{ "info": { "author": "Sean Kelly", "author_email": "sean.kelly@jpl.nasa.gov", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Environment :: Web Environment", "Framework :: Pyramid", "Intended Audience :: Healthcare Industry", "Intended Audience :: Science/Research", "License :: OSI Approved :: Apache Software License", "Operating System :: OS Independent", "Programming Language :: Python", "Topic :: Internet :: WWW/HTTP", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries :: Python Modules" ], "description": "**************\nedrn.labcas.ui\n**************\n\nUser interface for the Early Detection Research Network (EDRN_) Laboratory\nCatalog and Archive System (LabCAS_). Developed by the EDRN Informatics Center\n(IC_), operated by the Jet Propulsion Laboratory (JPL_), which itself is\noperated by the California Institute of Technology (CalTech_).\n\n\nRunning a Development Instance\n==============================\n\nEasy. First copy ``dev.cfg.in`` to ``dev.cfg`` and set the\n``ldap-manager-password`` in the ``[secrets]`` section. Then::\n\n 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\n python2.7 bootstrap.py -c dev.cfg\n bin/buildout -c dev.cfg\n bin/pserve --reload parts/templates/paste-dev.cfg \n\nThen visit http://localhost:6543/ with a browser.\n\n\n.. _EDRN: http://edrn.nci.nih.gov/\n.. _LabCAS: http://cancer.jpl.nasa.gov/documents/applications/laboratory-catalog-and-archive-service-labcas\n.. _IC: http://cancer.jpl.nasa.gov/\n.. _JPL: http://www.jpl.nasa.gov/\n.. _CalTech: http://www.caltech.edu/\n\n\n\nInstallation\n============\n\n1. Download the src\n2. Add [versions] in etc/versions/eggs.cfg\n3. Copy ops.cfg.in to ops.cfg; if you re-use last version's ops.cfg, *change*\n the session and authorization tokens!\n4. Run buildout\n5. Fix cronjob\n6. Run initial cron\n7. Fix symlink\n8. Restart web server\n9. Log in, hit Manage, set the settings\n\nMaybe when tagging a release we do both setup.py and [versions]?\n\n\nChangelog\n=========\n\nWhat follows is a history of changes from release to release. Where issue IDs\nare listed below, you can find out more about them by visiting the issue\ntracker at https://oodt.jpl.nasa.gov/jira/browse/CA.\n\n\n1.0.17 \u2014\u00a0The Oppression of the Hierarchy\n----------------------------------------\n\n\u2022 (Telecon) Download multiple files in a dataset (WIP)\n\u2022 (Luca's email) Limit size of thumbnail on file-level view\n\u2022 (Luca's email) Show multiple PIs\n\u2022 (Luca's & Paul's email) Show multiple PIs on public collections too\n\u2022 CA-1582: LabCAS Login - Reset Password\n\u2022 CA-1583: LabCAS link back to Portal\n\u2022 CA-1584: LabCAS update copyright date\n\u2022 CA-1585: Add About Tab to LabCAS\n\u2022 CA-1586: Update UI to support hierarchical datasets\n\n\n1.0.16 \u2014 Escape *all* the Credentials!\n--------------------------------------\n\n\u2022 (Various emails) Escape characters in Solr queries\n\u2022 (Various emails) When accessing a /download URL with a browser, prompt for\n credentials\n\n\n1.0.15 \u2014 API\n------------\n\n\u2022 (Various emails) Add a /download API endpoint with HTTP Basic authentication\n\u2022 (Observation) Remove hard-coding of EDRN group in dev mode\n\u2022 (Observation) Add a favicon.ico\n\n\n1.0.14 \u2014 WIP?\n-------------\n\n\u2022 (Status telecon) Add a border to thumbnails and limit their size\n\u2022 Add logging to support CA-1570\n\u2022 Add support for analytics\n\n\n1.0.13 \u2014 Thumbnails\n-------------------\n\n\u2022 Email, add thumbnails\n\n\n1.0.12 \u2014 Gimme Some Space\n-------------------------\n\n\u2022 Tag-up, Add Collaborative Group facet\n\u2022 Tag-up, Add Discipline facet\n\u2022 Tag-up, Put a little space between the tabs and the search results\n\n\n1.0.11 \u2014 Status\n---------------\n\n\u2022 Status meeting, Add the File's computed \"Description\" to the search results for Files\n\u2022 Status meeting, Remove the counts since we can't update them as checkboxes are checked/unchecked in search\n\n\n1.0.10 \u2014\u00a0Meeting\n----------------\n\n\u2022 Meeting, Truncate the description in search results with \"\u2026\"\n\u2022 Meeting, In search results, include collection name and dataset name for files; and collection name for datasets\n\u2022 Meeting, If description is unavailable, don't show \"No description available\".\n\u2022 Meeting, If cohort is unknown, don't show \"Unknown cohort\"\n\u2022 Meeting, Put collections, datasets, files back in order\n\u2022 Meeting, In file search results, add the content type\n\u2022 Meeting, Use tabs to separate facet controls\n\u2022 Meeting, Additional facets: organ, PI (collection); species (dataset)\n\n\n1.0.9 \u2014 Proof of Concept\n------------------------\n\n\u2022 Meeting, a proof-of-concept of facet controls on search results\n\n\n1.0.8 \u2014 Napster Downloads\n-------------------------\n\n\u2022 Email, Make temp directory configurable\n\u2022 Email, disable downloading of multiple files if size exceeds threshold\n\u2022 Email, master checkbox to select all files wasn't toggling child checkboxes\n\u2022 Inspection, management control panel using not using saved values as defaults\n\n\n1.0.7 \u2014 Descriptive\n-------------------\n\n\u2022 CA-1566, Show file-level \"Description\" field\n\n\n1.0.6 \u2014 Tidbits\n---------------\n\n\u2022 CA-1564, Wrong bread-crumbing for dataset\n\u2022 CA-1565, Show a better form for the FileType\n\n\n1.0.5 \u2014 Matin\u00e9e Performance\n---------------------------\n\n\u2022 CA-1531, Internal Server Error when downloading multiple files\n\u2022 CA-1556, Session cookie doesn't expire\n\u2022 CA-1562, LabCAS UI lacks a favicon.ico, fails to set \n\u2022 CA-1563, Cannot expand search results on additional datasets\n\u2022 Email, explain what \ud83d\udd34 means\n\n\n1.0.4 \u2014\u00a0The Daily\n-----------------\n\n\u2022 CA-1557, Create direct link to LabCAS Viewers\n\u2022 CA-1558, Hide \"Start Workflow\" options if there are no workflows to run\n\u2022 CA-1559, Identify which fields are required when uploading a dataset\n\u2022 (Daily, CA-1561) Use plain text boxes instead of rich text fields\n\u2022 (Daily) Delete null metadata keys before executing dynamic workflow\n\u2022 (Daily) Make the \"V\" (for version) smaller on search results\n\u2022 (Daily) On search, do a GET not a POST; or try a POST, redirect, GET\n\u2022 (Daily) On search results, add the breadcrumbs\n\u2022 (Daily) Have the UI drop any metadata items with None values, and let Luca\n know as soon as it's available\n\n\n1.0.3 \u2014 Dan's Other Email\n-------------------------\n\nThis release addresses points raised in another eamil from Dan. There are *no*\nJIRA issues.\n\n\n1.0.2 \u2014\u00a0Dan's Email\n-------------------\n\nThis release addresses points raised in Dan's email. There are *no* JIRA\nissues.\n\n\n1.0.1 \u2014 Free and Clear, Baby!\n-----------------------------\n\n\u2022 CA-1541, Implement guided selection of choices for NIST workflow\n\u2022 CA-1485, Do not display LabcasUpload2Workflow\n\u2022 CA-1503, Controlled vocabularies for discipline, institution, organ, species, specimen type\n\u2022 CA-1504, ProtoocolName metadata field doesn't appear\n\u2022 CA-1505, Pass identifiers based on names selected\n\u2022 CA-1506, DataCustodian should default\n\u2022 CA-1508, DatasetId should not be a UUID if a name is given\n\u2022 CA-1519, Support authorization cookie for labcas-backend\n\u2022 CA-1530, Use input.dataset.FIELD.order and input.dataset.FIELD.visible\n\u2022 CA-1532, Metadata ordering and URL type\n\u2022 CA-1533, SpeciesId, SpecimenType, and QAState not being sent\n\u2022 CA-1540, Update UI for NIST workflow\n\u2022 CA-1550, Free text search in LabCAS UI\n\n\n1.0.0 \u2014 Wait, That's Not His First Name?\n----------------------------------------\n\n\u2022 CA-1478, Suppress display of LabCAS Product and ECAS Product\n\u2022 CA-1479, Replace EDRN with MCL\n\u2022 CA-1480, Remove mentions of collaborative groups since MCL doesn't have them\n\u2022 CA-1481, Replace OrganSite with Organ\n\u2022 CA-1482, Do not display both Title and Name for a Collection (they are the\n same)\n\u2022 CA-1483, Do not display UNKNOWN fields\n\u2022 CA-1484, Missing metadata fields in UI display\n\n\n0.0.3 \u2014 Yes I Would Care to Make a Release\n------------------------------------------\n\n\u2022 CA-1475, LabCAS backend changes caused issues for UI\n\u2022 CA-1475, Permissions in LabCAS UI\n\u2022 CA-1474, Double collections/collections path in LabCAS UI\n\u2022 CA-1473, Remove pre-staged files from aborted uploads\n\u2022 CA-1472, Differentiate between upload and non-upload workflows\n\u2022 CA-1471, Use workflow's CollectionName to select the staging directory\n instead of asking for a target collection\n\u2022 CA-1422, Support browsing of collections / datasets / files\n\u2022 CA-1451, Display more human collection names\n\u2022 CA-1452, Use \"DownloadId\" to download files\n\u2022 CA-1457, Expose Data Upload on top-level page\n\u2022 CA-1458, Upload to sub-directory\n\u2022 CA-1461, Workflow invocation should not be hard-coded\n\n\n0.0.2 \u2014\u00a0TBD\n-----------\n\n\u2022 CA-1381, Increase the number of files displayed by LabCAS UI\n\u2022 CA-1382, Support for NIST dataset ID generation\n\u2022 CA-1384, Use pull-downs for menus with many choices\n\u2022 CA-1386, UI should respect the order of the field values (won't fix)\n\u2022 CA-1387, Labcas Upload UI does not send the ProtocolId\n\u2022 CA-1391, Cannot run UnivColoLungImage workflow on labcas-dev\n\u2022 CA-1392, CA-1393, Support rich text\n\u2022 CA-1394, LabCAS UI should generate dataset IDs\n\u2022 CA-1395, Change \"NormalizationMethod\" to \"Method\"\n\u2022 CA-1399, Remove HTML tags around DatasetDescription\n\u2022 CA-1403, Implement QAState=public in LabCAS UI\n\u2022 CA-1404, Chrome date input issue\n\u2022 CA-1405, Move Upload button to the top\n\u2022 CA-1408, URL to PI leads back to dataset, but with a \"#\" at the end\n\u2022 CA-1409, Collaborative Group URLs work only for two collaborative groups\n\n\n0.0.1 \u2014 Jackie\n--------------\n\n\u2022 CA-1332, fixed RNA sequence upload\n\u2022 CA-1333, added fields for booleans and URIs.\n\u2022 CA-1345, \"Date\" and \"ProtocolID\" fields not appearing in LabCAS UI\n\u2022 CA-1343, LabCAS UI should display images inline and not force the browser to\n download them\n\u2022 CA-1346, Double metadata entries\n\u2022 CA-1357, People and protocols not updating\n\u2022 CA-1354, Don't prompt for both Protocol Name and Protocol ID, but display\n both after uploading\n\u2022 CA-1356, Collaborative group metadata field is plain text, should be\n restricted values\n\u2022 CA-1355, \"OwnerGroup\" should be check boxes, not a free text field\n\u2022 CA-1358, On dataset list change \"Product\" in table header to \"Dataset\"\n\u2022 CA-1359, Add a N/A option to Collaborative Group\n\u2022 CA-1360, Change name of \"Owner Group\" to something like \"Share data with\u2026\"\n\u2022 CA-1362, Show all groups; default to groups of which you are a mamber\n\u2022 CA-1363, Disable upload button if you're not a member of any group, and add\n a contact notice\n\u2022 CA-1366, Help text when hovering over \"Share Data with\u2026\" is weird\n\u2022 CA-1373, \"Share data with\u2026\" field too error-prone\n\u2022 CA-1364, Who is currently logged in\n\u2022 CA-1365, No logout button\n\u2022 CA-1368, Data may not be immediately available\n\u2022 CA-1374, Make \"Generic LabCAS Dataset\" the first workflow and rename it to\n \"Standard LabCAS Dataset\"\n\u2022 CA-1377, Must distribute Plupload because of GPL\n\u2022 CA-1361, LabCAS UI no longer overrides title & description for \"OwnerGroup\"\n\n\n0.0.0 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