gigascience / gigadb-website

Source code for running GigaDB
http://gigadb.org
GNU General Public License v3.0
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[S781] Smoke tests the new staging deployed web site #747

Closed rija closed 5 months ago

rija commented 3 years ago

Updated table with results of 20th Jan 2022 checks

Thing to check check Dec version Check Jan20 version comments
login via email [y] [y]
login via affiliates [n] [n] Now there is no option to use affiliate login (which is correct for now)
automatic emails being sent on registration [n] [?] Unable to test as I am unable to delete any of my user accounts and I dont have any unused email addresses!, this is also a bug in the live version, create ticket
automatic emails being sent on dataset submission [n] [n] Error message returned when attempting to submit a prepared spreadsheet submission, see ticket #862
does the contact us form actually send us an email [n] [n] website says thanks for contacting us, but nothing is received in database@ mailbox, Not sure if there is meant to be a confirmation sent to the sender as well or not, but I didn't receive one of those either see #863
admin login gives access to admin pages [y] [y]
general user login does NOT give access to admin pages [y] [n] unable to check as I dont have a user account and the create account doesn't work
logout works [y] [y]
reset password works [n] [n] CDbException same error as registration (n1) see #859
change password works [n] [n] CDbException same error as registration (n1) see #859
Edit your personal details works as expected [n] [n] same 2 issues as Dec version; 1 you cant update password - see reset password issue above, 2 you cant unsubscribe from the mailing list! NB the account I was using was already subscribed so I dont know if it would be possible to subscribe via the edit personal details page? see #865
edit dataset link on Your datasets work [y] [y] the layout of the submission wizard is still a mess, see #933
delete dataset link on your datasets work [n] [n] bug still present, see #866
search bar on homepage works [n] [y] still slow, see #825
search bar in header works [y] [y] but still slow see #825
search results are returned by clicking dataset types or keywords or authors [y] [y] still slow, see #825
do all admin pages allow appropriate updates to the database? [n] [y] I think they are all working
Does Google analytics still works [n] [n] see ticket #942
When i add a news item with the current date does it display on the home page? [y] [y]
do the external links in headers and footer all work (e.g. facebook, twitter etc) [y] [y]
Are the numbers on the home page accurate? (number of datasets, samples, files and volume, as well as individual dataset types) [n] [n] data volume - known bug see #531
Is the number of datasets in the banner on homepage correct [y] [y]
Is the RSS feed on home page working [y] [y] it appears to be, but not sure how to check properly
able to download files from datasets [y] [y] confirmed #858 is fixed
able to download the templates for sample and files within submission wizard [n] [n] same Error 404. Unable to resolve the request "files/GigaDBUploadForm.xls". see #867
does hypothes.is work [n] [y] not sure if its related or not, but staging now seems slower than it was
do admin tables all work as expected? [n] [n] see #943, #944, #934
rija commented 2 years ago

@only1chunts probably will notice this to, but I've stumbled upon this issue now while working on #742, and it's not related to the issue that task is for, so putting it here: it seems github links are not appearing. See http://staging.gigadb.org/dataset/100640

only1chunts commented 2 years ago

n1 - CDbException when trying to update user password or register an account

CONVERTED THIS COMMENT TO TICKET #859

CDbException

CDbCommand failed to execute the SQL statement: SQLSTATE[22001]: String data, right truncated: 7 ERROR: value too long for type character varying(64). The SQL statement executed was: UPDATE "gigadb_user" SET "id"=:yp0, "email"=:yp1, "password"=:yp2, "first_name"=:yp3, "last_name"=:yp4, "affiliation"=:yp5, "role"=:yp6, "is_activated"=:yp7, "newsletter"=:yp8, "previous_newsletter_state"=:yp9, "facebook_id"=:yp10, "twitter_id"=:yp11, "linkedin_id"=:yp12, "google_id"=:yp13, "username"=:yp14, "orcid_id"=:yp15, "preferred_link"=:yp16 WHERE "gigadb_user"."id"=35. Bound with :yp0=35, :yp1='only1chunts@gmail.com', :yp2='$argon2id$v=19$m=65536,t=2,p=1$DrmhmKjMKz8k41rg9Wc9LA$E0rSktXtxL6msxt/VQeG6tqRSdXRxTTnDzZbLNCSnsk', :yp3='Chris', :yp4='Hunter', :yp5='GigaDB', :yp6='user', :yp7=true, :yp8=true, :yp9=false, :yp10=NULL, :yp11=NULL, :yp12=NULL, :yp13=NULL, :yp14='only1chunts@gmail.com', :yp15=NULL, :yp16='EBI'

/var/www/vendor/yiisoft/yii/framework/db/CDbCommand.php(358)

346         {
347             if($this->_connection->enableProfiling)
348                 Yii::endProfile('system.db.CDbCommand.execute('.$this->getText().$par.')','system.db.CDbCommand.execute');
349 
350             $errorInfo=$e instanceof PDOException ? $e->errorInfo : null;
351             $message=$e->getMessage();
352             Yii::log(Yii::t('yii','CDbCommand::execute() failed: {error}. The SQL statement executed was: {sql}.',
353                 array('{error}'=>$message, '{sql}'=>$this->getText().$par)),CLogger::LEVEL_ERROR,'system.db.CDbCommand');
354 
355             if(YII_DEBUG)
356                 $message.='. The SQL statement executed was: '.$this->getText().$par;
357 
358             throw new CDbException(Yii::t('yii','CDbCommand failed to execute the SQL statement: {error}',
359                 array('{error}'=>$message)),(int)$e->getCode(),$errorInfo);
360         }
361     }
362 
363     /**
364      * Executes the SQL statement and returns query result.
365      * This method is for executing an SQL query that returns result set.
366      * @param array $params input parameters (name=>value) for the SQL execution. This is an alternative
367      * to {@link bindParam} and {@link bindValue}. If you have multiple input parameters, passing
368      * them in this way can improve the performance. Note that if you pass parameters in this way,
369      * you cannot bind parameters or values using {@link bindParam} or {@link bindValue}, and vice versa.
370      * Please also note that all values are treated as strings in this case, if you need them to be handled as

Stack Trace

#0 | +  /var/www/vendor/yiisoft/yii/framework/db/ar/CActiveRecord.php(1756): CDbCommand->execute() -- | -- #1 | +  /var/www/vendor/yiisoft/yii/framework/db/ar/CActiveRecord.php(1130): CActiveRecord->updateByPk(35, array("id" => 35, "email" => "only1chunts@gmail.com", "password" => "$argon2id$v=19$m=65536,t=2,p=1$DrmhmKjMKz8k41rg9Wc9LA$E0rSktXtxL...", "first_name" => "Chris", ...)) #2 | +  /var/www/vendor/yiisoft/yii/framework/db/ar/CActiveRecord.php(811): CActiveRecord->update(null) #3 | –  /var/www/protected/models/ChangePasswordForm.php(46): CActiveRecord->save(false)41 $user->password = $this->password; 42 $user->password_repeat = $this->confirmPassword; 43 $user->newsletter = $this->newsletter; 44 $user->encryptPassword(); 45 46 if($user->save(false)) { 47 return true; 48 } 49 } 50 return false; 51 } #4 | –  /var/www/protected/controllers/UserController.php(406): ChangePasswordForm->changePass()401 402 if(isset($_POST['ChangePasswordForm'])) 403 { 404 $model->attributes=$_POST['ChangePasswordForm']; 405 $model->newsletter=$_POST['ChangePasswordForm']['newsletter']; 406 if($model->validate() && $model->changePass()) 407 $this->redirect('/user/view_profile'); 408 } 409 $model->password = $model->confirmPassword = ''; 410 $this->render('changePassword',array('model'=>$model)); 411 } #5 | +  /var/www/vendor/yiisoft/yii/framework/web/actions/CInlineAction.php(49): UserController->actionChangePassword() #6 | +  /var/www/vendor/yiisoft/yii/framework/web/CController.php(308): CInlineAction->runWithParams(array()) #7 | +  /var/www/vendor/yiisoft/yii/framework/web/filters/CFilterChain.php(134): CController->runAction(CInlineAction) #8 | +  /var/www/vendor/yiisoft/yii/framework/web/filters/CFilter.php(40): CFilterChain->run() #9 | +  /var/www/vendor/yiisoft/yii/framework/web/CController.php(1148): CFilter->filter(CFilterChain) #10 | +  /var/www/vendor/yiisoft/yii/framework/web/filters/CInlineFilter.php(58): CController->filterAccessControl(CFilterChain) #11 | +  /var/www/vendor/yiisoft/yii/framework/web/filters/CFilterChain.php(131): CInlineFilter->filter(CFilterChain) #12 | +  /var/www/vendor/yiisoft/yii/framework/web/CController.php(291): CFilterChain->run() #13 | +  /var/www/vendor/yiisoft/yii/framework/web/CController.php(265): CController->runActionWithFilters(CInlineAction, array("accessControl")) #14 | +  /var/www/vendor/yiisoft/yii/framework/web/CWebApplication.php(282): CController->run("changePassword") #15 | +  /var/www/vendor/yiisoft/yii/framework/web/CWebApplication.php(141): CWebApplication->runController("user/changePassword") #16 | +  /var/www/vendor/yiisoft/yii/framework/base/CApplication.php(185): CWebApplication->processRequest() #17 | –  /var/www/index.php(23): CApplication->run()18 require_once($composer); 19 20 # Run the Yii1.1 application 21 Yii::$enableIncludePath = false; 22 $config=dirname(__FILE__).'/protected/config/main.php'; 23 Yii::createWebApplication($config)->run();
2021-11-30 10:59:00 nginx/1.21.3 Yii Framework/1.1.20-yii2-2.0.15.1-migration
rija commented 2 years ago

Another problem I noticed, iframe in tabs that are not of type "Protocols.io","JBrowse","3D Models", "Code Ocean" won't load due to limitation of server side code. I discovered it as part of #742, but it's not related to CSP configuration so it won't be tackled in that issue.

only1chunts commented 2 years ago

n2 - Dataset Admin table sort not working.

CONVERTED COMMENT TO TICKET #860

None of the admin-dataset page table headers actually sort when clicked. The URL changes, but the table order remains the same, e.g. https://staging.gigadb.org/adminDataset/admin gives the same ordered table as all of these: https://staging.gigadb.org/adminDataset/admin/Dataset_sort/publication_date https://staging.gigadb.org/adminDataset/admin/Dataset_sort/identifier https://staging.gigadb.org/adminDataset/admin/Dataset_sort/manuscript_id https://staging.gigadb.org/adminDataset/admin/Dataset_sort/title https://staging.gigadb.org/adminDataset/admin/Dataset_sort/publication_date https://staging.gigadb.org/adminDataset/admin/Dataset_sort/modification_date

only1chunts commented 2 years ago

n3 - On the tables in most of the Admin pages the text filters do not work in any columns. the space is there at the top of the column to type in, but nothing happens when you click enter.

CONVERTED THIS COMMENT TO TICKET #861

image

Dataset_author - sort works, filters do not Dataset_Files - sort works, filters do not Dataset_Project - sort work, filters do not Dataset_Links - sort works (not DOI - but thats the same as the current live page!), filters do not Dataset_relations - sork works (not related_DOI - but thats the same as the current live page!), filters do not Dataset_Funders - sort work, filters do not Dataset_manuscript - sort works (not DOI - but thats the same as the current live page!), filters do not Authors - sort work, filters do not Species - sort work, filters do not Projects - sort work, filters do not External_links - sort work (as well as live), filters do not Link_prefixes - sort work, filters do not Funder - sort work, filters do not Attribute - sort work, filters do not Dataset_types - sort work (as well as live), filters do not Data_types - sort work, filters do not File_formats - sort work, filters do not Users - sort work, filters do not News_items - sort work, filters do not RSS_Messages - no data in table - probably do not even need this table in admin pages! Publishers - sort work, filters do not Update_logs - sort work (as well as live), filters do not

rija commented 5 months ago

This has served its purpose