PDB component integration into VF

[TomasKulhanek]

Dataset tab in filemanager switch to a prototype allowing to view, add, delete entries from selected repositories (currently PDB entries and Uniprot entries). It's possible to name a dataset and save it for further use.

• [x] litemol viewer of selected pdb file
• [x] pdb link component and other one entry components
• [x] prepare dataset panel, which allows to add entries from PDB using autocomplete component and refined by other component/viewers
• [x] widget to customize entity-id attribute for pdb-topology-viewer (N), data.firstelementofstructure[0].entity_id, filtering polypeptide molecules - issue #32
• [x] show/hide all components - encapsulate in dataset - change icon (T)
• [x] show/hide some of the components, within dataset (T)
• [x] distinguish between pdb and uniprot entry - show PDB UniProt Viewer (T)
• [x] litemol viewer in dataset (T)
• [x] howto effectively rebootstrap already existing pdb component - detach and attach -
• [x] pdb prints component and other multiple entries components

Tomas:

• [x] autocomplete component in Firefox
• [x] autocomplete component, works in chrome, test in chromium
• [ ] store submitted dataset as artifact of virtual folder - represent it as separated folder with metadata
• [ ] replacing the component in more elegant way (within entity-id, pdb-ids)
• [ ] jsonrender to show raw data from pdb summary and other APIs
• [x] autocomplete, fix when key press enter renders button click event

Nurul:

• [ ] accordion to hide all details
• [ ] make component to choose assembly-id, analogy of entity-id

[TomasKulhanek]

before submitting D5.5 report:

• [x] address https://portal.west-life.eu/virtualfolder/ shows error message pops up: "Sorry, error when connecting backend web service at /metadataservice/files error:{"ResponseStatus": "ErrorCode":"UnauthorizedAccessException","Message":"Attempted to perform an unauthorized operation.","Errors":[]}} status:UnauthorizedAccessException"
• [x] There is a link at the bottom of the page " Development documentation at internal-wiki.west-life.eu/w/index.php?title=WP6". This is not appropriate in a page that has been delivered.
• [x] The report says that there is a demo at https://portal.west-life.eu/virtualfolder/test/index-dataset.html. When I visit this I see:[an error occurred while processing the directive]
• [x] on that page I also see " PDB or related item to add:". There is no help text to suggest what I should enter. There should be a tooltip listing the possible responses, and a placeholder within the input element.
• [x] If I enter something unexpected, e.g. the gene name CFTR, then I get the unhelpful response "No hints.". Added tooltip "Enter PDB or UnitProt accession code, protein name or related terms."
• [x] I guessed that a PDB accession code is expected, and entered one. This gave a useful page but with some errors - failed PDB-REDO etc., failed pdb components should not be rendered, relates to issue #39
  • [x] Then when I click “Publish dataset” I get “Sorry. Dataset not submitted at undefined error:404 status:Not Found” - remove