diff options
| -rw-r--r-- | wqflask/wqflask/show_trait/SampleList.py | 44 |
1 files changed, 25 insertions, 19 deletions
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 92cea550..e4bbe5b9 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -32,7 +32,7 @@ class SampleList: for counter, sample_name in enumerate(sample_names, 1): sample_name = sample_name.replace("_2nd_", "") - # ZS: self.this_trait will be a list if it is a Temp trait + # self.this_trait will be a list if it is a Temp trait if isinstance(self.this_trait, list): sample = webqtlCaseData.webqtlCaseData(name=sample_name) if counter <= len(self.this_trait): @@ -47,7 +47,7 @@ class SampleList: name=sample_name, value=float(self.this_trait[counter - 1])) else: - # ZS - If there's no value for the sample/strain, + # If there's no value for the sample/strain, # create the sample object (so samples with no value # are still displayed in the table) try: @@ -63,29 +63,29 @@ class SampleList: sample.this_id = str(counter) - # ZS: For extra attribute columns; currently only used by + # For extra attribute columns; currently only used by # several datasets if self.sample_attribute_values: sample.extra_attributes = self.sample_attribute_values.get( sample_name, {}) - # ZS: Add a url so RRID case attributes can be displayed as links - if 'rrid' in sample.extra_attributes: + # Add a url so RRID case attributes can be displayed as links + if '36' in sample.extra_attributes: if self.dataset.group.species == "mouse": - if len(sample.extra_attributes['rrid'].split(":")) > 1: - the_rrid = sample.extra_attributes['rrid'].split(":")[ + if len(sample.extra_attributes['36'].split(":")) > 1: + the_rrid = sample.extra_attributes['36'].split(":")[ 1] - sample.extra_attributes['rrid'] = [ - sample.extra_attributes['rrid']] - sample.extra_attributes['rrid'].append( + sample.extra_attributes['36'] = [ + sample.extra_attributes['36']] + sample.extra_attributes['36'].append( webqtlConfig.RRID_MOUSE_URL % the_rrid) elif self.dataset.group.species == "rat": - if len(str(sample.extra_attributes['rrid'])): - the_rrid = sample.extra_attributes['rrid'].split("_")[ + if len(str(sample.extra_attributes['36'])): + the_rrid = sample.extra_attributes['36'].split("_")[ 1] - sample.extra_attributes['rrid'] = [ - sample.extra_attributes['rrid']] - sample.extra_attributes['rrid'].append( + sample.extra_attributes['36'] = [ + sample.extra_attributes['36']] + sample.extra_attributes['36'].append( webqtlConfig.RRID_RAT_URL % the_rrid) self.sample_list.append(sample) @@ -128,12 +128,13 @@ class SampleList: FROM CaseAttribute, CaseAttributeXRefNew WHERE CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.Id AND CaseAttributeXRefNew.InbredSetId = %s - ORDER BY lower(CaseAttribute.Name)''', (str(self.dataset.group.id),)) + ORDER BY CaseAttribute.Id''', (str(self.dataset.group.id),)) self.attributes = {} for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)): key, name = attr self.attributes[key] = Bunch() + self.attributes[key].id = key self.attributes[key].name = name self.attributes[key].distinct_values = [ item.Value for item in values] @@ -168,10 +169,13 @@ class SampleList: for sample_name, items in itertools.groupby(results.fetchall(), lambda row: row.SampleName): attribute_values = {} + # Make a list of attr IDs without values (that have values for other samples) + valueless_attr_ids = [self.attributes[key].id for key in self.attributes.keys()] for item in items: + valueless_attr_ids.remove(item.Id) attribute_value = item.Value - # ZS: If it's an int, turn it into one for sorting + # If it's an int, turn it into one for sorting # (for example, 101 would be lower than 80 if # they're strings instead of ints) try: @@ -179,8 +183,10 @@ class SampleList: except ValueError: pass - attribute_values[self.attributes[item.Id].name.lower( - )] = attribute_value + attribute_values[str(item.Id)] = attribute_value + for attr_id in valueless_attr_ids: + attribute_values[str(attr_id)] = "" + self.sample_attribute_values[sample_name] = attribute_values def get_first_attr_col(self): |