diff options
| -rwxr-xr-x | wqflask/base/trait.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/quick_search.html | 110 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 2 |
4 files changed, 12 insertions, 104 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7c1c035c..dde8b8d8 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -302,7 +302,7 @@ class GeneralTrait: #XZ: assign SQL query result to trait attributes. for i, field in enumerate(self.dataset.display_fields): - setattr(self, field, traitInfo[i]) + setattr(self, field, str(traitInfo[i])) if self.dataset.type == 'Publish': self.confidential = 0 diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 62fb0fbd..5bfc3a01 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -243,6 +243,8 @@ def run(pheno_vector, with Bench("LMM_ob fitting"): lmm_ob.fit() + print("genotype_matrix: ", genotype_matrix.shape) + with Bench("Doing GWAS"): t_stats, p_values = GWAS(pheno_vector, genotype_matrix, diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html index 5877a840..01588924 100644 --- a/wqflask/wqflask/templates/quick_search.html +++ b/wqflask/wqflask/templates/quick_search.html @@ -105,7 +105,7 @@ {% if result.result_fields['species'] == species %} <tr> <td> - <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}" + <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"> {{ result.result_fields['name'] }} </a> </td> @@ -114,7 +114,7 @@ <td>{{ result.result_fields['dataset_name'] }}</td> <td>{{ result.result_fields['symbol'] }}</td> <td>{{ result.result_fields['description'] }}</td> - <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td> + <td>Chr {{ result.result_fields['chr'] }}: {{ result.result_fields['mb'] }}</td> <td>{{ result.result_fields['mean'] }}</td> <td>{{ result.result_fields['lrs'] }}</td> </tr> @@ -168,105 +168,6 @@ {% endblock %} - {# - <table id="pheno_results" class="table table-hover table-striped table-bordered"> - <thead> - <tr> - <th>Id</th> - <th>Species</th> - <th>Group</th> - <th>Description</th> - <th>LRS</th> - <th>Year</th> - <th>Authors</th> - </tr> - </thead> - <tbody> - {% for result in results.phenotype %} - <tr> - <td>{{ result.result_fields['phenotype_id'] }}</td> - <td>{{ result.result_fields['species'] }}</td> - <td>{{ result.result_fields['group_name'] }}</td> - <td>{{ result.result_fields['description'] }}</td> - <td>{{ result.result_fields['lrs'] }}</td> - <td> - <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result.result_fields['pubmed_id'] }}&dopt=Abstract"> - {{ result.result_fields['year'] }} - </a> - </td> - <td>{{ result.result_fields['authors'] }}</td> - </tr> - {% endfor %} - </tbody> - </table> - </div> - <div class="tab-pane" id="tab2"> - <table id="mrna_assay_results" class="table table-hover table-striped table-bordered"> - <thead> - <tr> - <th>Record ID</th> - <th>Species</th> - <th>Group</th> - <th>Data Set</th> - <th>Symbol</th> - <th>Description</th> - <th>Location</th> - <th>Mean Expr</th> - <th>Max LRS</th> - </tr> - </thead> - <tbody> - {% for result in results.mrna_assay %} - <tr> - <td> - <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}" - {{ result.result_fields['name'] }} - </a> - </td> - <td>{{ result.result_fields['species'] }}</td> - <td>{{ result.result_fields['group_name'] }}</td> - <td>{{ result.result_fields['dataset_name'] }}</td> - <td>{{ result.result_fields['symbol'] }}</td> - <td>{{ result.result_fields['description'] }}</td> - <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td> - <td>{{ result.result_fields['mean'] }}</td> - <td>{{ result.result_fields['lrs'] }}</td> - </tr> - {% endfor %} - </tbody> - </table> - </div> - <div class="tab-pane" id="tab3"> - <table id="geno_results" class="table table-hover table-striped table-bordered"> - <thead> - <tr> - <th>Marker</th> - <th>Species</th> - <th>Group</th> - <th>Data Set</th> - <th>Location</th> - </tr> - </thead> - <tbody> - {% for result in results.genotype %} - <tr> - <td> - <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['marker_name'] }}&dataset={{ result.result_fields['dataset'] }}"> - {{ result.result_fields['marker_name'] }} - </a> - </td> - <td>{{ result.result_fields['species'] }}</td> - <td>{{ result.result_fields['group_name'] }}</td> - <td>{{ result.result_fields['dataset_name'] }}</td> - <td>{{ result.result_fields['chr'] }} : {{ result.result_fields['mb'] }}</td> - </tr> - {% endfor %} - </tbody> - </table> - </div> - #} - - {% block js %} <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script> @@ -274,9 +175,14 @@ <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> - <script type="text/javascript" charset="utf-8"> $(document).ready( function () { + + $("div[id^='tab'").bind('click', function(){ + tab_id = $(this).attr('id'); + $("a[href^='"+tab_id+"']").first().trigger('click'); + }); + $('#species_level ul li:first').addClass('active'); $('#trait_type_level ul li:first').addClass('active'); console.time("Creating table"); diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 1af324b2..4480e8da 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -80,7 +80,7 @@ def search_page(): print("key is:", pf(key)) with Bench("Loading cache"): result = Redis.get(key) - + if result: print("Cache hit!!!") with Bench("Loading results"): |