diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/data_set.py | 14 | ||||
| -rw-r--r-- | wqflask/runserver.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/api/gen_menu.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/dataset_menu_structure.json | 19 | ||||
| -rwxr-xr-x[-rw-r--r--] | wqflask/wqflask/templates/show_trait_mapping_tools.html | 0 |
6 files changed, 25 insertions, 15 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 8652e6b7..1f99df49 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -64,7 +64,7 @@ logger = getLogger(__name__ ) # Each subclass will add to this DS_NAME_MAP = {} -def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_samplelist = True, group_name = None): +def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None): if not dataset_type: dataset_type = Dataset_Getter(dataset_name) @@ -77,7 +77,7 @@ def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_sampleli class Dataset_Types(object): - def __init__(self, rebuild=False): + def __init__(self): """Create a dictionary of samples where the value is set to Geno, Publish or ProbeSet. E.g. @@ -93,13 +93,9 @@ Publish or ProbeSet. E.g. """ self.datasets = {} - if rebuild: #ZS: May make this the only option - data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) - #data = gen_menu.gen_dropdown_json() - else: - file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" - with open(file_name, 'r') as fh: - data = json.load(fh) + data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) + #data = gen_menu.gen_dropdown_json() + for species in data['datasets']: for group in data['datasets'][species]: diff --git a/wqflask/runserver.py b/wqflask/runserver.py index 7c06356b..15572d97 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -9,6 +9,7 @@ from wqflask import app + import logging import utility.logger logger = utility.logger.getLogger(__name__ ) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 9354ece6..2914d354 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -233,6 +233,7 @@ def show_settings(): # Cached values GN_VERSION = get_setting('GN_VERSION') HOME = get_setting('HOME') +SERVER_PORT = get_setting('SERVER_PORT') WEBSERVER_MODE = get_setting('WEBSERVER_MODE') GN2_BASE_URL = get_setting('GN2_BASE_URL') GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL') diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index 64a413c2..adf66fb5 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -36,11 +36,6 @@ def gen_dropdown_json(): types=types, datasets=datasets) - output_file = """./wqflask/static/new/javascript/dataset_menu_structure.json""" - - with open(output_file, 'w') as fh: - json.dump(data, fh, indent=3, sort_keys=True) - return data def get_species(): diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index daf818b1..679e38b0 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -5172,6 +5172,23 @@ "HSNIH-Rat-PL-RSeq-0818", "HSNIH-Palmer Prelimbic Cortex RNA-Seq (Aug18) rlog" ] + ], + "Prefrontal Cortex mRNA": [ + [ + "864", + "HSNIH-Rat-VoLo-RSeq-0818", + "HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) rlog" + ], + [ + "863", + "HSNIH-Rat-PL-RSeq-0818", + "HSNIH-Palmer Prelimbic Cortex RNA-Seq (Aug18) rlog" + ], + [ + "861", + "HSNIH-Rat-IL-RSeq-0818", + "HSNIH-Palmer Infralimbic Cortex RNA-Seq (Aug18) rlog" + ] ] }, "HSNIH-RGSMC": { @@ -7564,4 +7581,4 @@ ] } } -} \ No newline at end of file +} diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 777d4a2d..777d4a2d 100644..100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html |