From c05650476b4e925c2bf6e7369ab8d321ce83ad48 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 3 Jul 2019 22:10:03 -0500 Subject: Fixed bug for creating one of the third party links on the trait page Changed text in several pages (submit trait, mapping error) Changed header menu structure some --- wqflask/base/webqtlConfig.py | 2 +- wqflask/wqflask/show_trait/show_trait.py | 7 ++++++- wqflask/wqflask/templates/base.html | 29 +++++++++++++------------- wqflask/wqflask/templates/gsearch_gene.html | 9 ++++---- wqflask/wqflask/templates/gsearch_pheno.html | 5 ++--- wqflask/wqflask/templates/index_page_orig.html | 1 - wqflask/wqflask/templates/mapping_error.html | 6 ++++++ wqflask/wqflask/templates/submit_trait.html | 19 ++++++++--------- 8 files changed, 42 insertions(+), 36 deletions(-) diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index a08acb0a..b9e6abd8 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -53,7 +53,7 @@ ABA_URL = "http://mouse.brain-map.org/search/show?search_type=gene&search_term=% EBIGWAS_URL = "https://www.ebi.ac.uk/gwas/search?query=%s" WIKI_PI_URL = "http://severus.dbmi.pitt.edu/wiki-pi/index.php/search?q=%s" ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s" -DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s' +DBSNP = 'http://ensembl.org/Mus_musculus/Variation/Population?v=%s' # Temporary storage (note that this TMPDIR can be set as an # environment variable - use utility.tools.TEMPDIR when you diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 5178ece8..5c349bf3 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -291,7 +291,12 @@ class ShowTrait(object): FROM GeneList_rn33 WHERE geneSymbol = '{}'""".format(self.this_trait.symbol) - kgId, chr, transcript_start, transcript_end = g.db.execute(query).fetchall()[0] if len(g.db.execute(query).fetchall()) > 0 else None + results = g.db.execute(query).fetchone() + if results: + kgId, chr, transcript_start, transcript_end = results + else: + kgId = chr = transcript_start = transcript_end = None + if chr and transcript_start and transcript_end and kgId: transcript_start = int(transcript_start*1000000) # Convert to bases from megabases transcript_end = int(transcript_end*1000000) diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 3fd9faf5..b1977b7f 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -44,10 +44,19 @@ Intro
  • - Search + +
  • - Submit Trait + Submit Data
  • Collections @@ -61,18 +70,6 @@
  • SNP Browser
    • -
  • - - -
  • {% if g.user_session.logged_in %} Sign out @@ -80,11 +77,13 @@ Sign in {% endif %}
    • +
  • - Use GeneNetwork 1 + Use GN1
    • diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 70390830..9b584ea5 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -9,7 +9,7 @@
    -

    GN searched 754 datasets and 39765944 traits across 10 species, and found {{ trait_count }} results that match your query. +

    GN searched 754 datasets and 39,765,944 traits across 10 species, and found {{ trait_count }} results that match your query. You can filter these results by adding key words in the fields below and you can also sort results on most columns.

    To study a record, click on its Record ID below.
    Check records below and click Add button to add to selection.

    @@ -21,14 +21,13 @@ -
    -
    -
    + - +

    +
    diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index 42bf1b64..609c1852 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -21,14 +21,13 @@ -
    -
    - +
    +
    diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 30e3f2f6..251a816f 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -181,7 +181,6 @@

    Affiliates

    diff --git a/wqflask/wqflask/templates/mapping_error.html b/wqflask/wqflask/templates/mapping_error.html index b73a2c31..884d4df8 100644 --- a/wqflask/wqflask/templates/mapping_error.html +++ b/wqflask/wqflask/templates/mapping_error.html @@ -5,7 +5,13 @@ {{ header("An error occurred during mapping") }}
    +

    There is likely an issue with the genotype file associated with this group/RISet. Please contact Zach Sloan (zachary.a.sloan@gmail.com) or Arthur Centeno (acenteno@gmail.com) about the data set in question.

    +

    +
    +

    +

    Try mapping using interval mapping instead; some genotype files with many columns of NAs have issues with GEMMA or R/qtl.

    +

    diff --git a/wqflask/wqflask/templates/submit_trait.html b/wqflask/wqflask/templates/submit_trait.html index c9f716bf..0dd38fe5 100644 --- a/wqflask/wqflask/templates/submit_trait.html +++ b/wqflask/wqflask/templates/submit_trait.html @@ -8,7 +8,7 @@ {{ flash_me() }}
    -
    +

    Introduction

    @@ -33,7 +33,7 @@

    Trait Submission Form

    -

    1. Choose cross or RI set:

    +

    1. Choose Species and Group:


    @@ -52,7 +52,6 @@
    -

    2. Enter Trait Data:

    @@ -66,9 +65,9 @@

    From a File: You can enter data by entering a file name here. The file should contain a series of numbers representing trait values. - The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each progeny individual - or recombinant inbred line. Represent missing values with a non-numeric character such as "x". If you have chosen a recombinant inbred set, - when you submit your data will be displayed in a form where you can confirm and/or edit them. If you enter a file name here, any data that + The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each progeny individual + or recombinant inbred line. Represent missing values with a non-numeric character such as "x". If you have chosen a recombinant inbred set, + when you submit your data will be displayed in a form where you can confirm and/or edit them. If you enter a file name here, any data that you paste into the next section will be ignored.

    @@ -77,10 +76,10 @@

    Paste or Type Multiple Values: You can enter data by pasting a series of numbers representing trait values into this area. - The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each progeny individual - or recombinant inbredline. Represent missing values with a non-numeric character such as "x". If you have chosen a recombinant inbred set, - when you submit your data will be displayed in a form where you can confirm and/or edit them. If you enter a file name in the previous section, - any data that you paste here will be ignored. Check sample data for the correct format. + The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each individual + or line. Use an "x" for missing values. If you have chosen a set of inbred strains, then your data will be displayed in a form in + which you can confirm and/or edit. If you enter a file name in the previous section, + any data that you paste here will be ignored. Check sample data for the correct format.

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