66: Write comments, refactor error storage
    
    * #66: Write jsdoc-style function comments
    
    Documented functions, removed unused mock response function, and
    refactored testing slightly to remove repetition.
    
    * #66: Move article to its own route
    
    * #25: Remove console.logs, add reusable spinner
    roryschadler authored Feb 21, 2022
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Commits on Feb 22, 2022

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  2. Merge pull request #120 from Duke-MatSci/#97_Header_tab_panel

    #97 Header Tab Panel
    aswallace authored Feb 22, 2022
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  6. Merge pull request #121 from Duke-MatSci/#113_Refactor_templated_view…

    …_Sample
    
    RFC(#113): refactor templated view sample
    kevinzunigacuellar authored Feb 22, 2022
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Commits on Feb 25, 2022

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  3. #28: Link MM/teams to teams page (#122)

    * #28: Link MM/teams to teams page
    
    * #28: Update reference to about, how, news
    roryschadler authored Feb 25, 2022
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  7. #61: Add gallery page

    stouffers committed Feb 25, 2022
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  10. fix lint errors

    stouffers committed Feb 25, 2022
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  14. remove console.log in test

    stouffers committed Feb 25, 2022
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  15. Merge pull request #108 from Duke-MatSci/#61_Templated_View_-_Images

    feat(#61): Add gallery page
    stouffers authored Feb 25, 2022
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Commits on Mar 4, 2022

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Commits on Mar 8, 2022

  1. feat(#100): knowledge graph rest endpoint (#138)

    * #100: Add logger service
    
    * #100: Updated secrets default and increased token validity to 8hours
    
    * #100: testing script for isInternal middleware service
    
    * #100: Add isInternal middleware service to validate internal calls
    
    * #100: Re-usable logger service for unit test
    
    * #100: Moved logger service to initialize first
    
    * #100: renamed filestorage directory and added a method to ensure unique file names
    
    * #100: Updated test with log service
    
    * #100: Added unique name generator to package.json
    
    * #100: Added knowledge graph endpoint method
    
    * #100: Add KG wrapper route to REST service
    
    * #100: Append KG route to server initialization
    
    * #100: Re-installed app
    
    * #43: Add fuseki service to container
    
    * #43: Fuseki volume mount
    
    * #43: Add fuseki critical files to ignore
    
    * #100: Updated nginx to use a preferred version
    
    * #100: File renaming and linter error fixes
    
    * #100: Update environment variables
    tholulomo authored Mar 8, 2022
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Commits on Mar 9, 2022

  1. #25 migrate tools (#128)

    * #25: initial ModuleTools commit
    
    Replaced vuetify elements with vue-material and simplified layout.
    
    * #25: Refactored module tools page to use store
    
    Moved module tools data into store, refactored tool card into component
    for reuse in simulationTools as well.
    
    * #25: Initial simulation tools commit
    
    Changed module tools getter name to avoid overlap, added simulation
    tools store data and getter, added simulation tools assets.
    
    * #25: Linting fix
    
    * #25: Write tests for simulation, module, ToolCard
    
    * #25: Initial chemprops commit
    
    Rewrote chemProps.html to use `vue-material`, removed `Axios` and
    commented out Smiles.vue and Auth.js in chemProps.js. Still need to
    implement SMILES API, so that chemProps form works -- future ticket.
    
    * #25: Initial chempropsapitoken commit
    
    Missing Duke shibboleth authorization and chemprops in general, so can't
    implement the api token functionality just yet.
    
    * #25: fix typo, switch to md-layout
    
    * #25: Initial csvPlotter commit
    
    File upload and display works, but no tests have been written yet.
    Includes a new dependency, `d3`.
    
    * #25: Fix typo
    
    * #25: Fix typo in router path
    
    * #25: Create reusable ReferenceContainer component
    
    * #25: Initial MCR tool commit
    
    Migrated MCR tool homepage over, factoring out the references into the
    new reusable container and migrating the tool descriptions into reusable
    ToolCard components
    
    * #25: Rename state getters to avoid overlap
    
    Also added ReferenceContainer to chemProps
    
    * #25: Make mcrTools plural
    
    * #25: Replace v-bind with shorthand where possible
    
    * #25: Linting fix
    
    * #25: Added support for external links to ToolCard
    
    * #25: Initial dynamfit commit
    
    Same deal as other initial commits. New store module for references,
    migrating vuetify tags to vue-material tags. Added JobMgr.js module,
    which dynamfit uses. Changed Axios implementation to fetch
    implementation, mocked auth module as it is not implemented yet.
    
    * #25: Fix bug in ToolCard internal link checker
    
    Using `new URL()` to test links threw errors (expected) but jest didn't
    like that. Replaced with a simple externalLink flag that defaults to
    false unless the store explicitly sets it true.
    
    * #25: Fix error thrown by CSV Plotter when mounting, removing data
    
    CSV Plotter was trying to display undefined data. Fixed that, in the
    process also fixed (mostly) removing data. Some style changes too
    
    * #25: Fixed CSV Plotter drag and drop
    
    * #25: Iterate on csv plotter layout, drag ability
    
    Entire "drag file here" section now works as expected. Line spacing
    leaves something to be desired, but I'll come back to it once I
    understand the `vue-material` syntax better. Prettified the HTML too.
    
    * #25: Initial Dynamfit addons commit
    
    * #25: Migrate dynamfit example pages
    
    Previously we had three separate files for dynamfit and its two pages of
    tutorial, which were all very similar except for a few instructions,
    some disabled fields, and some extra images. I flattened them into one
    file.
    
    * #25: package.json auto-alphabetized
    
    * #25: Migrate dynamfit result page
    
    Job Manager still not working, that's next. Once it's working, it should
    provide the content for this page.
    
    * #25: Fix/catch dynamfit mounting errors
    
    * #25: Simplify button link
    
    * #25: Update chemprops to use the new dialog box, and prep for SMILES
    
    * #25: Initial SMILES commit
    
    Functionality depends on the API being up and running, to return
    results.
    
    * #25: Move LineChart to components
    
    * #25: Clear input element, chart on file remove
    
    By tying the LineChart key to the filename, removing the file using the
    button also resets the LineChart.
    
    * #25: Refactor store to simplify tools
    
    Half of the refactor is in this commit, flattening the `tools/` subdir
    as it seems unnecessary. moduleTools store will be added next.
    
    * #25: Create unified tools store
    
    Every tool is now stored consistently. Dynamfit was moved from its own
    directory into this one and updated to store its own display info.
    Getters are a first guess at what will work, debugging that will happen
    once this store migration is complete.
    
    * #25: Create unified toolset store
    
    Store toolsets as supersets of tools and other toolsets. Again, getters
    are a first pass, and will be debugged next.
    
    * #25: Wrote toolset store for moduletools
    
    Also added a pageContent getter and updated MCRTools variable names to
    match standard
    
    * #25: Rename moduleTools to tools in preparation
    
    Will eventually move simulationTools under the tools store umbrella,
    getting ready for that now so I don't have to rename it everywhere
    
    * #25: Added missing info to tools, getters, index
    
    Some tools were missing namespace flags, some missing image files.
    One getter needed updating to include external link flag and image
    filepath, and Dynamfit needed to be added to the index.
    
    * #25: Fixed bug in calling rootGetters
    
    I had gotten the syntax for calling getters wrong.
    
    * #25: Nest tools under nanomine, not metamine
    
    * #25: Create reusable tool and toolset pages
    
    * #25: Fix typos
    
    * #25: move link nesting to getters for easy changes
    
    * #25: Fix toolset page not reloading on route change
    
    Also add base component for toolsets, tools
    
    * #25: Rolling back MCR tool work to revisit later
    
    * #25: Nest tools to /nm/tools, update mentions
    
    * #25: Move simulation tools under toolsettemplate
    
    * #25: Fix references not showing/erroring when empty
    
    * #25: Move dynamfit to tools root, remove mcr home
    
    MCR homepage is now handled by toolsettemplate
    
    * #25: update webpack chunk names
    
    * #25: fix typo
    
    * #25: tag auth mocks more obviously
    
    * #25: Fix typos
    
    * #25: Move references to separate file
    
    Easier to remove duplicates from a reference list if you can generate
    the set of all references in a repeatable way. By referring to
    references with DOI/ISBN numbers, we set the stage for pulling
    reference info from semantic scholar as well.
    
    * #25: Wrote ReferenceContainer unit test
    
    Also updated ToolCard unit test to test for link rendering correctly.
    
    * #25: Remove old tests for moduletools, simulation
    
    Those pages are now handled by ToolSetTemplate, no need for their own
    specs.
    
    * #25: Write unit test for LineChart
    
    Had to add a moduleNameMapper to the jest config in order for it to
    recognize `d3`, which LineChart uses to draw the graph.
    
    * #25: Further refactor reference handling
    
    Move references to ReferenceContainer store module, for easier
    replacement later with a SemanticScholar API call or other form of
    reference checking. Use DOIs (or ISBN in one case so far) as key.
    
    * #25: Initial SmilesCanvas unit test
    
    For some reason, SmilesCanvas is not able to reach the same document as
    the jest harness is providing the test, so it errors out when trying to
    render the SMILES output. Haven't been able to debug, this is a
    placeholder test that I'll come back to when I'm able to figure it out.
    
    * #25: Move CanvasWrapper into SmilesCanvas
    
    CanvasWrapper is not used anywhere else in the old repo -- pulled its
    functionality (not very much) into SmilesCanvas.
    
    * #25: Write ToolSetTemplate unit test
    
    * #25: Write initial Dynamfit unit test
    
    Return to this once the Dynamfit/JobMgr API is completed to write tests
    for the form logic
    
    * #25: Write initial DynamfitResult unit test
    
    Return to this once the Dynamfit/JobMgr API is completed to write tests
    for the API response logic
    
    * #25: Remove skipped unit test
    
    * #25: Fix bug in testing md-button with `to` attr
    
    `RouterLinkStub` (used in `createWrapper` for jest tests) doesn't play
    nicely with the `md-button` implementation of `router-link`.
    (`md-button` is using deprecated attributes of `router-link`, and is
    throwing console.warnings.) So I wrapped `md-button`s in `router-link`s
    explicitly, which solved the testing bug too.
    
    * #25: attempt at spacing toolcards
    
    * #25: Remove broken tests
    
    Using RouterLinkStub in createWrapper breaks these tests, which aren't
    testing our code anyway so it's not a big deal.
    
    * #25: Move tools that won't use ToolTemplate out
    
    Prep for moving all the tools from state into their own components, more
    like they were stored in previous repo.
    
    * #25: Move tools from state into components
    
    Each tool now has its own component, instead of its own state module as
    discussed with Tolu. Each component uses the ToolTemplate component for
    display, which has two separate views: a card view for ToolSets, and
    a space for an upcoming tool instruction view for the Tool itself.
    
    * #25: Move ToolSets from state to components
    
    Each toolset now has its own component, instead of its own state module
    as discussed with Tolu. Each component uses the ToolSetTemplate
    component for display, which like the ToolTemplate has two views, a card
    view and a toolset page view. This does involve some recursive
    components which seem to be working fine.
    
    * #25: Fix ToolSetTemplate Test
    
    ToolSetTemplate no longer includes References (they're only accessible
    to the Tools that cite them), so the ReferenceContainer test was
    removed. It also no longer calls store getters to retrieve card content.
    
    * #25: Fix filepath typo
    
    * #25: Cleaning up old files
    
    Removed commented out code and console.logs, and parameterized a
    function
    
    * #25: Moved global suppressing to test-setup.js
    
    Set up `test-setup.js` to be run before each test file is executed.
    Moved the suppressing of global.console.log and global.fetch to there,
    rather than repeating it in every test.
    roryschadler authored Mar 9, 2022
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Commits on Mar 22, 2022

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Commits on Mar 25, 2022

  1. #24 migrate upload (#147)

    * #24: Initial XML Uploader commit
    
    Converted vuetify to vue-material, added references to the reference
    store.
    
    * #24: Fix old references to xml-uploader
    
    * #24: Remove mock dataset from testing
    
    * #24: Write unit test for dataset viewer
    
    * #24: Rename DatasetCreateOrSelect to DatasetViewer
    
    * #24: Updated dialog rendering, removed autologin
    roryschadler authored Mar 25, 2022
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  2. #132 write slot driven templates (#142)

    * #132: Add MCR specific tool page
    
    Renamed tool template to specify that it is MCR tool specific -- at
    least given the tools we've added so far. Added a dependency for
    EditImage.vue, a component of ImageUpload.vue that is itself a component
    of MCRToolTemplate.vue. Removed the old MCR homepage.
    
    Added a pageContent getter for tools as well.
    
    * #132: tag auth mock more obviously
    
    * #132: Use MCRToolTemplate in all tools, add socket
    
    Job Manager uses vue-socket.io -- copied config from old repo and added
    this and socket.io-client as well. Updated MCRToolTemplate to account
    for move from state to components -- added card, moved reference
    container.
    
    * #132: Remove old ToolTemplate
    
    * #132: Update MCRToolTemplate to use tool prop
    
    Also add spinner for loading results
    
    * #132: Fix typos
    
    * #132: Add optional mocks to test wrapper
    
    `$socket` needed to be mocked for some tests, added that functionality
    to `createWrapper`.
    
    * #132: Write Tool Card that uses slots, not props
    
    * #132: Move major tool page content to slots
    
    Not all content could be moved, as some is needed for job management,
    but major display content was turned into slots for template HTML.
    
    * #132: Move Toolset content from data to slots
    
    * #132: Wrote tests of new templates
    
    Also updated the wrapper function to allow for user-defined stubs
    
    * #132: Remove replacement-tool-page slot
    
    Was created for Dynamfit, ChemProps, but those really should be separate
    components, so I removed the slot.
    
    * #132: Make tool cards full-width
    
    * #132: Convert Module Tools page to new system
    
    * #133: Convert Binarization tools and homepage
    
    Moved tool data from the `data` field to slots in the tool page template
    and moved the homepage data from `data` to the toolset page template
    slots.
    
    * #133: Fix seeming typo in ImageUpload.vue
    
    I may be wrong, but the way the selects prop is used in the template
    seems like it should be an Array, not an Object. All the selects fields
    in each tool are Arrays as far as I remember. Certainly for the
    binarization tools.
    
    * #134: Convert Characterization tools
    
    * #135: Convert reconstruction tools
    
    * #136: Convert Intelligent characterization tool
    
    * #139: Remove ChemProps, Dynamfit from template
    
    ChemProps and Dynamfit rewrite all the job management code already, so
    they should really be separate components.
    
    * #139: Wrap lifecycle events in `this.card` checks
    
    If a component is being rendered as a card, it doesn't need to check for
    authorization or commit its header. Also removed unused minWidth param
    from renderDialog.
    
    * #132: Convert MCR homepage
    
    * #132: Remove unnecessary index files
    
    ToolSetTemplate no longer needs to keep all tools as components, so the
    index files that centralized them were removed.
    
    * #132: Tweak ToolCard size, layout
    
    * #132: Write test for MCRToolTemplate
    
    * #132: Remove typos and testing code
    
    * #132: Attempt at cleaning up scoped styles
    
    * #132: Migrate SimulationTools, Polymerizer
    
    Add fallback content for toolset pages, if description is not present.
    
    * #132: Change submit button implementation
    
    You can't listen to events on slots, so the button was moved to the
    tool template, and the slot only provides the button text now.
    
    * #132: Typo in styles import
    
    * #132: Fix MathML syntax
    
    * #132: Move tool, toolset routes to own module
    
    * #132: Replace MathML with MathJax
    
    Includes a CDN script tag in index.html, and a new component, but now
    math will render in all browsers.
    
    * #132: Combine tool scss files into one
    
    * #132: Fix style imports for new consolidated file
    
    * #132: Updated vue-advanced-cropper version
    
    * #132: Wrap styles to avoid overflow
    roryschadler authored Mar 25, 2022
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  3. #29 migrate meta mine tools (#148)

    * #29: Initial PixelUnit commit
    
    Converted all vuetify to vue-material, cleaned up JS a little bit. Had
    to replace the static file reference with a link to the live website's
    version of the file, as we don't yet have a way to serve static files
    that I know of.
    
    * #29: Update PixelUnit route
    
    * #29: Remove console.logs
    
    * #29: Write template unit test for PixelUnit
    
    Once file storage is implemented, the config file can be loaded for the
    test as well, which will allow testing of the page's function
    
    * #29: Remove commented console.logs
    
    * #29: Comment out test rather than skip it
    
    * #29: Fix likely location of CI test fail
    
    Added dummy catch block to the promise I think is causing the issue.
    
    * #29: Remove PixelUnit test from test suite
    
    Didn't completely remove it, so that it can be tackled in a future TD
    ticket.
    
    * #29: Move scoped styles to _tools.scss
    
    * #29: Wrap styles to avoid overflow
    roryschadler authored Mar 25, 2022
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  4. #125 refactor sparql js (#150)

    * #125: Throw errors instead of failing quietly
    
    * #125: Add combined query and parse function
    
    Could export it as the default if we want? No need to, of course.
    
    * #125: Throw error on response failure
    
    * #125: Simplify rethrowing errors
    roryschadler authored Mar 25, 2022
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Commits on Mar 30, 2022

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Commits on Apr 4, 2022

  1. fix(#140): general technical debt (#152)

    * #126: add functions for chart id resolution
    
    * #126 remove scoped styles
    
    * Initial commit #98
    
    Currently using duplicated/modified code from Gallery.
    Added initial standard styling for #114, #115, #118
    
    * #98: Add styling for sample images #115
    
    * #98: Minor styling and linting fixes
    
    * #98: Start developing state management for explorer results
    
    * #98: Fix linting errors
    
    * #140: app scroll behaviour fixes
    
    * #140: Ignoring mongodump folder
    
    * #140: Update mongo init file to create indexes
    
    * #50: Restore shell script replaced with syncdb.sh
    
    * #140: Mongodb restore and sync script
    
    * #140: Add syncdb shell to script
    
    * #140: Add Elastic search to docker compose services
    
    * #140: Add Elastic search to docker compose services
    
    * #140: Add ES config payload
    
    * #140: Add article mappings payload
    
    * #140: td - under dev
    
    * #140: Fix conflicts
    
    * #140: pre-checks commit
    
    * #140: pre-checks commit -2
    
    * #140: pre-check temp udates
    
    * #140: Update docker compose file  port mappings
    
    * #140: Remove dependency and added environment variables
    
    * #140: Updating frontend nginx settings
    
    * #140: Updating frontend nginx settings
    
    * #140: Redirect all 50x error back to index page
    
    * #140: Rest services update, test fixes, and deployment updates
    
    * #140: Changed logger directory
    
    * #140: Linter fixes
    
    * #140: typo fixes
    
    Co-authored-by: Sam Stouffer <samuellstouffer@gmail.com>
    Co-authored-by: Anya Wallace <aswallace98@gmail.com>
    3 people authored Apr 4, 2022
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  6. Merge pull request #110 from Duke-MatSci/#89_Setup_Whyis_Docker_Conta…

    …iner
    
    #89 setup whyis docker container
    mjpalmeri authored Apr 5, 2022
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Commits on Apr 11, 2022

  1. #156: Updating icos (#157)

    * #156: Updating icos
    
    * #150: Upgraded node version
    
    * #150: Re-install node module after upgrade
    
    * #150: Blocked out fuseki standalone service implementation
    
    * #150: Upgraded node version on BE
    
    * #150: Update to specific version of body-parser
    
    * #156: Updated log file creation
    
    * #156: Updated ES to log pings
    tholulomo authored Apr 11, 2022
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Commits on Apr 21, 2022

  1. Merge pull request #167 from Duke-MatSci/#145_Parameterized_query

    #145: add parameterized query page
    mjpalmeri authored Apr 21, 2022
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  2. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #160_chart_overlap_on_small_screens
    aswallace committed Apr 25, 2022
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  3. Merge pull request #173 from Duke-MatSci/#172_mrs_tutorial_menu_link

    Add menu item MRS2022 to PageHeader.vue
    bingyinh authored Apr 26, 2022
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  2. Merge pull request #166 from Duke-MatSci/#158-sample-pages-not-rendering

    #158: fix undefined data return from sparql
    kevinzunigacuellar authored Apr 28, 2022
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  2. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #164_data_voyager_clarity
    aswallace committed May 2, 2022
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  2. #165: Fix linting error

    aswallace committed May 3, 2022
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  3. fix(#156): Update ico fix (#169)

    * #156: Add unwanted whyis files to gitignore
    
    * #156: Add host port to client services
    
    * #156: update env variable deployment and update readme file
    
    * #156: Update environment variable readme file with additional info
    
    * #156: Update readme with information for environment variable deployment
    
    * #156: Update search url
    
    * #156: Update api url
    
    * #156: Disable websocket
    
    * #156: temporary service disable
    
    * #156: fix connection time
    
    * #156: Update api call to use new service port environment variable
    
    * #156: Update search url
    
    * #156: empty commit to trigger new build
    
    * #156: Pull upstream
    
    * #156: Update readme on environment variable deployment
    tholulomo authored May 3, 2022
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  7. Merge pull request #171 from Duke-MatSci/#161_chart_overlap_on_small_…

    …screens
    
    #161: Fix vega chart responsiveness
    aswallace authored May 3, 2022
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  9. Merge pull request #170 from Duke-MatSci/#162_footer_styling_on_tools…

    …_pages
    
    #162: Fix overlap in tool styling
    aswallace authored May 3, 2022
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  11. Merge pull request #178 from Duke-MatSci/#175_two_prop_parameterized_…

    …query
    
    #175: add two-property parameterized query
    stouffers authored May 3, 2022
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  12. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #165_data_voyager_clarity
    aswallace committed May 3, 2022
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Commits on May 4, 2022

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  2. Fix linting errors

    aswallace committed May 4, 2022
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Commits on May 9, 2022

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Commits on May 10, 2022

  1. #160 #180 Dialog box styling fixes

     #160: Dialog box now fits screen when expands to full screen for
    mobile responsiveness
     #180: Clicking outside causes unwanted behavior, so instead added
    scrolling so that close button is always visible
    aswallace committed May 10, 2022
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Commits on May 11, 2022

  1. Remove unit

    aswallace committed May 11, 2022
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  2. Merge pull request #183 from Duke-MatSci/#179_chartimage_gallery_routing

    #179: Fix dropdown links for galleries
    aswallace authored May 11, 2022
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  5. Merge pull request #181 from Duke-MatSci/#165_data_voyager_clarity

    #165 data voyager clarity
    aswallace authored May 11, 2022
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  2. Merge pull request #168 from Duke-MatSci/#164_side_drawer_routes

    #164: fix visualize and Module Tools routes
    aswallace authored May 19, 2022
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  4. Merge pull request #200 from Duke-MatSci/#160#180_dialog_box_styling

    #160#180 dialog box styling
    aswallace authored May 19, 2022
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Commits on Jun 2, 2022

  1. chore(#155): Fixes (#211)

    * #155: add backup to git ignore
    
    * #155: Add node modules to ignore
    
    * #155: Add a new library for pixel unit testing
    
    * #155: Re-enable pixel unit test
    
    * #155: Re-enable pixel unit test
    
    * #177: Add 404 page and updated app router
    
    * #177: Styling 404 page
    
    * #155: updated search, testing and dv link
    
    * #155: fix typos and update creation page to use curate
    
    * #155: Add header to page not found
    
    * #155: update unit test for page-not-found
    
    * #155: Updated code owners
    
    * #155: Update home link
    tholulomo authored Jun 2, 2022
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Commits on Jun 7, 2022

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Commits on Jun 9, 2022

  1. Merge pull request #222 from Duke-MatSci/#205_pq_safari

    #205: Recommendation for regex fix for safari
    aswallace authored Jun 9, 2022
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  3. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #176_param_names_pq_to_dv
    aswallace committed Jun 9, 2022
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Commits on Jun 16, 2022

  1. #210: Add some of missing properties to pq dropdown

    Still needs additional work. Dielectric constant won't return results due to not having units, breakdown strength is not directly curated as a property of the samples
    aswallace committed Jun 16, 2022
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Commits on Jun 17, 2022

  1. Merge pull request #223 from Duke-MatSci/#176_param_names_pq_to_dv

    #176 Parameterized query variable names match selected option
    aswallace authored Jun 17, 2022
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Commits on Jun 29, 2022

  1. add sample metadata author and year (#221)

    * add sample metadata author and year
    
    * add nullish coalesing
    
    * lint code
    
    * add container to metadata and user computed sampleId
    kevinzunigacuellar authored Jun 29, 2022
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Commits on Jul 1, 2022

  1. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #210_Add_properties_to_PQ_dropdown
    aswallace committed Jul 1, 2022
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Commits on Jul 7, 2022

  1. Merge pull request #234 from Duke-MatSci/#210_Add_properties_to_PQ_dr…

    …opdown
    
    #210 Add properties to parameterized query dropdowns
    aswallace authored Jul 7, 2022
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Commits on Jul 18, 2022

  1. Staging (#227)

    * #220: UI fixes
    
    * #220: styling changes
    
    * #220: Add Curae home page and updated parameterized query
    
    * #220: Add Curae home page and updated parameterized query
    
    * #220: Add Curae home page and updated parameterized query
    
    * #190: Update with require library
    
    * #190: Remove placeholder files
    
    * #190: Migrate globalmiddleware file to index.js
    
    * #190: Add validators and global error handlers
    
    * #190: Add schema and resolver for user and user management
    
    * #190: Allow setting jwt expiration arg
    
    * #190: Add image migration logic
    
    * #190: Add pagination handler
    
    * #190: Update eslint for rest services
    
    * #190: Remove unused services
    
    * #190: Update auth token source
    
    * #190: linter fixes
    
    * #190: Update auth token source
    
    * #190: Update server file with additional services at startup
    
    * #190: Add testing for graphql service pt1
    
    * #190: update test import
    
    * #190: Renamed graph resolver
    
    * #190: Renamed graph resolver
    
    * #190: removed unused import
    
    * #190: Install ws package
    
    * #155: Work in progress
    
    * #220: Update styles for page opt
    
    * #220: Added an icon to filter panel
    
    * #220: Add parameterized query as tab and remove it as a button
    
    * #220: Add image gallery to list of routes
    
    * #220: create an image gallery components
    
    * #220: test WIP
    
    * #190: Refactor graphql and define user, api and image gallery schemas and resolver
    
    * #190: Centralizing error for graphql operations
    
    * #190: Adding appollo server and remove express-graphql
    
    * 190: Modified restful tests
    
    * #190: Update rest server config, middleware services and graphql init
    
    * #190: Add xmldata model for xmldata collection
    
    * #190: Add a new params to pass env var
    
    * #190: Ignoring node_modules in docker
    
    * #190: Ignore fuseki files
    
    * #190: Update validations and add new login controller - wip
    
    * WIP: frontend testing
    
    * #190: Add proxy to rest environment variables
    
    * #190: Rename imageContent method to file content
    
    * #190: Renamed expected file param
    
    * #190: Separated file controller from admin controller
    
    * #190: Update import and added file routes handler
    
    * #190: Renamed files
    
    * #190: Add single image resolver and updated search resolvers
    
    * #190: Add query pipelines directory and image query pipeline
    
    * #190: Renamed file
    
    * #190: New file route handler for file related services
    
    * #190: Renamed files
    
    * #190: Update image query with image keywords
    
    * #220: Revert ES6 Syntax and Image Gallery WIP
    
    * #190: Image gallery
    
    * #190: update parameterized query page link
    
    * #190: Linter fixes
    
    * #190: update gql fetch policy
    
    * #190: linter fixes
    
    * #190: Linter error fixes
    
    * #190: Fix failing tests
    
    * #190: Remove path import from vueconfig
    
    * #190: Remove optional chaining causing error
    
    * #190: Bug fixes for search box
    
    * #190: Remove output logs
    
    * #190: Update base url
    
    * #190: Add logic for image not found
    
    * #190: Refactored image base URL - API
    
    * #215: Work in progress
    
    * #215: remove empty return and linter fixes
    
    * #215: gallery unit test WIP
    
    * #215: gallery unit test WIP
    
    * #220: Add text reducer and image reducer to mixin
    
    * #220: Update unit testing
    
    * #220: Update docker image setup for UI
    
    * #220: general UI optimization update
    
    * #220: Linter fixes
    
    * #220: Updated UI docker config
    
    * #220: Re-install npm library
    
    * #220: Update text description for null values
    tholulomo authored Jul 18, 2022
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Commits on Aug 1, 2022

  1. fix (#235): Update Drawer with Curation (#240)

    * #235: Add test for side drawer
    
    * #235: Update side drawer with curation menu options
    
    * #235: Linter fixes
    tholulomo authored Aug 1, 2022
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  2. feat(#238): Contact us page api (#243)

    * #238: Created a new mongodb schema for contact
    
    * #238: Refactor error formatter to return error instead of throw
    
    * #238: Add sinon lib for unit testing
    
    * #238: Refactored to return error instead of throwing
    
    * #238: Added unit testing for contact and refactored existing test
    
    * #238: Added contact query/mutation and schema
    tholulomo authored Aug 1, 2022
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Commits on Aug 10, 2022

  1. #241: MVP of metamaterial visualization tool

    Important TD: data access is very inefficient right now and needs lots of work
    
    - csv needs to be stored on rest, not frontend
    - should be stored in local storage after initial pull
    - needs geometry visualization
    
    Currently mockup2 is the more up-to-date version
    aswallace committed Aug 10, 2022
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Commits on Aug 16, 2022

  1. Whyis Integration 1 of 8 (#246)

    * #156: Add unwanted whyis files to gitignore
    
    * #156: Add host port to client services
    
    * #156: update env variable deployment and update readme file
    
    * #156: Update environment variable readme file with additional info
    
    * #156: Update readme with information for environment variable deployment
    
    * #156: Update search url
    
    * #156: Update api url
    
    * #156: Disable websocket
    
    * #156: temporary service disable
    
    * #156: fix connection time
    
    * #156: Update api call to use new service port environment variable
    
    * #156: Update search url
    
    * #156: empty commit to trigger new build
    
    * #156: Pull upstream
    
    * #156: Update readme on environment variable deployment
    
    * WIP
    
    * Switched back over to the whyis fuseki install.
    
    * resolved conflict
    
    * Got fuseki working with fast instance and summary views
    
    * whyis integration 1 of 8
    
    * Update CI
    
    Co-authored-by: Jamie McCusker <mccusj2@rpi.edu>
    Co-authored-by: Jamie McCusker <mccusker@gmail.com>
    3 people authored Aug 16, 2022
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  2. #241: Remove mockup

    aswallace committed Aug 17, 2022
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Commits on Aug 19, 2022

  1. update CI (#247)

    tholulomo authored Aug 19, 2022
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  2. fix(#236): Update image gallery search (#244)

    * #236: Refactored unit test
    
    * #236: Add search functionality to image gallery
    
    * #236: Refactor image gallery
    
    * #236: Update container image
    tholulomo authored Aug 19, 2022
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  3. chore (#237): Add descriptions to existing query and mutation resolve…

    …rs (#245)
    
    * #237: Add descriptions to existing query and mutation resolvers
    
    * #237: Update schema text descriptions
    tholulomo authored Aug 19, 2022
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  2. Linting errors

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Commits on Aug 29, 2022

  1. #229: dataset curation

    tholulomo committed Aug 29, 2022
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  2. Fix linting error

    aswallace committed Aug 30, 2022
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  3. #241: Metamaterial viz feedback

    - Add constituent material info under the unit cell image
    - Temporarily switch to using Papaparse for csv to json conversion since my implementation was buggy
    aswallace committed Aug 30, 2022
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  1. #229: WIP

    tholulomo committed Aug 31, 2022
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  3. #229: dataset unit testing

    tholulomo committed Sep 5, 2022
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  1. #250: UI fixes for demo

    aswallace committed Sep 26, 2022
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  2. #250: Remove click event

    aswallace committed Sep 26, 2022
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Commits on Sep 27, 2022

  1. #229 spreadsheet file interface (#249)

    * #229: dataset curation
    
    * #229: WIP
    
    * #229: added a resolver for dataset upload
    
    * #229: Add file upload and update data stream
    
    * #229: dataset unit testing
    
    * #250: UI fixes for demo
    
    * #250: Remove click event
    
    * #229: Updates to remove explorer home page latency
    
    * #229: Test requires refactoring, passed sanity checks
    
    Co-authored-by: Anya Wallace <aswallace98@gmail.com>
    tholulomo and aswallace authored Sep 27, 2022
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  3. #252: Linter fixes

    tholulomo committed Sep 30, 2022
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  3. feat(#252): Add resolver for pixelated data and updated unit test (#257)

    * #252: Add resolver for pixelated data and updated unit test
    
    * #252: Validate user before allowing upload
    
    * #252: Linter fixes
    
    * #252: Re adding missing library
    tholulomo authored Oct 1, 2022
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Commits on Oct 5, 2022

  1. #241: Pixelated metamaterial viz updates

    - Switch to using apollo graphql for data
    - Temporarily remove color coding until datasets have label or title
    - Temporarily limit to 10x10 OR 50x50, not both
    - Add loading spinner, fix async behavior
    aswallace committed Oct 5, 2022
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  2. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #241_metamine_visualization_tool
    aswallace committed Oct 5, 2022
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  1. Remove console.log

    aswallace committed Oct 7, 2022
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  2. Merge pull request #258 from Duke-MatSci/#241_metamine_visualization_…

    …tool
    
    #241 metamine visualization tool
    aswallace authored Oct 7, 2022
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  2. Fix linting error

    aswallace committed Oct 11, 2022
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  3. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #241_metamine_visualization_tool
    aswallace committed Oct 11, 2022
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  3. Merge pull request #262 from Duke-MatSci/#261_metamine_header

    #261: Fix MetaMine header styling and add viz link
    aswallace authored Oct 12, 2022
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Commits on Oct 13, 2022

  1. Fix (#252): Updates (#263)

    * #252: Updated graphql schema description
    
    * #252: Add changes to automatically create storage at RESTAPI start up
    tholulomo authored Oct 13, 2022
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  2. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #229_spreadsheet_file_interface
    aswallace committed Oct 13, 2022
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  1. Fix(#252): Updates (#264)

    * #252: Updated graphql schema description
    
    * #252: Add changes to automatically create storage at RESTAPI start up
    
    * #252: Refactored pixel data endpoint
    
    * #252: Added a centralized log writer
    tholulomo authored Oct 17, 2022
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  2. #252 updates (#265)

    * #252: Updated graphql schema description
    
    * #252: Add changes to automatically create storage at RESTAPI start up
    
    * #252: Refactored pixel data endpoint
    
    * #252: Added a centralized log writer
    
    * #252: Refactor isAuth to remove file anytime auth fails
    tholulomo authored Oct 17, 2022
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  4. Merge pull request #260 from Duke-MatSci/#241_metamine_visualization_…

    …tool
    
    Metamine visualization tool: #259 combine timeouts
    aswallace authored Oct 17, 2022
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Commits on Oct 18, 2022

  1. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #229_spreadsheet_file_interface
    aswallace committed Oct 18, 2022
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  2. Linting errors

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  2. #229: update failing test

    tholulomo committed Nov 1, 2022
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  4. Update decryptENVARFile.sh (#248)

    Co-authored-by: tholulomo <94853475+tholulomo@users.noreply.github.com>
    kevinzunigacuellar and tholulomo authored Nov 1, 2022
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  5. [Hotfix] #229: Fixed datasetId mutation bug (#267)

    * #229: Fixed datasetId mutation bug
    
    * #229: update failing test
    
    * #229: Fix error messsage
    tholulomo authored Nov 1, 2022
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  6. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #229_spreadsheet_file_interface
    aswallace committed Nov 1, 2022
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Commits on Nov 3, 2022

  1. #229: XML Spreadsheet upload wip

    400 error in createDataset file upload: `BAD_USER_INPUT`
    aswallace committed Nov 3, 2022
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Commits on Nov 7, 2022

  1. #229: Fix curation upload route issues (#268)

    * #229: Fix curation upload route issues
    
    * #229: Add validations for curation upload routes
    tholulomo authored Nov 7, 2022
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  2. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #229_spreadsheet_file_interface
    aswallace committed Nov 7, 2022
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  1. #229 fix upload (#269)

    * #229: Fix curation upload route issues
    
    * #229: Add validations for curation upload routes
    
    * #229: Refactor uploadfile to remove middleware service
    
    * #229: Pull upstream update
    tholulomo authored Nov 8, 2022
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  2. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #229_spreadsheet_file_interface
    aswallace committed Nov 8, 2022
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Commits on Nov 17, 2022

  1. Fix (#229): Fix upload (#274)

    * #229: Fix curation upload route issues
    
    * #229: Add validations for curation upload routes
    
    * #229: Refactor uploadfile to remove middleware service
    
    * #229: Pull upstream update
    
    * #272: Fix dialog box styling and typos
    
    * #272: Rename class to reflect use case
    
    * #272: Reduce scope of dialog icon styling
    
    * #229: Bug fixes
    
    * #272: Merge upstream fixes
    
    * #229: Update Nodejs version
    
    * #229: CI update
    
    * #229: Update vue
    
    * #229: Docker updates
    
    Co-authored-by: Anya Wallace <aswallace98@gmail.com>
    tholulomo and aswallace authored Nov 17, 2022
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  2. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #229_spreadsheet_file_interface
    aswallace committed Nov 17, 2022
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Commits on Nov 18, 2022

  1. #26 migrate contact us (#140)

    * #26: change contact link from src to nm
    
    * #26: create contactus page
    
    * #26: apply lint
    
    * #26: add contactus route to nm
    
    * #26: add contact page tests
    
    * #26: remove list style
    
    * #26: add error validation html
    
    * #26: add validation and onSubmit methods
    
    * #26: add post method
    
    * #26: add rendering tests for inputs
    
    * #26: add platform flag
    
    * delete event prevent default
    
    * resolve router conflicts
    
    * #26: add validation for platform
    
    * #26: uncooment platform post data
    
    * #30: add test for user inputs
    
    * add spacing
    
    * rename webpack code chunk name
    
    * add contact query
    
    * add apollo query
    
    * add $ to input
    
    Co-authored-by: tholulomo <94853475+tholulomo@users.noreply.github.com>
    kevinzunigacuellar and tholulomo authored Nov 18, 2022
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  5. #275: Remove comments

    aswallace committed Nov 18, 2022
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  6. Merge pull request #276 from Duke-MatSci/#275_apollo_client_module

    #275: Separate apolloClient into module
    aswallace authored Nov 18, 2022
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  7. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #229_spreadsheet_file_interface
    aswallace committed Nov 18, 2022
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Commits on Nov 23, 2022

  1. [Hotfix]: Dataset curation updates (#278)

    * [Hotfix]: dataset curation updates
    
    * [Hotfix]: Deprecate fields that are no longer supported in GQL
    
    * [Hotfix]: Update gql schema test
    tholulomo authored Nov 23, 2022
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Commits on Nov 28, 2022

  1. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #229_spreadsheet_file_interface
    aswallace committed Nov 28, 2022
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Commits on Dec 5, 2022

  1. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #229_spreadsheet_file_interface
    aswallace committed Dec 5, 2022
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  3. #229: Fix linting

    aswallace committed Dec 5, 2022
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  2. [MINOR]: #279 contact page BE integration (#280)

    * #279: Update form UI and added contact link to metamine page
    
    * #279: Remove console.log statement
    
    * #279: Integrated BE with contact page and updated unit test
    tholulomo authored Dec 6, 2022
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  5. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

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    aswallace committed Dec 6, 2022
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Commits on Dec 13, 2022

  1. #207 material data filter search (#287)

    * #207: Update unit test to run in band
    
    * #207: Update to remove facet dialog for smaller screen
    
    * #207: Add materials property to facet search
    
    * #207, #212: Total count fix and added materials property fetch actions
    
    * #207: Remove facet call at home page load
    
    * #207: Refactor BE api to support materials property functionality on UI
    
    * #207: Backend unit testing for admin controller apis
    
    * #207: Added unit test for materials property and searchtableresult component
    
    * #207: Linter and error fixes
    
    * #207: Fix import typo
    
    * #207: Upgrade node version
    
    * #207: Refactor  name to
    
    * :bug #207: Update CI node version
    
    * 🐛 #207: Downgrade CI node version
    tholulomo authored Dec 13, 2022
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Commits on Dec 14, 2022

  1. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

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    aswallace committed Dec 14, 2022
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  3. Merge pull request #282 from Duke-MatSci/#229_spreadsheet_file_interface

    #229 Spreadsheet File Interface
    aswallace authored Dec 14, 2022
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Commits on Dec 15, 2022

  1. Fix readme typo

    Update readme ICO
    tholulomo authored Dec 15, 2022
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Commits on Jan 2, 2023

  1. #289 snackbar for error handling (#290)

    * #289: Implement snackbar two ways
    
    * #289: Fix linting
    
    * #289: Add Snackbar to App.vue
    
    * #289: Add snackbar unit test and an example for calling from vuex
    aswallace authored Jan 2, 2023
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Commits on Jan 25, 2023

  1. #293 UI & BE Enhancements (#294)

    * #293: Add coverage to gitignore and update readme icon
    
    * #293: Fixed parameterized query UI inconsistency
    
    * #293: Sticky header bug fix
    
    * #293: Update unit test for viz page
    
    * #293: Add new filter types and removed undefined from image response
    
    * #293: Refactor auth middleware to use the centralized error writer
    
    * 293: Add 404 controller to backend to manage unavailable routes and page not found
    
    * #293: Fix mobile bug in viz page
    
    * #293: Update to return authors as part of image response
    tholulomo authored Jan 25, 2023
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Commits on Feb 6, 2023

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Commits on Feb 9, 2023

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Commits on Feb 11, 2023

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Commits on Feb 21, 2023

  1. [MAJOR] #300: Shibb auth (#308)

    * #300: Add names for each container
    
    * 🔥[hotfix]: FE Bug fixes
    
    * 🔥[hotfix]: Linter fixes
    
    * #300: BE auth service setup
    
    * #300: Refactor FE with auth flow implementation
    
    * #300: Add auth service to proxy
    
    * #300: Update docker environment variables
    
    * #300: Linter fix
    
    * #300: Refactor failing component and fix test failures
    
    * #300: Fixed merged conflict
    
    * #300: Add additional logger to auth service
    
    * #300: Add additional logger to auth service
    
    * #300: Remove unused logger from auth service
    
    * #300: Remove unused logger from auth service
    
    * #300: Update failed auth response
    
    * #300: Refactor login button
    
    * #300: Remove sparql query menu
    
    * #300: Update logout actions
    
    * #300: Update unit test assertions
    
    * #300: Remove skipped unit test
    tholulomo authored Feb 21, 2023
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Commits on Feb 28, 2023

  1. Merge branch 'develop' of https://github.com/Duke-MatSci/materialsmine

    …into #292_visualization_gallery_ui_bugs
    aswallace committed Feb 28, 2023
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Commits on Mar 1, 2023

  1. Feat(#309): Prod CICD (#310)

    * feat(upgrade): #309 Add rest coverage report to gitignore
    
    * feat(upgrade): #309 Setup coverage testing report for backend
    
    * feat(core): #309 Add release versioning to CI pipeline
    
    * feat(ci/cd): #309 Update CI pipeline for prod release
    
    * feat(ci/cd): #309 Re-enabled image build and deployment for QA CI  environment
    tholulomo authored Mar 1, 2023
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  2. fix(#292): modify page input and selection styling

    make the page number input smaller to match surrounding labels,
    move the selection to the same line as buttons and match styling
    aswallace committed Mar 1, 2023
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  4. Merge pull request #297 from Duke-MatSci/#292_visualization_gallery_u…

    …i_bugs
    
    fix(#292): update visualization image gallery
    aswallace authored Mar 1, 2023
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