From d0074e832dbf8739bca1e29f1714ecf9e14af574 Mon Sep 17 00:00:00 2001 From: learner97 Date: Tue, 7 May 2024 14:28:54 -0600 Subject: [PATCH 1/4] adding althome to sbh1 and backend --- lib/views/admin/theme.js | 1 + lib/views/setup.js | 8 ++++++++ templates/views/setup.jade | 4 ++++ 3 files changed, 13 insertions(+) diff --git a/lib/views/admin/theme.js b/lib/views/admin/theme.js index 51f7ee3a..72f4f2c3 100644 --- a/lib/views/admin/theme.js +++ b/lib/views/admin/theme.js @@ -41,6 +41,7 @@ function form (req, res) { uriPrefix: config.get('databasePrefix'), frontPageText: config.get('frontPageText'), firstLaunch: config.get('firstLaunch'), + altHome: config.get('altHome'), currentTheme: currentTheme, themeParameters: themeParameters } diff --git a/lib/views/setup.js b/lib/views/setup.js index 3052622c..9b0b5b05 100644 --- a/lib/views/setup.js +++ b/lib/views/setup.js @@ -22,6 +22,7 @@ const settingsSchema = Joi.object({ frontendURL: requiredString('Please enter the frontend URL of your instance'), instanceUrl: requiredString('Please enter the backend URL of your instance'), uriPrefix: requiredString('Please enter the URI prefix of your instance'), + altHome: requiredString('Please enter your alternate homepage'), frontPageText: requiredString('Please enter some welcome text for your homepage'), userPassword: requiredString('Please enter a password for the initial user account', { trim: false }), userPasswordConfirm: requiredString("Passwords didn't match", { trim: false }).valid(Joi.ref('userPassword')), @@ -58,6 +59,7 @@ module.exports = function (req, res) { frontendURL: req.protocol + '://' + req.get('Host') + '/', instanceUrl: req.protocol + '://' + req.get('Host') + '/', uriPrefix: req.protocol + '://' + req.get('Host') + '/', + altHome: req.protocol + '://' + req.get('Host') + '/', userName: '', affiliation: '', userFullName: '', @@ -96,6 +98,7 @@ async function setupPost (req, res, settings) { frontendURL: req.body.frontendURL, instanceUrl: req.body.instanceUrl, uriPrefix: req.body.uriPrefix, + altHome: req.body.altHome, userName: req.body.userName, affiliation: req.body.affiliation, userFullName: req.body.userFullName, @@ -129,6 +132,10 @@ async function setupPost (req, res, settings) { updatedSettings.uriPrefix += '/' } + if (updatedSettings.altHome && updatedSettings.altHome[updatedSettings.altHome.length - 1] !== '/') { + updatedSettings.altHome += '/' + } + if (error) { if (req.accepts('text/html')) { return setupForm(req, res, updatedSettings, { @@ -156,6 +163,7 @@ async function setupPost (req, res, settings) { config.set('frontPageText', updatedSettings.frontPageText) config.set('allowPublicSignup', updatedSettings.allowPublicSignup) config.set('databasePrefix', updatedSettings.uriPrefix) + config.set('altHome', updatedSettings.altHome) config.set('triplestore', { ...config.get('triplestore'), diff --git a/templates/views/setup.jade b/templates/views/setup.jade index 77ee42e3..7f66bd46 100644 --- a/templates/views/setup.jade +++ b/templates/views/setup.jade @@ -66,6 +66,10 @@ block body | We need to know how to prefix URIs of objects stored in this SynBioHub. Its default is the same as the URL, and should only be changed if you are shadowing another instance. label URI Prefix input.form-control(name='uriPrefix',value=settings.uriPrefix) + p + | We need to know where if you would like to set up your own home page. + label Alternate Home Page + input.form-control(name='altHome',value=settings.altHome) p | We need to know where the Virtuoso INI is stored. We have guessed it to be b #{config.triplestore.virtuosoINI} From 7ac35cee73dcd90e1b68183fc7ae4eeee7e4a8dc Mon Sep 17 00:00:00 2001 From: learner97 Date: Thu, 9 May 2024 13:43:26 -0600 Subject: [PATCH 2/4] cahnged some setup stuff back to account for no frontend setting for sbh1 --- lib/views/admin/theme.js | 7 +++++++ lib/views/setup.js | 8 ++++---- templates/views/setup.jade | 12 +----------- tests/first_time_setup.py | 2 +- tests/previousresults/getrequest_setup_.html | 13 +------------ 5 files changed, 14 insertions(+), 28 deletions(-) diff --git a/lib/views/admin/theme.js b/lib/views/admin/theme.js index 72f4f2c3..d7ddc54d 100644 --- a/lib/views/admin/theme.js +++ b/lib/views/admin/theme.js @@ -113,6 +113,13 @@ function post (req, res) { publishUpdate = true } + console.log(typeof (req.body)) + + if (typeof req.body === 'object' && 'altHome' in req.body && req.body.altHome !== config.get('altHome')) { + config.set('altHome', req.body.altHome) + publishUpdate = true + } + if (publishUpdate) { updateWor() } diff --git a/lib/views/setup.js b/lib/views/setup.js index 9b0b5b05..3a2606bd 100644 --- a/lib/views/setup.js +++ b/lib/views/setup.js @@ -19,10 +19,10 @@ const settingsSchema = Joi.object({ userName: requiredString('Please enter a username for the initial user account'), userFullName: requiredString('Please enter a full name for the initial user account'), userEmail: requiredString('Please enter a valid e-mail address for the initial user account').email(), - frontendURL: requiredString('Please enter the frontend URL of your instance'), + frontendURL: Joi.string().allow(''), instanceUrl: requiredString('Please enter the backend URL of your instance'), uriPrefix: requiredString('Please enter the URI prefix of your instance'), - altHome: requiredString('Please enter your alternate homepage'), + altHome: Joi.string().allow(''), frontPageText: requiredString('Please enter some welcome text for your homepage'), userPassword: requiredString('Please enter a password for the initial user account', { trim: false }), userPasswordConfirm: requiredString("Passwords didn't match", { trim: false }).valid(Joi.ref('userPassword')), @@ -56,10 +56,10 @@ module.exports = function (req, res) { const settings = { instanceName: 'My SynBioHub', - frontendURL: req.protocol + '://' + req.get('Host') + '/', + frontendURL: '', instanceUrl: req.protocol + '://' + req.get('Host') + '/', uriPrefix: req.protocol + '://' + req.get('Host') + '/', - altHome: req.protocol + '://' + req.get('Host') + '/', + altHome: '', userName: '', affiliation: '', userFullName: '', diff --git a/templates/views/setup.jade b/templates/views/setup.jade index 7f66bd46..d8719596 100644 --- a/templates/views/setup.jade +++ b/templates/views/setup.jade @@ -50,26 +50,16 @@ block body br h2 2. Some technical details div.form-group - p - | Frontend Url: We need to know where this SynBioHub instance is is displayed. If the URL below is incorrect, please change it - b #{settings.frontendURL} - |, but if this is incorrect, please change it here. - label Frontend URL - input.form-control(name='frontendURL',value=settings.frontendURL) p | Backend Url: We need to know where this SynBioHub instance is hosted so we can assign URLs to your submissions. The instance URL has been automatically guessed as b #{settings.instanceUrl} |, but if this is incorrect, please change it here. label Instance URL - input.form-control(name='instanceURL',value=settings.instanceUrl) + input.form-control(name='instanceUrl',value=settings.instanceUrl) p | We need to know how to prefix URIs of objects stored in this SynBioHub. Its default is the same as the URL, and should only be changed if you are shadowing another instance. label URI Prefix input.form-control(name='uriPrefix',value=settings.uriPrefix) - p - | We need to know where if you would like to set up your own home page. - label Alternate Home Page - input.form-control(name='altHome',value=settings.altHome) p | We need to know where the Virtuoso INI is stored. We have guessed it to be b #{config.triplestore.virtuosoINI} diff --git a/tests/first_time_setup.py b/tests/first_time_setup.py index 9240a5a3..767198b9 100644 --- a/tests/first_time_setup.py +++ b/tests/first_time_setup.py @@ -25,7 +25,7 @@ def test_post(self): 'userEmail': 'test@user.synbiohub', 'userPassword': 'test', 'userPasswordConfirm': 'test', - 'instanceName': 'Test Synbiohub', 'frontendURL': 'http://localhost:7777', + 'instanceName': 'Test Synbiohub', 'instanceUrl': 'http://localhost:7777/', 'uriPrefix': 'http://localhost:7777/', 'color': '#D25627', diff --git a/tests/previousresults/getrequest_setup_.html b/tests/previousresults/getrequest_setup_.html index 388a5b5b..e0ec142a 100644 --- a/tests/previousresults/getrequest_setup_.html +++ b/tests/previousresults/getrequest_setup_.html @@ -100,17 +100,6 @@

2. Some technical details

-

- Frontend Url: We need to know where this SynBioHub instance is is displayed. If the URL below is incorrect, please change it - - http://localhost:7777/ - - , but if this is incorrect, please change it here. -

-

Backend Url: We need to know where this SynBioHub instance is hosted so we can assign URLs to your submissions. The instance URL has been automatically guessed as @@ -120,7 +109,7 @@

We need to know how to prefix URIs of objects stored in this SynBioHub. Its default is the same as the URL, and should only be changed if you are shadowing another instance. From 863a41ef7ccb7f564c9e929af79f03eb9d0ae6df Mon Sep 17 00:00:00 2001 From: learner97 Date: Thu, 9 May 2024 14:02:25 -0600 Subject: [PATCH 3/4] made a change to allow frontendURL to be empty (cannot set on SBH1) --- lib/views/setup.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/views/setup.js b/lib/views/setup.js index 3a2606bd..a6590e84 100644 --- a/lib/views/setup.js +++ b/lib/views/setup.js @@ -95,7 +95,7 @@ async function setupPost (req, res, settings) { { ...settings, instanceName: req.body.instanceName, - frontendURL: req.body.frontendURL, + frontendURL: req.body.frontendURL || '', instanceUrl: req.body.instanceUrl, uriPrefix: req.body.uriPrefix, altHome: req.body.altHome, From 13a115ccba8f84e0a4931bcf735240c0287ede80 Mon Sep 17 00:00:00 2001 From: learner97 Date: Mon, 13 May 2024 11:28:54 -0400 Subject: [PATCH 4/4] fixed issue with setup with althome --- lib/views/setup.js | 2 +- ...:collectionId-:displayId-:version-gff_.xml | 438 +++++++++--------- ...collectionId-:displayId-:version-omex_.xml | Bin 7542 -> 7552 bytes ...collectionId-:displayId-:version-sbol_.xml | 60 +-- ...llectionId-:displayId-:version-sbolnr_.xml | 16 +- ..._public-:collectionId-:displayId-sbol_.xml | 60 +-- ...ublic-:collectionId-:displayId-sbolnr_.xml | 60 +-- ...:collectionId-:displayId-:version-gff_.xml | 432 ++++++++--------- ...collectionId-:displayId-:version-omex_.xml | Bin 7625 -> 7597 bytes tests/test_functions.py | 2 +- 10 files changed, 535 insertions(+), 535 deletions(-) diff --git a/lib/views/setup.js b/lib/views/setup.js index a6590e84..8fb2912a 100644 --- a/lib/views/setup.js +++ b/lib/views/setup.js @@ -98,7 +98,7 @@ async function setupPost (req, res, settings) { frontendURL: req.body.frontendURL || '', instanceUrl: req.body.instanceUrl, uriPrefix: req.body.uriPrefix, - altHome: req.body.altHome, + altHome: req.body.altHome || '', userName: req.body.userName, affiliation: req.body.affiliation, userFullName: req.body.userFullName, diff --git a/tests/previousresults/get_file_public-:collectionId-:displayId-:version-gff_.xml b/tests/previousresults/get_file_public-:collectionId-:displayId-:version-gff_.xml index 2d25d7d0..209926df 100644 --- a/tests/previousresults/get_file_public-:collectionId-:displayId-:version-gff_.xml +++ b/tests/previousresults/get_file_public-:collectionId-:displayId-:version-gff_.xml @@ -1,5 +1,82 @@ + + + part_pIKE_Toggle_1 + 1 + LacI/TetR Toggle Switch + LacI/TetR Toggle Switch + + + + + + + + pIKELeftCassette_1 + 1 + + + + + + + + + + pIKERightCassette_1 + 1 + + + + + + + + + + anno2 + 1 + + + + + + location2 + 1 + + + 1286 + 2834 + + + + + + + + + + anno1 + 1 + + + + + + location1 + 1 + + + 1 + 1285 + + + + + + + BBa_R0040 @@ -48,6 +125,42 @@ + + + ECK120033736 + 1 + ECK120033736 + Terminator2 + + + + + + + + + BBa_C0040 + 1 + tetR + tetR coding sequence + + + + + + + + + BBa_J61130 + 1 + BBa_J61101 RBS + RBS2 + + + + + + part_pIKERightCassette_1 @@ -59,36 +172,36 @@ - - - BBa_C0040 + + + BBa_J61130 1 - + - - - BBa_R0010 + + + ECK120033736 1 - + - - - BBa_J61130 + + + BBa_J61120 1 - + @@ -103,69 +216,69 @@ - - - BBa_J61120 + + + BBa_R0010 1 - + - - - ECK120033736 + + + BBa_C0040 1 - + - - - anno6 + + + anno2 1 - - - location6 + + + location2 1 - 1464 - 1554 + 56 + 68 - + - - - anno3 + + + anno6 1 - - - location3 + + + location6 1 - 69 - 729 + 1464 + 1554 - + @@ -191,25 +304,25 @@ - - - anno2 + + + anno5 1 - - - location2 + + + location5 1 - 56 - 68 + 743 + 1463 - + @@ -235,51 +348,51 @@ - - - anno5 + + + anno3 1 - - - location5 + + + location3 1 - 743 - 1463 + 69 + 729 - + - - - ECK120033736 + + + BBa_J61120 1 - ECK120033736 - Terminator2 - + BBa_J61101 RBS + RBS2 + - - + + - - - BBa_C0040 + + + BBa_J61101 1 - tetR - tetR coding sequence - + BBa_J61101 RBS + RBS1 + - - + + @@ -292,14 +405,14 @@ - - - BBa_R0040 + + + BBa_C0012 1 - + @@ -325,58 +438,36 @@ - - - BBa_C0012 + + + BBa_R0040 1 - + - - - anno1 - 1 - - - - - - location1 - 1 - - - 1 - 55 - - - - - - - - - - anno3 + + + anno4 1 - - - location3 + + + location4 1 - 69 - 1197 + 1198 + 1288 - + @@ -402,138 +493,47 @@ - - - anno4 + + + anno3 1 - - - location4 + + + location3 1 - 1198 - 1288 + 69 + 1197 - + - - - - BBa_J61130 - 1 - BBa_J61101 RBS - RBS2 - - - - - - - - - BBa_J61120 - 1 - BBa_J61101 RBS - RBS2 - - - - - - - - - BBa_J61101 - 1 - BBa_J61101 RBS - RBS1 - - - - - - - - - part_pIKE_Toggle_1 - 1 - LacI/TetR Toggle Switch - LacI/TetR Toggle Switch - - - - - - - - pIKELeftCassette_1 - 1 - - - - - - - - - - pIKERightCassette_1 - 1 - - - - - - - - + + anno1 1 - + - - + + location1 1 - + 1 - 1285 - - - - - - - - - - anno2 - 1 - - - - - - location2 - 1 - - - 1286 - 2834 + 55 - + diff --git a/tests/previousresults/get_file_public-:collectionId-:displayId-:version-omex_.xml b/tests/previousresults/get_file_public-:collectionId-:displayId-:version-omex_.xml index 6e56bf2102c412830c0df4088c957a13370f881f..4aa7a4d5e85320696d21aaec021e055b6f5ca27f 100644 GIT binary patch literal 7552 zcmai3_j8=p6ZDaRSKz 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a/tests/previousresults/get_file_public-:collectionId-:displayId-:version-sbol_.xml +++ b/tests/previousresults/get_file_public-:collectionId-:displayId-:version-sbol_.xml @@ -11,24 +11,24 @@ - - - pIKERightCassette_1 + + + pIKELeftCassette_1 1 - + - - - pIKELeftCassette_1 + + + pIKERightCassette_1 1 - + @@ -87,6 +87,17 @@ + + + + ECK120029600 + 1 + + + + + + @@ -120,17 +131,6 @@ - - - - ECK120029600 - 1 - - - - - - @@ -230,6 +230,17 @@ + + + + BBa_J61130 + 1 + + + + + + @@ -285,17 +296,6 @@ - - - - BBa_J61130 - 1 - - - - - - diff --git a/tests/previousresults/get_file_public-:collectionId-:displayId-:version-sbolnr_.xml b/tests/previousresults/get_file_public-:collectionId-:displayId-:version-sbolnr_.xml index 34190c27..fcbedbe9 100644 --- a/tests/previousresults/get_file_public-:collectionId-:displayId-:version-sbolnr_.xml +++ b/tests/previousresults/get_file_public-:collectionId-:displayId-:version-sbolnr_.xml @@ -11,24 +11,24 @@ - - - pIKERightCassette_1 + + + pIKELeftCassette_1 1 - + - - - pIKELeftCassette_1 + + + pIKERightCassette_1 1 - + diff --git a/tests/previousresults/get_file_public-:collectionId-:displayId-sbol_.xml b/tests/previousresults/get_file_public-:collectionId-:displayId-sbol_.xml index e7cef170..2e3a41fd 100644 --- a/tests/previousresults/get_file_public-:collectionId-:displayId-sbol_.xml +++ b/tests/previousresults/get_file_public-:collectionId-:displayId-sbol_.xml @@ -11,24 +11,24 @@ - - - pIKERightCassette_1 + + + pIKELeftCassette_1 1 - + - - - pIKELeftCassette_1 + + + pIKERightCassette_1 1 - + @@ -87,6 +87,17 @@ + + + + ECK120029600 + 1 + + + + + + @@ -120,17 +131,6 @@ - - - - ECK120029600 - 1 - - - - - - @@ -230,6 +230,17 @@ + + + + BBa_J61130 + 1 + + + + + + @@ -285,17 +296,6 @@ - - - - BBa_J61130 - 1 - - - - - - diff --git a/tests/previousresults/get_file_public-:collectionId-:displayId-sbolnr_.xml b/tests/previousresults/get_file_public-:collectionId-:displayId-sbolnr_.xml index e7cef170..2e3a41fd 100644 --- a/tests/previousresults/get_file_public-:collectionId-:displayId-sbolnr_.xml +++ b/tests/previousresults/get_file_public-:collectionId-:displayId-sbolnr_.xml @@ -11,24 +11,24 @@ - - - pIKERightCassette_1 + + + pIKELeftCassette_1 1 - + - - - pIKELeftCassette_1 + + + pIKERightCassette_1 1 - + @@ -87,6 +87,17 @@ + + + + ECK120029600 + 1 + + + + + + @@ -120,17 +131,6 @@ - - - - ECK120029600 - 1 - - - - - - @@ -230,6 +230,17 @@ + + + + BBa_J61130 + 1 + + + + + + @@ -285,17 +296,6 @@ - - - - BBa_J61130 - 1 - - - - - - diff --git a/tests/previousresults/get_file_user-:userId-:collectionId-:displayId-:version-gff_.xml b/tests/previousresults/get_file_user-:userId-:collectionId-:displayId-:version-gff_.xml index 810a2487..f19df8bc 100644 --- a/tests/previousresults/get_file_user-:userId-:collectionId-:displayId-:version-gff_.xml +++ b/tests/previousresults/get_file_user-:userId-:collectionId-:displayId-:version-gff_.xml @@ -24,38 +24,129 @@ - - - part_pIKELeftCassette_1 + + + BBa_R0010 1 - TetR Inverter - TetR Inverter - + pLacI + pLacI promoter + + + + + + + + + BBa_J61101 + 1 + BBa_J61101 RBS + RBS1 + + + + + + + + + BBa_C0012 + 1 + lacI + lacI coding sequence + + + + + + + + + part_pIKE_Toggle_1 + 1 + LacI/TetR Toggle Switch + LacI/TetR Toggle Switch + - - - BBa_R0040 + + + pIKERightCassette_1 1 - + - + - - - BBa_J61101 + + + pIKELeftCassette_1 1 - + - + + + + + anno2 + 1 + + + + + + location2 + 1 + + + 1286 + 2834 + + + + + + + + + + anno1 + 1 + + + + + + location1 + 1 + + + 1 + 1285 + + + + + + + + + + part_pIKELeftCassette_1 + 1 + TetR Inverter + TetR Inverter + + + + @@ -67,6 +158,17 @@ + + + + BBa_R0040 + 1 + + + + + + @@ -78,6 +180,17 @@ + + + + BBa_J61101 + 1 + + + + + + @@ -101,25 +214,25 @@ - - - anno3 + + + anno2 1 - - - location3 + + + location2 1 - 69 - 1197 + 56 + 68 - + @@ -145,64 +258,28 @@ - - - anno2 + + + anno3 1 - - - location2 + + + location3 1 - 56 - 68 + 69 + 1197 - + - - - BBa_R0010 - 1 - pLacI - pLacI promoter - - - - - - - - - BBa_J61101 - 1 - BBa_J61101 RBS - RBS1 - - - - - - - - - BBa_C0012 - 1 - lacI - lacI coding sequence - - - - - - ECK120033736 @@ -262,91 +339,91 @@ - - - ECK120033736 + + + BBa_J61120 1 - + - - - BBa_J61130 + + + BBa_R0010 1 - + - - - BBa_E0040 + + + ECK120033736 1 - + - - - BBa_R0010 + + + BBa_C0040 1 - + - - - BBa_J61120 + + + BBa_J61130 1 - + - - - BBa_C0040 + + + BBa_E0040 1 - + - - - anno6 + + + anno5 1 - - - location6 + + + location5 1 - 1464 - 1554 + 743 + 1463 - + @@ -372,168 +449,91 @@ - - - anno1 + + + anno2 1 - - - location1 + + + location2 1 - 1 - 55 + 56 + 68 - + - - - anno5 + + + anno6 1 - - - location5 + + + location6 1 - 743 - 1463 + 1464 + 1554 - + - - - anno3 + + + anno1 1 - - - location3 + + + location1 1 - 69 - 729 + 1 + 55 - + - - - anno2 + + + anno3 1 - - - location2 + + + location3 1 - 56 - 68 - - - - - - - - - - part_pIKE_Toggle_1 - 1 - LacI/TetR Toggle Switch - LacI/TetR Toggle Switch - - - - - - - - pIKELeftCassette_1 - 1 - - - - - - - - - - pIKERightCassette_1 - 1 - - - - - - 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