diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 74 |
1 files changed, 49 insertions, 25 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 255e3b74..ccdafa14 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -35,7 +35,7 @@ import json from flask import Flask, g -from htmlgen import HTMLgen2 as HT +import htmlgen as HT from base import webqtlConfig from base.GeneralObject import GeneralObject @@ -88,35 +88,60 @@ class HtmlGenWrapper: """Wrapper Methods for HTML gen""" @staticmethod def create_image_tag(**kwargs): - return HT.Image(**kwargs) + image = HT.Image("", "") + for key, value in list(kwargs.items()): + image.set_attribute(key, value) + return image @staticmethod def create_form_tag(**kwargs): - return HT.Form(**kwargs) + form = HT.Form("POST", "") # Default method is POST + + for key, value in list(kwargs.items()): + if key == "submit": + form.append(value) + continue + form.set_attribute(key.replace("cgi", "action"), str(value)) + return form @staticmethod def create_p_tag(**kwargs): - return HT.Paragraph(**kwargs) + paragraph = HT.Paragraph() + for key, value in list(kwargs.items()): + paragraph.set_attribute(key, value) + return paragraph @staticmethod def create_br_tag(): - return HT.BR() + return HT.VoidElement("br") @staticmethod def create_input_tag(**kwargs): - return HT.Input(**kwargs) + input_ = HT.Input() + for key, value in list(kwargs.items()): + input_.set_attribute(key.lower().replace("_", ""), value) + return input_ @staticmethod def create_area_tag(**kwargs): - return HT.Area(**kwargs) + area = HT.VoidElement("area") + for key, value in list(kwargs.items()): + area.set_attribute(key, value) + return area @staticmethod def create_link_tag(href, content, **kwargs): - return HT.Href(href, content, **kwargs) + link = HT.Link(href, content) + for key, value in list(kwargs.items()): + link.set_attribute(key, value) + return link @staticmethod def create_map_tag(**kwargs): - return HT.Map(**kwargs) + map_ = HT.Element("map") + for key, value in list(kwargs.items()): + map_.set_attribute(key, value) + return map_ class DisplayMappingResults(object): @@ -554,7 +579,6 @@ class DisplayMappingResults(object): src="/image/{}.png".format(self.filename), border="0", usemap='#WebQTLImageMap' ) - self.intImg = intImg #Scales plot differently for high resolution if self.draw2X: @@ -575,12 +599,12 @@ class DisplayMappingResults(object): cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=showLocusForm, - submit=HtmlGenWrapper.create_input_tag(type='hidden')) + submit=HtmlGenWrapper.create_input_tag(type_='hidden')) hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'} for key in hddn.keys(): showLocusForm.append(HtmlGenWrapper.create_input_tag( - name=key, value=hddn[key], type='hidden')) + name=key, value=hddn[key], type_='hidden')) showLocusForm.append(intImg) else: showLocusForm = intImg @@ -1002,7 +1026,7 @@ class DisplayMappingResults(object): COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift, yPaddingTop+kstep*15, rectWidth+2+rightShift+nameWidth, yPaddingTop+10+kstep*15,) HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name) Areas = HtmlGenWrapper.create_area_tag(shape='rect', coords=COORDS, href=HREF) - gifmap.areas.append(Areas) ### TODO + gifmap.append(Areas) ### TODO def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1): im_drawer = ImageDraw.Draw(canvas) @@ -1404,7 +1428,7 @@ class DisplayMappingResults(object): COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT)) # NL: 06-02-2011 Rob required to display NCBI info in a new window - gifmap.areas.append( + gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=COORDS, @@ -1578,7 +1602,7 @@ class DisplayMappingResults(object): COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT)) TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart)) HREF = '' - gifmap.areas.append( + gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=COORDS, @@ -1702,7 +1726,7 @@ class DisplayMappingResults(object): WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0) WEBQTL_TITLE = "Click to view this section of the genome in WebQTL" - gifmap.areas.append( + gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=WEBQTL_COORDS, @@ -1724,7 +1748,7 @@ class DisplayMappingResults(object): else: PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen" - gifmap.areas.append( + gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=PHENOGEN_COORDS, @@ -1745,7 +1769,7 @@ class DisplayMappingResults(object): else: UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser" - gifmap.areas.append( + gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=UCSC_COORDS, @@ -1767,7 +1791,7 @@ class DisplayMappingResults(object): else: ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser" - gifmap.areas.append(HtmlGenWrapper.create_area_tag( + gifmap.append(HtmlGenWrapper.create_area_tag( shape='rect', coords=ENSEMBL_COORDS, href=ENSEMBL_HREF, @@ -2011,7 +2035,7 @@ class DisplayMappingResults(object): href=HREF, target="_blank", title="Locus : {}".format(Lname)) - gifmap.areas.append(Areas) + gifmap.append(Areas) ##piddle bug if j == 0: im_drawer.line( @@ -2227,8 +2251,8 @@ class DisplayMappingResults(object): shape='rect', coords=sig_coords, title=sig_title) - gifmap.areas.append(Areas1) - gifmap.areas.append(Areas2) + gifmap.append(Areas1) + gifmap.append(Areas2) start_pos_x += (chr_length_dist+self.GraphInterval)*plotXScale return start_pos_x @@ -2682,7 +2706,7 @@ class DisplayMappingResults(object): shape='rect', coords=COORDS, href=HREF) - gifmap.areas.append(Areas) + gifmap.append(Areas) startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale return plotXScale @@ -2768,7 +2792,7 @@ class DisplayMappingResults(object): this_row = [] #container for the cells of each row selectCheck = HtmlGenWrapper.create_input_tag( - type="checkbox", + type_="checkbox", name="selectCheck", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") # checkbox for each row @@ -2887,7 +2911,7 @@ class DisplayMappingResults(object): for gIndex, theGO in enumerate(geneCol): this_row = [] # container for the cells of each row selectCheck = str(HtmlGenWrapper.create_input_tag( - type="checkbox", + type_="checkbox", name="selectCheck", Class="checkbox trait_checkbox")) # checkbox for each row |