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User interface for LabCAS, for EDRN

Project Description

User interface for the Early Detection Research Network (EDRN) Laboratory Catalog and Archive System (LabCAS). Developed by the EDRN Informatics Center (IC), operated by the Jet Propulsion Laboratory (JPL), which itself is operated by the California Institute of Technology (CalTech).

Running a Development Instance

Easy. First copy dev.cfg.in to dev.cfg and set the ldap-manager-password in the [secrets] section. Then:

ssh -L 9000:localhost:9000 -L 9001:localhost:9001 -L 9002:localhost:9002 -L 8080:localhost:8080 -L 8983:localhost:8983 labcas-dev.jpl.nasa.gov
python2.7 bootstrap.py -c dev.cfg
bin/buildout -c dev.cfg
bin/pserve --reload parts/templates/paste-dev.cfg

Then visit http://localhost:6543/ with a browser.

Installation

  1. Download the src
  2. Add [versions] in etc/versions/eggs.cfg
  3. Copy ops.cfg.in to ops.cfg; if you re-use last version’s ops.cfg, change the session and authorization tokens!
  4. Run buildout
  5. Fix cronjob
  6. Run initial cron
  7. Fix symlink
  8. Restart web server
  9. Log in, hit Manage, set the settings

Maybe when tagging a release we do both setup.py and [versions]?

Changelog

What follows is a history of changes from release to release. Where issue IDs are listed below, you can find out more about them by visiting the issue tracker at https://oodt.jpl.nasa.gov/jira/browse/CA.

1.0.16 — Escape all the Credentials!

  • (Various emails) Escape characters in Solr queries
  • (Various emails) When accessing a /download URL with a browser, prompt for credentials

1.0.15 — API

  • (Various emails) Add a /download API endpoint with HTTP Basic authentication
  • (Observation) Remove hard-coding of EDRN group in dev mode
  • (Observation) Add a favicon.ico

1.0.14 — WIP?

  • (Status telecon) Add a border to thumbnails and limit their size
  • Add logging to support CA-1570
  • Add support for analytics

1.0.13 — Thumbnails

  • Email, add thumbnails

1.0.12 — Gimme Some Space

  • Tag-up, Add Collaborative Group facet
  • Tag-up, Add Discipline facet
  • Tag-up, Put a little space between the tabs and the search results

1.0.11 — Status

  • Status meeting, Add the File’s computed “Description” to the search results for Files
  • Status meeting, Remove the counts since we can’t update them as checkboxes are checked/unchecked in search

1.0.10 — Meeting

  • Meeting, Truncate the description in search results with “…”
  • Meeting, In search results, include collection name and dataset name for files; and collection name for datasets
  • Meeting, If description is unavailable, don’t show “No description available”.
  • Meeting, If cohort is unknown, don’t show “Unknown cohort”
  • Meeting, Put collections, datasets, files back in order
  • Meeting, In file search results, add the content type
  • Meeting, Use tabs to separate facet controls
  • Meeting, Additional facets: organ, PI (collection); species (dataset)

1.0.9 — Proof of Concept

  • Meeting, a proof-of-concept of facet controls on search results

1.0.8 — Napster Downloads

  • Email, Make temp directory configurable
  • Email, disable downloading of multiple files if size exceeds threshold
  • Email, master checkbox to select all files wasn’t toggling child checkboxes
  • Inspection, management control panel using not using saved values as defaults

1.0.7 — Descriptive

  • CA-1566, Show file-level “Description” field

1.0.6 — Tidbits

  • CA-1564, Wrong bread-crumbing for dataset
  • CA-1565, Show a better form for the FileType

1.0.5 — Matinée Performance

  • CA-1531, Internal Server Error when downloading multiple files
  • CA-1556, Session cookie doesn’t expire
  • CA-1562, LabCAS UI lacks a favicon.ico, fails to set <title>
  • CA-1563, Cannot expand search results on additional datasets
  • Email, explain what 🔴 means

1.0.4 — The Daily

  • CA-1557, Create direct link to LabCAS Viewers
  • CA-1558, Hide “Start Workflow” options if there are no workflows to run
  • CA-1559, Identify which fields are required when uploading a dataset
  • (Daily, CA-1561) Use plain text boxes instead of rich text fields
  • (Daily) Delete null metadata keys before executing dynamic workflow
  • (Daily) Make the “V” (for version) smaller on search results
  • (Daily) On search, do a GET not a POST; or try a POST, redirect, GET
  • (Daily) On search results, add the breadcrumbs
  • (Daily) Have the UI drop any metadata items with None values, and let Luca know as soon as it’s available

1.0.3 — Dan’s Other Email

This release addresses points raised in another eamil from Dan. There are no JIRA issues.

1.0.2 — Dan’s Email

This release addresses points raised in Dan’s email. There are no JIRA issues.

1.0.1 — Free and Clear, Baby!

  • CA-1541, Implement guided selection of choices for NIST workflow
  • CA-1485, Do not display LabcasUpload2Workflow
  • CA-1503, Controlled vocabularies for discipline, institution, organ, species, specimen type
  • CA-1504, ProtoocolName metadata field doesn’t appear
  • CA-1505, Pass identifiers based on names selected
  • CA-1506, DataCustodian should default
  • CA-1508, DatasetId should not be a UUID if a name is given
  • CA-1519, Support authorization cookie for labcas-backend
  • CA-1530, Use input.dataset.FIELD.order and input.dataset.FIELD.visible
  • CA-1532, Metadata ordering and URL type
  • CA-1533, SpeciesId, SpecimenType, and QAState not being sent
  • CA-1540, Update UI for NIST workflow
  • CA-1550, Free text search in LabCAS UI

1.0.0 — Wait, That’s Not His First Name?

  • CA-1478, Suppress display of LabCAS Product and ECAS Product
  • CA-1479, Replace EDRN with MCL
  • CA-1480, Remove mentions of collaborative groups since MCL doesn’t have them
  • CA-1481, Replace OrganSite with Organ
  • CA-1482, Do not display both Title and Name for a Collection (they are the same)
  • CA-1483, Do not display UNKNOWN fields
  • CA-1484, Missing metadata fields in UI display

0.0.3 — Yes I Would Care to Make a Release

  • CA-1475, LabCAS backend changes caused issues for UI
  • CA-1475, Permissions in LabCAS UI
  • CA-1474, Double collections/collections path in LabCAS UI
  • CA-1473, Remove pre-staged files from aborted uploads
  • CA-1472, Differentiate between upload and non-upload workflows
  • CA-1471, Use workflow’s CollectionName to select the staging directory instead of asking for a target collection
  • CA-1422, Support browsing of collections / datasets / files
  • CA-1451, Display more human collection names
  • CA-1452, Use “DownloadId” to download files
  • CA-1457, Expose Data Upload on top-level page
  • CA-1458, Upload to sub-directory
  • CA-1461, Workflow invocation should not be hard-coded

0.0.2 — TBD

  • CA-1381, Increase the number of files displayed by LabCAS UI
  • CA-1382, Support for NIST dataset ID generation
  • CA-1384, Use pull-downs for menus with many choices
  • CA-1386, UI should respect the order of the field values (won’t fix)
  • CA-1387, Labcas Upload UI does not send the ProtocolId
  • CA-1391, Cannot run UnivColoLungImage workflow on labcas-dev
  • CA-1392, CA-1393, Support rich text
  • CA-1394, LabCAS UI should generate dataset IDs
  • CA-1395, Change “NormalizationMethod” to “Method”
  • CA-1399, Remove HTML tags around DatasetDescription
  • CA-1403, Implement QAState=public in LabCAS UI
  • CA-1404, Chrome date input issue
  • CA-1405, Move Upload button to the top
  • CA-1408, URL to PI leads back to dataset, but with a “#” at the end
  • CA-1409, Collaborative Group URLs work only for two collaborative groups

0.0.1 — Jackie

  • CA-1332, fixed RNA sequence upload
  • CA-1333, added fields for booleans and URIs.
  • CA-1345, “Date” and “ProtocolID” fields not appearing in LabCAS UI
  • CA-1343, LabCAS UI should display images inline and not force the browser to download them
  • CA-1346, Double metadata entries
  • CA-1357, People and protocols not updating
  • CA-1354, Don’t prompt for both Protocol Name and Protocol ID, but display both after uploading
  • CA-1356, Collaborative group metadata field is plain text, should be restricted values
  • CA-1355, “OwnerGroup” should be check boxes, not a free text field
  • CA-1358, On dataset list change “Product” in table header to “Dataset”
  • CA-1359, Add a N/A option to Collaborative Group
  • CA-1360, Change name of “Owner Group” to something like “Share data with…”
  • CA-1362, Show all groups; default to groups of which you are a mamber
  • CA-1363, Disable upload button if you’re not a member of any group, and add a contact notice
  • CA-1366, Help text when hovering over “Share Data with…” is weird
  • CA-1373, “Share data with…” field too error-prone
  • CA-1364, Who is currently logged in
  • CA-1365, No logout button
  • CA-1368, Data may not be immediately available
  • CA-1374, Make “Generic LabCAS Dataset” the first workflow and rename it to “Standard LabCAS Dataset”
  • CA-1377, Must distribute Plupload because of GPL
  • CA-1361, LabCAS UI no longer overrides title & description for “OwnerGroup”

0.0.0 — Unreleased

  • CA-1331, Release to operations
Release History

Release History

This version
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1.0.16

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1.0.15

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1.0.14

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1.0.13

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1.0.12

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1.0.11

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1.0.10

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1.0.9

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1.0.8

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1.0.7

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1.0.6

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1.0.5

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1.0.4

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1.0.3

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1.0.2

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1.0.1

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1.0.0

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0.0.3

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0.0.2

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0.0.1

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0.0.0

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