diff options
| -rw-r--r-- | wqflask/wqflask/parser.py | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 33 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/export_trait_data.py | 12 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.coffee | 24 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 9 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/index_page.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/new_index_page.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 25 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 31 |
9 files changed, 87 insertions, 66 deletions
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py index 67325b56..e34992a0 100644 --- a/wqflask/wqflask/parser.py +++ b/wqflask/wqflask/parser.py @@ -36,10 +36,11 @@ def parse(pstring): print(pf(items)) return(items) -parse("foo=(3 2 1)") -parse("shh") -parse("shh grep") -parse("LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)") -parse("sal1 LRS=(9 99 Chr4 122 155) sal2 cisLRS=(9 999 10)") -parse("sal1 sal3 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9 999 10)") -parse("sal1 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9, 999, 10)") \ No newline at end of file +if __name__ == '__main__': + parse("foo=(3 2 1)") + parse("shh") + parse("shh grep") + parse("LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)") + parse("sal1 LRS=(9 99 Chr4 122 155) sal2 cisLRS=(9 999 10)") + parse("sal1 sal3 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9 999 10)") + parse("sal1 LRS=(9 99 Chr4 122 155) wiki=bar sal2 go:foobar cisLRS=(9, 999, 10)") \ No newline at end of file diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 4cca6492..585deb8f 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -60,6 +60,7 @@ class SearchResultPage(templatePage): nkeywords = 0 def __init__(self, fd): + self.fd = fd if not self.openMysql(): return @@ -98,9 +99,15 @@ class SearchResultPage(templatePage): #userExist = None for individualDB in self.database: - self.cursor.execute('''SELECT Id, Name, FullName, confidentiality, - AuthorisedUsers FROM %sFreeze WHERE Name = %s''', ( - self.database[0].type, individualDB)) + # Can't use paramater substitution for table names apparently + db_type = self.database[0].type + "Freeze" + print("db_type [%s]: %s" % (type(db_type), db_type)) + + query = '''SELECT Id, Name, FullName, confidentiality, + AuthorisedUsers FROM %s WHERE Name = %%s''' % (db_type) + + self.cursor.execute(query, (individualDB,)) + (indId, indName, indFullName, @@ -175,6 +182,8 @@ class SearchResultPage(templatePage): 'RefSeq_TranscriptId'] elif self.dbType == "Geno": self.searchField = ['Name','Chr'] + + self.do_search() ########################################### # Search Options @@ -545,7 +554,6 @@ class SearchResultPage(templatePage): _log.info("Done executing queries") - #searchCountQuery retrieve all the results, for counting use only if searchCountQuery != searchQuery: for item in searchQuery: @@ -558,7 +566,6 @@ class SearchResultPage(templatePage): return nresults - def assembleQuery(self): self.query = [] if self.ANDQuery or self.ORQuery: @@ -635,13 +642,15 @@ class SearchResultPage(templatePage): return 0 + def do_search(self): + print("fd.search_terms:", self.fd['search_terms']) + self.search_terms = parser.parse(self.fd['search_terms']) + print("After parsing:", self.search_terms) + #print("ORkeyword is:", pf(self.ORkeyword)) + #self.ANDkeyword2 = parser.parse(self.ANDkeyword) + #self.ORkeyword2 = parser.parse(self.ORkeyword) + #print("ORkeyword2 is:", pf(parser.parse(self.ORkeyword))) - def normalSearch(self): - print("ORkeyword is:", pf(self.ORkeyword)) - self.ANDkeyword2 = parser.parse(self.ANDkeyword) - self.ORkeyword2 = parser.parse(self.ORkeyword) - print("ORkeyword2 is:", pf(parser.parse(self.ORkeyword))) - #self.ANDkeyword2 = re.sub(self._1mPattern, '', self.ANDkeyword) #self.ANDkeyword2 = re.sub(self._2mPattern, '', self.ANDkeyword2) #self.ANDkeyword2 = re.sub(self._3mPattern, '', self.ANDkeyword2) @@ -649,7 +658,7 @@ class SearchResultPage(templatePage): ###remove remain parethesis, could be input with syntax error #self.ANDkeyword2 = re.sub(re.compile('\s*\([\s\S]*\)'), '', self.ANDkeyword2) #self.ANDkeyword2 = self.encregexp(self.ANDkeyword2) - # + #self.ORkeyword2 = re.sub(self._1mPattern, '', self.ORkeyword) #self.ORkeyword2 = re.sub(self._2mPattern, '', self.ORkeyword2) #self.ORkeyword2 = re.sub(self._3mPattern, '', self.ORkeyword2) diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index e5f2035d..f7f2d6d4 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -4,21 +4,13 @@ import operator import simplejson as json -#import xlwt from pprint import pformat as pf def export_sample_table(targs): - #print("* keys0 args is:", targs[0].keys()) - - - #test_export_file = open("/home/zas1024/gene/wqflask/wqflask/show_trait/export_test.txt", "w") - # - #for key, item in targs.iteritems(): - # print("[arrow] key is:", key) - + sample_data = json.loads(targs['export_data']) final_sample_data = [] - + for sample_group in ['primary_samples', 'other_samples']: for row in sample_data[sample_group]: sorted_row = dict_to_sorted_list(row) diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index c7dc7c88..b1cca461 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -295,6 +295,10 @@ $ -> samples.other_samples = other_samples return samples + ##End Get Sample Data from Table Code + + ##Export Sample Table Data Code + export_sample_table_data = -> sample_data = get_sample_table_data() console.log("sample_data is:", sample_data) @@ -302,27 +306,19 @@ $ -> console.log("json_sample_data is:", json_sample_data) $('input[name=export_data]').val(json_sample_data) - console.log("export_data is", $('input[name=export_data]').val()) - $('#trait_data_form').attr('action', '/export_trait_csv') + format = $('#export_format').val() + if format == "excel" + $('#trait_data_form').attr('action', '/export_trait_excel') + else + $('#trait_data_form').attr('action', '/export_trait_csv') console.log("action is:", $('#trait_data_form').attr('action')) + $('#trait_data_form').submit() - - #$.ajax( - # url: '/export_trait_csv' - # type: 'POST' - # data: "json_data=" + json_sample_data - #) $('#export').click(export_sample_table_data) - - - ##End Get Sample Data from Table Code - - ##Export Sample Table Data Code - ##End Export Sample Table Data Code diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 5729eb22..5aadedef 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -334,14 +334,19 @@ return samples; }; export_sample_table_data = function() { - var json_sample_data, sample_data; + var format, json_sample_data, sample_data; sample_data = get_sample_table_data(); console.log("sample_data is:", sample_data); json_sample_data = JSON.stringify(sample_data); console.log("json_sample_data is:", json_sample_data); $('input[name=export_data]').val(json_sample_data); console.log("export_data is", $('input[name=export_data]').val()); - $('#trait_data_form').attr('action', '/export_trait_csv'); + format = $('#export_format').val(); + if (format === "excel") { + $('#trait_data_form').attr('action', '/export_trait_excel'); + } else { + $('#trait_data_form').attr('action', '/export_trait_csv'); + } console.log("action is:", $('#trait_data_form').attr('action')); return $('#trait_data_form').submit(); }; diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index a209f302..db0b2d9e 100644 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -96,7 +96,7 @@ <td width="3%"></td> <td nowrap width="85%" align="left"><input class="input-medium search-query" - id="tfor" name="ORkeyword" style= + id="tfor" name="search_terms" style= "width:420px; background-color:white; font-family:verdana; font-size:14px" type="text" maxlength="500"></td> </tr><!-- GET ANY HELP --> diff --git a/wqflask/wqflask/templates/new_index_page.html b/wqflask/wqflask/templates/new_index_page.html index 3d6d3f3f..f2178f3c 100644 --- a/wqflask/wqflask/templates/new_index_page.html +++ b/wqflask/wqflask/templates/new_index_page.html @@ -125,7 +125,7 @@ <label for="tfor">Search:</label> <input class="search-query" - id="tfor" name="ORkeyword" + id="tfor" name="search_terms" type="text" maxlength="500"> <!-- GET ANY HELP --> diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 1e1d8b8f..d48f9487 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -1253,10 +1253,18 @@ </div> {% endif %} <br> - <input type="button" id="hide_no_value" class="btn" value="Hide No Value"> - <input type="button" id="block_outliers" class="btn" value="Block Outliers"> - <input type="button" id="reset" class="btn btn-inverse" value="Reset"> - <input type="button" id="export" class="btn" value="Export"> + <div> + <input type="button" id="hide_no_value" class="btn" value="Hide No Value"> + <input type="button" id="block_outliers" class="btn" value="Block Outliers"> + <input type="button" id="reset" class="btn btn-inverse" value="Reset"> + <span class="input-append"> + <input type="button" id="export" class="btn" value="Export"> + <select id="export_format" class="select optional span2"> + <option value="excel">Excel</option> + <option value="csv">CSV</option> + </select> + </span> + </div> </fieldset> <br> <div> @@ -1272,17 +1280,16 @@ </div> </div> <br> - - - - + + + <div style="width:80%;margin:0;padding:0;border:none;"> {% for sample_type in sample_groups %} <div style="float:left;width:50%;"> <h2>{{ sample_type.header }}</h2> <div id="{{ sample_type.sample_group_type }}"> - <table class="not_tablesorter" {# Todo: Turn tablesorter back on #} + <table class="table table-hover not_tablesorter" {# Todo: Turn tablesorter back on #} id="{{ 'sortable%i' % (loop.index) }}" cellpadding="0" cellspacing="0"> <tr> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 693b863a..2933b428 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -90,6 +90,25 @@ def show_trait_page(): print("show_trait template_vars:", pf(template_vars.__dict__)) return render_template("show_trait.html", **template_vars.__dict__) +@app.route('/export_trait_csv', methods=('POST',)) +def export_trait_excel(): + """Excel file consisting of the sample data from the trait data and analysis page""" + print("In export_trait_excel") + print("request.form:", request.form) + sample_data = export_trait_data.export_sample_table(request.form) + + print("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) + + buff = StringIO.StringIO() + writer = csv.writer(buff) + for row in sample_data: + writer.writerow(row) + csv_data = buff.getvalue() + buff.close() + + return Response(csv_data, + mimetype='text/csv', + headers={"Content-Disposition":"attachment;filename=test.csv"}) @app.route('/export_trait_csv', methods=('POST',)) def export_trait_csv(): @@ -97,7 +116,7 @@ def export_trait_csv(): print("In export_trait_csv") print("request.form:", request.form) sample_data = export_trait_data.export_sample_table(request.form) - + print("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) buff = StringIO.StringIO() @@ -106,20 +125,12 @@ def export_trait_csv(): writer.writerow(row) csv_data = buff.getvalue() buff.close() - + return Response(csv_data, mimetype='text/csv', headers={"Content-Disposition":"attachment;filename=test.csv"}) -#@app.route("/export_trait_data", methods=('POST',)) -#def export_sample_table(): -# """CSV file consisting of the sample data from the trait data and analysis page""" -# print("In export_sample_table") -# print("request.form:", request.form) -# template_vars = export_trait_data.export_sample_table(request.form) - - @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): #print("In corr_compute, request.args is:", pf(request.form)) |