Views

The models are located at dcc/modeldcc/views.py.

modeldcc.views.AppliedAssayDetail(request, appliedassay_id)

Render a page with applied assay details to a given appliedassay_id, including related items.

modeldcc.views.AssayDetail(request, assay_id)

Render a page with assay details to a given assay_id, including related items.

modeldcc.views.BiosampleDetail(request, biosample_id)

Render a page with biosample details to a given biosample_id, including related items.

modeldcc.views.CombinedView(request, *args, **kwargs)

A deprecated table view, to show all the data for each section.

modeldcc.views.DataDetail(request, data_id)

Render a page with data details to a given data_id, including related items.

modeldcc.views.SequencingDetail(request, sequencing_id)

Render a page with sequencing details to a given sequencing_id, including related items.

modeldcc.views.SeriesChildTable(request, series_id)

Returns a list of biosamples and assays for the given series_id to be used in the table on the seriesDetail page.

modeldcc.views.SeriesDetail(request, series_id)

Render a page with series details to a given series_id, including related items.

modeldcc.views.addAnalyzedData(request, *args, **kwargs)

Add and upload analyzed data objects to the DCC and return a flag if they already exist and their data ids.

modeldcc.views.addAppliedAssay(request, *args, **kwargs)

Add applied assay objects to the DCC and return an array of their ids for the webinterface.

modeldcc.views.addAssay(request, *args, **kwargs)

Add assay objects to the DCC and return an array of their ids for the webinterface.

modeldcc.views.addBiosample(request, *args, **kwargs)

Add biosample and corresponding biosmaple replicate objects to the DCC and return an array of their ids for the webinterface.

modeldcc.views.addData(request, *args, **kwargs)

Add data objects to the DCC, upload or move the files (via url or a filepath), change the series status to COMPLETED_UPLOAD_STATUS and return the corresponding series id.

modeldcc.views.addFreezeTag(request, *args, **kwargs)

Update the version field for a given data id, previous version numbers are concatenated with the new one.

modeldcc.views.addLab(request, *args, **kwargs)

Add a lab to the DCC system.

modeldcc.views.addSequencing(request, *args, **kwargs)

Add sequencing objects to the DCC and return an array of their ids for the webinterface.

modeldcc.views.addSeries(request, *args, **kwargs)

Add a series object to the DCC and return a list of available assay and labs for the web interface.

modeldcc.views.announcements(request)

Render the announcements page.

modeldcc.views.batchUpload(request, *args, **kwargs)

Handle the batch upload by reading in the csv file, validating it and if all tests pass, staging the upload for final submission.

modeldcc.views.commitBatch(request, *args, **kwargs)

If all checks passed and the user also checked parsing of the csv file, add the batch staged annotations including the sequencing files to the DCC

modeldcc.views.createDataExportJSON(request, *args, **kwargs)

Create and save a json file with all available data sets and their metadata. Used in the react dataExport app.

modeldcc.views.createindexJSON(request, *args, **kwargs)

Create a json file with data of assays and labs in the currently database. Used for the plot in _index.js

modeldcc.views.csv_export(request)

Create and send a csv file containing all the metadata for a given series_id

and it’s connected sections.

modeldcc.views.delete(request, *args, **kwargs)

Mark a series as deleted, i.e. reset it’s status to INITIAL_UPLOAD_STATUS.

modeldcc.views.deleteFiles(request, *args, **kwargs)

Delete files from the DCC via an ajax request with the corresponding dataids.

modeldcc.views.deleteFilesByPath(request, *args, **kwargs)

Delete files from the systme via an ajax request with the corresponding filepath.

modeldcc.views.filePaths(request)

Render a list of the available files to help during a file upload, when files are in the UPLOAD_PATH directory.

modeldcc.views.getURLs(request)

Create and send a file, where each line contains the url to a file on the server requested via their relative filepaths.

modeldcc.views.getZippedFiles(request)

Create and send a .tar archive of requested filepaths.

modeldcc.views.get_file_object(data_url, data_local_path)

Helper function to get a file either via an url or via a file path on the server

modeldcc.views.get_fk_model(model, fieldname)

Helper function to get the foreignKey for a given fieldname in a given model.

modeldcc.views.get_plot_sizeDevelopment()

Generate and send a json file containing the data for the area plot to show the cummulative development of the amount of data in the DCC over time.

modeldcc.views.get_plot_stages2assay()

generate and send a json file contains a nested list of the amount of data per lab per assay. Used to render the bar graph on the index page.

modeldcc.views.get_plot_stages2chip()

Generate and send a json file containing the stages and targets for the ChiP-seq data, used in the bar plot on the visualzations page

modeldcc.views.helpPage(request)

Render help page.

modeldcc.views.hideEmptyColumns(data, table)

Helper function to hide otherwise empty columns in the table views in the detail pages.

modeldcc.views.importDNANexus(request, *args, **kwargs)

Render the interface to upload analyzed data (originally via DNANexus).

modeldcc.views.index(request)

Render the index page.

modeldcc.views.is_member(user)

Check if user is part of GROUP.

Args:

user (User)

Returns:

True if user is part of GROUP

modeldcc.views.login_interface(request)

Log in as a user with a POST request (mainly used for cypress tests).

Returns:

“fine”, if login is successful “incactive”, if user is not activated yet “bad”, if login was unsuccessful

modeldcc.views.policyPage(request)

Render the data policy page.

modeldcc.views.termsPage(request)

Render page with all controlled vocabulary terms as tables attached.

modeldcc.views.updateAnalyzedData(request)

Update analyzed data objects, if certain fields were missing or incorrect during their initial upload.

modeldcc.views.updateFile(request, *args, **kwargs)

Replace the current file attached to a data instance with a new file.

modeldcc.views.updateFilePaths(request, *args, **kwargs)

Rename/move and move files to reflect changes in their annotations. Moves them first to the new position with a __tmp attached to the file name. modeldcc.views.updateTemporaryFilePaths() converts the name to the final form.

modeldcc.views.updateTemporaryFilePaths(request, *args, **kwargs)

Remove the __tmp suffix of the updated file names.

modeldcc.views.visualization(request)

Render the visualization page and send the data files required for the visualzations along with it.