Arvados: Issueshttps://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422011-02-11T17:42:02ZArvados
Redmine GET-Evidence - Bug #466 (New): xmlrpc server is careless with huge temp fileshttps://dev.arvados.org/issues/4662011-02-11T17:42:02ZTom Cleggtom@curii.com
<p>For example, if processing aborts due to insufficient disk space while writing a huge temp file, the huge temp file (and perhaps other temp files) do not get deleted, and the disk stays full for no good reason.</p>
<p>Ideally, the processing code should use pipelines instead of temp files, or do "foreach record: foreach plugin: ..." instead of "foreach plugin: foreach record: ...".</p> longupload - Bug #451 (New): handle xmlhttprequest timeouts gracefullyhttps://dev.arvados.org/issues/4512011-01-13T19:04:50ZTom Cleggtom@curii.com
<p>Currently, browser may stall for a long time if a "send block to server" operation fails. Perhaps some browsers won't even call the onreadystatechange handler. The "send block" code should use a timer to detect this sort of thing and retry, like it does now after receiving a "fail" message from the server.</p> GET-Evidence - Feature #517 (New): Genome links should indicate which data set(s) actually suppor...https://dev.arvados.org/issues/5172010-06-18T18:04:38ZTom Cleggtom@curii.com
<p>Currently, if two data sets are available for one person, and one of the data sets has variant X-A1T, the X-A1T variant page will link to both Trait-o-matic data set pages, leaving the user to figure out which one actually lists the variant.</p> GET-Evidence - Bug #515 (New): 'Undefined' noticeshttps://dev.arvados.org/issues/5152010-06-11T12:19:15ZMadeleine Ballmpball@gmail.com
<p>There are many notices of the 'Undefined' variable variety. These mask real warnings about real bugs, hampering quality control.</p>
<p>These warnings are currently so numerous as to be unwieldy and must be shut off on development platforms via the following setting in php.ini:</p>
<p>error_reporting = E_ALL & ~E_DEPRECATED& ~E_NOTICE</p>
<p>However, server/compiler warnings are useful for quality control and should never be ignored, so developers should instead be using the following setting:</p>
<p>error_reporting = E_ALL | E_STRICT</p>
<p>To facilitate the setting above, current warnings should each be tracked down and fixed and new warnings addressed as they arise.</p> GET-Evidence - Bug #514 (New): ereg Deprecated in PHP 5.3.0https://dev.arvados.org/issues/5142010-06-11T11:55:56ZMadeleine Ballmpball@gmail.com
<p>There are many files using ereg (eregi, ereg_replace, etc.). These should be replaced with preg, as specified in the PHP manual:</p>
<p>"Note: As of PHP 5.3.0, the regex extension is deprecated in favor of the PCRE extension. Calling this function will issue an E_DEPRECATED notice. See the list of differences for help on converting to PCRE.</p>
<p>Note: preg_match(), which uses a Perl-compatible regular expression syntax, is often a faster alternative to ereg(). "</p>
<p>Perl-compatible extension (PCRE) doc is here:<br /><a class="external" href="http://www.php.net/manual/en/book.pcre.php">http://www.php.net/manual/en/book.pcre.php</a></p>
<p>Differences between ereg and preg are here:<br /><a class="external" href="http://www.php.net/manual/en/reference.pcre.pattern.posix.php">http://www.php.net/manual/en/reference.pcre.pattern.posix.php</a></p> GET-Evidence - Bug #506 (New): Standardize gene names (correctly)https://dev.arvados.org/issues/5062010-05-23T20:47:30ZMadeleine Ballmpball@gmail.com
<p>Some attempt at using standard gene names has occurred, but there's mistakes in the implementation -- there are cases when a name is both a standard name, and an alias that could point to a different standard name. The most conservative thing to do in these cases would be to accept the given name and not change it. One might also use the positions associated with gene names to distinguish between the two cases.</p>
<p>Right now it's been implemented incorrectly somewhere, resulting in gene names inconsistent with the position (in other words, moved to a new standard name when the old name was correct and standard).</p>
<p>The current GET-Evidence GJA9 L422F is a variant in ABT at chr1 39113094. According to genenames.org, this is both a standard name (to a gene on chr1) and an alias to another standard name, "GJD2" (on chr 15). So based on the position we can infer that "GJA9" is the correct, standard name for this.</p>
<p>But GET-Evidence incorrectly has this variant entered under GJD2: <a class="external" href="http://evidence.personalgenomes.org/GJD2-L422F">http://evidence.personalgenomes.org/GJD2-L422F</a></p> GET-Evidence - Bug #504 (New): Import aachanges containing periods (eg. HGC6.3-N156S)https://dev.arvados.org/issues/5042010-05-23T15:17:58ZMadeleine Ballmpball@gmail.com
<p>Although all amino acid changes in the genomes should have been imported, GET-Evidence is missing amino acid changes from genes containing a period (".") in their name.</p>
<p>Example (some missing aachanges from AK1, the anonymous Korean genome):<br />HGC6.3-V127G not found it GET-Evidence<br />HGC6.3-N156S not found it GET-Evidence<br />RP11-529I10.4-L156S not found it GET-Evidence</p> GET-Evidence - Bug #503 (New): Import aachanges starting with termination (eg. METTL8-X379R)https://dev.arvados.org/issues/5032010-05-23T15:05:32ZMadeleine Ballmpball@gmail.com
<p>Although all amino acid changes in the genomes should have been imported, GET-Evidence is missing amino acid changes starting (but not ending) with "X".</p>
<p>Example (some missing aachanges from ABT):<br />METTL8-X379R not found it GET-Evidence<br />ACTN3-X577R not found it GET-Evidence<br />HERC6-X123R not found it GET-Evidence<br />ZNF761-X526R not found it GET-Evidence<br />TMEM120A-X44Q not found it GET-Evidence<br />TSGA10IP-X21R not found it GET-Evidence<br />SYNM-X272R not found it GET-Evidence<br />SEC22B-X39Q not found it GET-Evidence</p> GET-Evidence - Feature #497 (New): Import and process raw reads for YRI trio datahttps://dev.arvados.org/issues/4972010-05-13T15:17:38ZMadeleine Ballmpball@gmail.com
<p><a class="external" href="http://developer.amazonwebservices.com/connect/entry.jspa?externalID=2899&categoryID=279">http://developer.amazonwebservices.com/connect/entry.jspa?externalID=2899&categoryID=279</a></p>
<p>"The YRI Trio Dataset provides complete genome sequence data for three Yoruba individuals from Ibadan, Nigeria, which represent the first human genomes sequenced using Illumina’s next generation Sequence-by-Synthesis technology. For each genome, the dataset contains >30x average depth of paired 35-base reads.</p>
<p>This data set can be used for the following applications:</p>
<p>The development of alignment algorithms<br />The development of de novo assembly algorithms<br />The development of algorithms that define genetic regions of interest, sequence motifs, structural variants, copy number variations, and site-specific polymorphisms<br />To test the viability of annotation engines that start with raw sequence data"</p> GET-Evidence - Feature #496 (New): Import and process raw reads for Jay Flatley genomehttps://dev.arvados.org/issues/4962010-05-13T13:11:36ZMadeleine Ballmpball@gmail.com
<p><a class="external" href="http://developer.amazonwebservices.com/connect/entry.jspa?externalID=3357&categoryID=279">http://developer.amazonwebservices.com/connect/entry.jspa?externalID=3357&categoryID=279</a></p>
<p>We should import and process reads for this genome.</p>
<p>"This data set contains the raw export files of the first genome sequenced by Illumina Individual Genome Service using Illumina’s Genome Analyzer technology of paired 75-base reads. 92,254,659,274 bases were used to generate a consensus sequence with coverage of 32x average depth. The genome was obtained via peripheral blood of Jay Flatley, CEO of Illumina."</p> GET-Evidence - Bug #495 (New): Allele frequency missing for rs41281314https://dev.arvados.org/issues/4952010-05-12T16:03:48ZMadeleine Ballmpball@gmail.com
<p>This is in 1000Genomes preliminary data according to dbSNP:<br /><a class="external" href="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ss.cgi?ss=ss130398918">http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ss.cgi?ss=ss130398918</a></p>
<p>But we don't have the allele frequency showing up in GET-Evidence page: <br /><a class="external" href="http://evidence.personalgenomes.org/CDH23-T1209A">http://evidence.personalgenomes.org/CDH23-T1209A</a></p>
<p>(Allele frequency of 0.120 in pilot.1.YRI - WEST AFRICA)</p> GET-Evidence - Feature #493 (New): Variant and Gene Removalhttps://dev.arvados.org/issues/4932010-05-10T15:21:03ZMadeleine Ballmpball@gmail.com
<p>The ability to remove genes and/or variants from the GET evidence database either if they are entered incorrectly or perhaps even if they are "retracted" in the literature. RSID A13T is an example of something incorrectly entered (and manually removed using the mysql command line client).</p> GET-Evidence - Feature #485 (New): Don't let users add variant pages for genes that aren't in kno...https://dev.arvados.org/issues/4852010-05-07T18:53:13ZTom Cleggtom@curii.com
<p>(If they're not in knownGene, they can never appear in variant reports...)</p> GET-Evidence - Bug #478 (New): Keep "overall odds ratio" updated when editing individual sets of ...https://dev.arvados.org/issues/4782010-05-07T18:47:29ZTom Cleggtom@curii.com
<p>Keep "overall odds ratio" updated when editing individual sets of OR figures</p> GET-Evidence - Feature #476 (New): allow “lab members” group to upload/view publication PDFshttps://dev.arvados.org/issues/4762010-05-07T17:31:32ZTom Cleggtom@curii.com
<p>allow “lab members” group to upload/view publication PDFs</p>