From cddae6a6593a3f65cdb9565207a9a58c338e9024 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Wed, 17 Nov 2021 01:19:00 +0300 Subject: temp disable query caching --- wqflask/base/data_set.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 70c58136..768ad49b 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -754,8 +754,8 @@ class DataSet: # Postgres doesn't have that limit, so we can get rid of this after we transition chunk_size = 50 number_chunks = int(math.ceil(len(sample_ids) / chunk_size)) - cached_results = fetch_cached_results(self.name, self.type) - # cached_results = None + # cached_results = fetch_cached_results(self.name, self.type) + cached_results = None if cached_results is None: trait_sample_data = [] for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks): @@ -800,8 +800,6 @@ class DataSet: results = g.db.execute(query).fetchall() trait_sample_data.append([list(result) for result in results]) - cache_dataset_results( - self.name, self.type, trait_sample_data) else: trait_sample_data = cached_results -- cgit v1.2.3 From f5dd4b9f6b02ebe20733df0e8bd5e1b5e89f9e93 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Wed, 17 Nov 2021 01:31:38 +0300 Subject: temp disable traits metadata cache --- wqflask/wqflask/correlation/show_corr_results.py | 21 +-------------------- 1 file changed, 1 insertion(+), 20 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 42010a1e..55915a74 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -86,30 +86,17 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe corr_results = correlation_data['correlation_results'] results_list = [] - file_name = f"{target_dataset['name']}_metadata.json" - - file_path = os.path.join(TMPDIR, file_name) - new_traits_metadata = {} - - try: - with open(file_path,"r+") as file_handler: - dataset_metadata = json.load(file_handler) - - except FileNotFoundError: - Path(file_path).touch(exist_ok=True) - dataset_metadata = {} for i, trait_dict in enumerate(corr_results): trait_name = list(trait_dict.keys())[0] trait = trait_dict[trait_name] - target_trait = dataset_metadata.get(trait_name) + target_trait = None if target_trait is None: target_trait_ob = create_trait(dataset=target_dataset_ob, name=trait_name, get_qtl_info=True) target_trait = jsonable(target_trait_ob, target_dataset_ob) - new_traits_metadata[trait_name] = target_trait if target_trait['view'] == False: continue results_dict = {} @@ -184,12 +171,6 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe results_list.append(results_dict) - - if bool(new_traits_metadata): - # that means new traits exists - dataset_metadata.update(new_traits_metadata) - with open(file_path,"w+") as file_handler: - json.dump(dataset_metadata, file_handler) return json.dumps(results_list) -- cgit v1.2.3 From 9577152dfed7ae3fab2fb677a89b78ed88b9e127 Mon Sep 17 00:00:00 2001 From: jgart Date: Wed, 17 Nov 2021 02:37:17 -0500 Subject: update jupyter notebook link name This does not point to the launcher app but to the curated notebooks. --- wqflask/wqflask/templates/base.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 6e922f24..a3bd1b63 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -87,7 +87,7 @@
  • Systems Genetics PheWAS
  • Genome Browser
  • BXD Power Calculator
    • -
  • Jupyter Notebook Launcher
    • +
  • Jupyter Notebooks
  • Interplanetary File System
    • -- cgit v1.2.3 From ea2ce4c05f9b367510ba60a9adc5da9e8337f032 Mon Sep 17 00:00:00 2001 From: jgart Date: Wed, 17 Nov 2021 02:47:52 -0500 Subject: update live jupyter notebooks --- wqflask/wqflask/jupyter_notebooks.py | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/jupyter_notebooks.py b/wqflask/wqflask/jupyter_notebooks.py index dbea04dd..7d76828e 100644 --- a/wqflask/wqflask/jupyter_notebooks.py +++ b/wqflask/wqflask/jupyter_notebooks.py @@ -6,16 +6,12 @@ jupyter_notebooks = Blueprint('jupyter_notebooks', __name__) def launcher(): links = ( { - "main_url": "http://notebook.genenetwork.org/51091/tree?", - "notebook_name": "COVID-19 in mybinder.org federation", - "src_link_url": "https://github.com/jgarte/covid19_in_binder"}, + "main_url": "http://notebook.genenetwork.org/34301/notebooks/genenetwork-api-using-r.ipynb", + "notebook_name": "R notebook showing how to query the GeneNetwork API.", + "src_link_url": "https://github.com/jgarte/genenetwork-api-r-jupyter-notebook"}, { - "main_url": "http://notebook.genenetwork.org/35639/tree?", - "notebook_name": "Simple requirements.txt based example", - "src_link_url": "https://github.com/jgarte/requirements"}, - { - "main_url": "http://notebook.genenetwork.org/40733/tree?", - "notebook_name": "Guile Jupyter Notebook Querying GeneNetwork API", - "src_link_url": "https://github.com/jgarte/guile-notebook-genenetwork-api"}) + "main_url": "http://notebook.genenetwork.org/57675/notebooks/genenetwork.ipynb", + "notebook_name": "Querying the GeneNetwork API declaratively with python.", + "src_link_url": "https://github.com/jgarte/genenetwork-jupyter-notebook-example"}) return render_template("jupyter_notebooks.html", links=links) -- cgit v1.2.3 From 747544906c4d331a8d46ed692070e0f9d335191b Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 17 Nov 2021 18:31:59 +0000 Subject: Fixes gene global search error caused by some genes not having a symbol (not sure why this is in the DB; seems to have only happened recently) --- wqflask/wqflask/gsearch.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 2516e4fb..bf44408e 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -82,12 +82,13 @@ class GSearch: this_trait['species'] = line[0] this_trait['group'] = line[1] this_trait['tissue'] = line[2] - this_trait['symbol'] = line[6] + this_trait['symbol'] = "N/A" + if line[6]: + this_trait['symbol'] = line[6] + this_trait['description'] = "N/A" if line[7]: this_trait['description'] = line[7].decode( 'utf-8', 'replace') - else: - this_trait['description'] = "N/A" this_trait['location_repr'] = 'N/A' if (line[8] != "NULL" and line[8] != "") and (line[9] != 0): this_trait['location_repr'] = 'Chr%s: %.6f' % ( -- cgit v1.2.3 From 3325440faef1161da90d51444543d8d847fb9cdd Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 17 Nov 2021 18:27:56 +0000 Subject: Fix issue where gene global search throws an error due to some traits not having a gene symbol (not sure why they don't in the DB, but the code defaults it to N/A now) --- wqflask/wqflask/gsearch.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index bf44408e..31f3305c 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -89,7 +89,7 @@ class GSearch: if line[7]: this_trait['description'] = line[7].decode( 'utf-8', 'replace') - this_trait['location_repr'] = 'N/A' + this_trait['location_repr'] = "N/A" if (line[8] != "NULL" and line[8] != "") and (line[9] != 0): this_trait['location_repr'] = 'Chr%s: %.6f' % ( line[8], float(line[9])) -- cgit v1.2.3 From dea1afa01025026a0754de60615b974a5cb3fd24 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 17 Nov 2021 21:53:20 +0000 Subject: Changed the URL for editing trait metadata to use the dataset group ID instead of the PublishFreezeId --- wqflask/wqflask/templates/show_trait_details.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 6b125221..4e9ea0fb 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -236,7 +236,7 @@ {% if admin_status != None and admin_status.get('metadata', DataRole.VIEW) > DataRole.VIEW %} {% if this_trait.dataset.type == 'Publish' %} - + {% endif %} {% if this_trait.dataset.type == 'ProbeSet' %} -- cgit v1.2.3