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all_questions.json
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"body": "<!---\r\nINSTRUCTIONS: Our intent is to use github as an open forum to help community members connect.\r\nIf you are looking to do any of the following, you are in the right place! and Thank You!\r\n - Ask for help/documentation/clarification of Tripal Functionality and Site Building/Management\r\n - Discuss controlled vocabulary terms for your data\r\n - Ask for input on site/module design questions\r\n - State your intent to develop a specific extension module\r\n - Really any type of discussion or question -we want to hear from you!\r\n--->\r\n\r\nHi,\r\nI have some custom descriptions for genes recorded in the GFF files as \"description=XXXXXX\" or \"product=XXXXXXX\", is it possible to show these information in the result-table of \"search gene\" or \"search sequence\" tools ?\r\nBesides, the `mRNA` sequences from the alignment failed to wrapped (concatenated by \" \" rather than \"\\n\" every 50 characters), while manually uploaded sequences and `CDS` sequences from alignment were correctly wrapped, how to fix that? \r\n\r\nThank you"
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"title": "Tried to import GO get type_id violates not-null constraint for goslim_agr",
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"body": "\r\nI have a brand spanking new tripal3 install with the rapid installer. I replaced the tripal module dir with the github repo today.\r\n\r\nThe very first thing I have tried is to import GO. I am getting an error. Should I have done something else before this. What did I miss???\r\n\r\nIs this critical? Or something I can ignore?\r\n\r\nThanks,\r\nSofia\r\n\r\n```\r\nRunning 'OBO Vocabulary Loader' importer\r\nNOTE: Loading of file is performed using a database transaction.\r\nIf it fails or is terminated prematurely then all insertions and\r\nupdates are rolled back and will not be found in the database\r\n\r\n[site http://default] [TRIPAL ERROR] [TRIPAL_CHADO] chado_select_record: the foreign key definition for 'dbxref_id' on table 'cvterm' returned no results where the definition supplied was Array( [db_id] => Array ( [name] => NCIT ) [accession] => C25693)\r\n[site http://default] [TRIPAL ERROR] [TRIPAL_CHADO] chado_select_record: the foreign key definition for 'dbxref_id' on table 'cvterm' returned no results where the definition supplied was Array( [db_id] => Array ( [name] => rdfs ) [accession] => comment)\r\nDownloading URL http://purl.obolibrary.org/obo/go.obo, saving to /tmp/obo_dgoYXf\r\nStep 1: Preloading File /tmp/obo_dgoYXf...\r\nFound the following namespaces: gene_ontology, biological_process, molecular_function, cellular_component, external.\r\nStep 2: Examining relationships...\r\nStep 3: Loading type defs...: 344,098,144 bytes.\r\nStep 4: Loading terms... %. Memory: 344,102,064 bytes.\r\nCannot add subset, \"goslim_agr\" to term: GO:0000003. ERROR: ChadoRecord::insert(). Could not insert a record into the table, cvtermprop, with the following values: Array\r\n(\r\n [cvterm_id] => 2982\r\n [type_id] =>\r\n [value] => goslim_agr\r\n)\r\n. ERROR: SQLSTATE[23502]: Not null violation: 7 ERROR: null value in column \"type_id\" violates not-null constraint\r\nDETAIL: Failing row contains (569, 2982, null, goslim_agr, 0)..\r\n[site http://default] [TRIPAL ERROR] [TRIPAL_JOB] Cannot add subset, \"goslim_agr\" to term: GO:0000003. ERROR: ChadoRecord::insert(). Could not insert a record into the table, cvtermprop, with the following values: Array( [cvterm_id] => 2982 [type_id] => [value] => goslim_agr). ERROR: SQLSTATE[23502]: Not null violation: 7 ERROR: null value in column \"type_id\" violates not-null constraintDETAIL: Failing row contains (569, 2982, null, goslim_agr, 0)..\r\n```"
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"body": "CentOS 7.2.15.11\r\ntripal-7.x-2.1-beta2 --> tripal-7.x-3.0-rc3\r\n\r\nWe are getting errors pretty early on in our upgrade. We are following the instructions on [tripal.info](https://tripal.readthedocs.io/en/latest/user_guide/install_tripal/upgrade_from_tripal2.html).\r\n\r\nWhen we disable tripal-core we find that we are missing many views. What should we do to repair this?\r\n\r\nThank you,\r\nSofia\r\n\r\n\r\n```\r\n[drupal@cuttingclass-test html]$ drush pm-disable tripal_core\r\nThe following theme is missing from the file system: <em [warning]\r\nclass=\"placeholder\">tripal</em>. For information about how to fix\r\nthis, see <a href=\"https://www.drupal.org/node/2487215\">the\r\ndocumentation page</a>. bootstrap.inc:1143\r\nThe following extensions will be disabled: tripal_core, chado_search, tripal_views, tripal_db, tripal_cv, tripal_analysis, tripal_organism, tripal_feature, tripal_analysis_blast, tripal_bulk_loader, tripal_daemon\r\nDo you really want to continue? (y/n): y\r\ntripal_organism was disabled successfully. [ok]\r\ntripal_analysis_blast was disabled successfully. [ok]\r\ntripal_bulk_loader was disabled successfully. [ok]\r\ntripal_cv was disabled successfully. [ok]\r\ntripal_daemon was disabled successfully. [ok]\r\ntripal_db was disabled successfully. [ok]\r\ntripal_core was disabled successfully. [ok]\r\ntripal_feature was disabled successfully. [ok]\r\ntripal_views was disabled successfully. [ok]\r\ntripal_analysis was disabled successfully. [ok]\r\nchado_search was disabled successfully. [ok]\r\nUnable to find a view by the name of 'tripal_bulk_loading_jobs'. [error]\r\nUnable to disable this view.\r\nUnable to find a view by the name of 'tripal_bulk_loader_templates'. [error]\r\nUnable to disable this view.\r\nUnable to find a view by the name of 'tripal_feature_user_feature'. [error]\r\nUnable to disable this view.\r\nUnable to find a view by the name of 'tripal_feature_admin_features'.[error]\r\nUnable to disable this view.\r\nUnable to find a view by the name of [error]\r\n'tripal_organism_user_organisms'. Unable to disable this view.\r\nUnable to find a view by the name of [error]\r\n'tripal_organism_admin_organisms'. Unable to disable this view.\r\nUnable to find a view by the name of 'tripal_analysis_user_analyses'.[error]\r\nUnable to disable this view.\r\nUnable to find a view by the name of [error]\r\n'tripal_analysis_admin_analyses'. Unable to disable this view.\r\nUnable to find a view by the name of 'tripal_cv_admin_cvs'. Unable to[error]\r\ndisable this view.\r\nUnable to find a view by the name of 'tripal_cv_admin_cvterms'. [error]\r\nUnable to disable this view.\r\nUnable to find a view by the name of 'tripal_db_admin_dbs'. Unable to[error]\r\ndisable this view.\r\nUnable to find a view by the name of 'tripal_db_admin_dbxrefs'. [error]\r\nUnable to disable this view.\r\n```"
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"body": "branch: Tripal 3\r\n\r\nI tried to create a Drupal view that would allow me to display both data from Chado and Drupal on a same page without any success. On Tripal 2, this could be achieved using Drupal views relationship between Drupal node and the corresponding Chado table. On Tripal 3, I didn't find the possibility to join those 2 sides.\r\n\r\nI can only either create a view on \"Chado stock\" or create a view on \"Accession\" for instance, but none of them can \"reach the other side of the database\".\r\n\r\nIf you create a \"Chado stock\"-based view, how could you provide a link to the corresponding Drupal entity?\r\n\r\nIf you create a \"Accession\"-based view (\"Accession\" being the Tripal entity that is related to a type of Chado stock), how could you display the related organism common name (stock.organism_id->organism.organism_id, organism.common_name) for each record or a specific picture (stock.stock_id->stock_dbxref.stock_id/dbxref_id->dbxref.dbxref_id/db_id->db.db_id by filtering on a given db.name)?\r\n\r\nI used to do it a lot on my Tripal 2 views but this issue prevents me from migrating to Tripal 3 at the moment.\r\n"
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"body": "Hi there! \r\nI'm trying to follow the manual for functional annotation: \r\nhttps://tripal.readthedocs.io/en/latest/user_guide/example_genomics/func_annots/setup.html\r\n\r\nWhen checking for new fields in STructure--> Tripal Content Types, the manual says check manage fields in mRNA but the image shows the fields in Gene. Anyway, when I do it in both places, I don't see anything similar to the example. No new fields related to functional modes showing. \r\nBut, if I go to \r\nStructure --> Content Types: \r\n\r\n\r\nI find there content for Blast and Interpro. \r\n\r\nIs this how its supposed to be? \r\n\r\n Thanks.\r\n"
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"body": "Hello!\r\n\r\nI am attempting to upload a GFF file on Tripal 7.x-2.x (https://github.com/tripal/tripal.git). However, the job keeps stalling at around 37% of parsed lines.\r\n\r\nThere is no error output from the Drush command. The Tripal Jobs list just says, \"Error.\" So I'm not sure how to troubleshoot.\r\n\r\nI first increased the PHP memory_limit value, as advised in the tutorial, to 2048M. I then raised it to 5120M. Both times, the job stalled at about 37% (36.74% for the former, 37.71% for the latter). It seems like the difference should have been much different if that was the issue, but I don't know.\r\n\r\nPlease advise if you have any advice on how to move past this stalling, with no clear error message, of a GFF load.\r\n\r\nThank you!"
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"body": "hi! \r\nI'm trying to get a file similar to the hier.tar.gz in the KEGG annotation example. I cannot run Kaas locally cause FTP is not free anymore, and when I do the analysis in the server: https://www.genome.jp/tools/kaas/ I dont see how to download anything similar. Do I need to download manually all the .keg files and then compress? \r\nThanks in advance.\r\n"
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"title": "\"max_locks_per_transaction\" memory setting for Chado load (Tripal v2)?",
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"body": "Hello!\r\n\r\nI am installing Tripal v2 using the tutorial. At the Chado installation process, I ran into the following Error regarding memory. (Note: This is a re-installation of Chado, as we had previously installed with Tripal v7.x-2.1; we removed that and replaced it with v7.x-2.x from Github in order to get it to work with the Views patch.)\r\n\r\n> WD tripal_core: SQLSTATE[53200]: Out of memory: 7 ERROR: out of shared memory [error]\r\n> HINT: You might need to increase max_locks_per_transaction.\r\n> [site http://default] [TRIPAL ERROR] [TRIPAL_CORE] SQLSTATE[53200]: Out of memory: 7 ERROR: out of shared memoryHINT: You might need to increase max_locks_per_transaction.\r\n\r\nSo, my question: What level should that max_locks_per_transaction stting for SQL be set to?\r\n\r\nThanks,\r\nMichael"
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"body": "Hello!\r\n\r\nWe are installing Tripal v2 using the tutorial, and it's a little unclear here (http://tripal.info/tutorials/v2.x/installation/tripal) on the ontologies to load. It lists three (Chado feature properties, Sequence ontology, Gene ontology), but the next paragraph says, \"Repeat this process for each of the FOUR ontologies.\" Is there a fourth that needs to be loaded? If so, which one?\r\n\r\nAlso, I submitted the job for loading the Gene Ontology yesterday, and it's still \"running\" at 99% completed nearly a day later. I know it says it could take a while, but is that normal, or is there likely something not working?\r\n\r\nThank you!\r\n--Michael"
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"body": "Hi there!\r\nI'm using tripal v3.0 (latest), Ubuntu 18.04.\r\n\r\nI'm a bit confused with the tripal legacy thing. If I understood well, legacy contains the previous tripal versions modules? in my new db I'm building, when I go to Find Tripal Content, I see what I am creating (organism, analyses, features.. etc). but in my home page, I see a Navigation panel, \r\n\r\n\r\nbut it seems to me that links me to \"legacy\" content? \r\nwhen I click in for example.. features: \r\n\r\nI dont see the blue links until I dont sync Features going to Tripal- Tripal Legacy - Features - Sync.\r\nand then I see them.\r\n\r\n\r\n\r\nso, if I am right.. my question is: How can I have my Navigation Panel actually pointing to the same links than when I go to Find Tripal Content? is that even possible? is it necessary then to sync everything all the time? \r\n\r\nThanks! \r\n\r\n\r\n\r\n"
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"body": "Hi\r\nUsing UBUNTU 18.04 and last Tripal v3.0 Release installation\r\nI'm trying to follow the tutorial of the citrus example: \r\n\r\nWhen creating the organism, my link to CrossReference never works.. \r\n\r\n\r\n\r\n\r\nshould link to: \r\npurl.obolibrary.org/obo/ncbitaxon#NCBITaxon:2711\r\nnever loads. \r\nis that an issue of the OBO or my tripal crossreference config? \r\n\r\n\r\nThanks! \r\n"
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"body": "\r\nHi\r\nUsing UBUNTU 18.04 and last Tripal v3.0 Release installation\r\nI'm trying to follow the tutorial of the citrus example: \r\n\r\nWhen creating the analysis, using Filtered HTML doesnt work, I don't get the description text formatted\r\n. In the text guidelines, by the way, it's written 'Description (Set to Full HTML)' , shouldn't be Set to Filtered HTML?\r\n\r\nThanks! \r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n"
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"body": "Hi, I'm about to install v3 from scratch. \r\nI will follow instructions here\r\nhttps://tripal.readthedocs.io/en/latest/user_guide/install_tripal/server_setup.html\r\n\r\n- is it ok to download the default php 7.2 (ubuntu 18.04) (sudo apt-get install php php-dev php-cli libapache2-mod-php) or will I have compatibility issues? (I tried in a first attempt to downgrade to 7.1 but apparently I didnt do it very well, and then no further steps worked for me, thats why I'm restarting)\r\n\r\nThanks! \r\n\r\n \r\n"
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"body": "Hi, \r\nI'm trying with no success to follow the tutorial for functional Annotation Modules (https://tripal.info/node/106), though I'm using Tripal v3 (I didnt find a tutorial for this version, is there any?).\r\n\r\nI came across several issues: \r\n\r\n_BLAST Module:\r\n After following the instruction for loading the BLAST results: \r\n \r\n Database: ExPASy SwissProt\r\n BLAST XML File/Directory: /var/www/html/sites/default/files/Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_uniprot_sprot.fasta.out\r\n Query Type: mRNA\r\n Parameters: -p blastx -e 1e-6 -m 7\r\n Submit a job to parse the XML output: checked\r\n Keywords for custom search: checked\r\n Click the Save button. You can now see our new Analysis._\r\n\r\nI see the Analysis, but when running the job to parse the BLAST results I get the following Error message: \r\n\r\n PDOException: SQLSTATE[42P01]: Undefined table: 7 ERROR: relation \"chado.blast_hit_data\" does not exist LINE 1: DELETE FROM chado.blast_hit_data WHERE analysisfeature_id =... ^: DELETE FROM chado.blast_hit_data WHERE analysisfeature_id = :analysisfeature_id ; Array ( [:analysisfeature_id] => 157384 ) in chado_query() (line 1715 of /var/www/html/sites/all/modules/tripal/tripal_chado/api/tripal_chado.query.api.inc).\r\n\r\nInterProScan Module: \r\nEverything seems to work fine, but I don't see the \"Interpro Report\" link anywhere.\r\nI also cannot follow the link http://[localhost]/orange1.1g015615m\r\n\r\nKEGG Module works fine! \r\n\r\nThanks in advance.\r\n\r\nBy the way, I'm not using Tripal via git.. should I? \r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n \r\n\r\n"
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"body": "Hello All,\r\n\r\nI have a question about how others are handling sequence feature versions.\r\n\r\nI have a group that is developing gene/mRNA models. They are using an ensembl like system for versioning of gene and transcript id. And they want to maintain a history of previous versions.\r\n\r\nThey plan on incrementing a digit after the id when a new version is generated.\r\n\r\ngene nv2m00005394.1\r\nmRNA nv2m00005394.1.mRNA.1\r\n\r\n```\r\nChr11\tGFF3Conv\tgene\t3598792\t3603486\t.\t-\t.\tAlias=Sox9;Name=nv2m00005394.1;ID=nv2m00005394.1\r\nChr11\tGFF3Conv\tmRNA\t3598792\t3603486\t.\t-\t.\tID=nv2m00005394.1.mRNA.1;Parent=nv2m00005394.1\r\n```\r\n\r\n\r\nHow should I handle this? Create a new feature for each version and mark the old one obsolete? How do I make it easy for users to find the correct ID when they don't know there has been an update? I have some ideas, but it would require the geneID and mRNAIDs to have different bases, ie nv2g00005394 (change g->m) for gene and nv2m00005394 for mRNA.\r\n\r\nAny advice would be fantastic!!!\r\n\r\nThank you!\r\nSofia\r\n\r\n\r\n"
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"body": "How do I change the $feature->all_relationships variable, if the data about relationships come from a custom table or if I use feature_relationshipprop in addition to feature_relationship? Using it in the template file tripal_feature_relationships.tpl.php."
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