[WIP][Private Data] JGI Credentials

app.py

@@ -77,14 +77,9 @@
                 ],
                 className="mb-3",
             ),
-            dbc.InputGroup(
-                [
-                    dbc.InputGroupAddon("Dataset Password (if private MSV) - Beta Feature", addon_type="prepend"),
-                    dbc.Input(id='dataset_password', placeholder="Enter Dataset Password", type="password", value=""),
-                ],
-                className="mb-3",
-            ),
+            dbc.Button("Enter Credentials", block=False, size="sm", id="credentials_modal_button"),
             html.Br(),
+            html.Hr(),
             dbc.Row([
                 dbc.Col(
                     dbc.FormGroup(
@@ -226,13 +221,53 @@
     )
 ]
 
+PRIVATE_CREDENTIALS_MODAL = [
+    dbc.Modal(
+        [
+            dbc.ModalHeader("Credentials (Beta)"),
+            dbc.ModalBody([
+                dbc.InputGroup(
+                    [
+                        dbc.InputGroupAddon("Dataset Password (if private MSV)", addon_type="prepend"),
+                        dbc.Input(id='dataset_password', placeholder="Enter Dataset Password", type="password", value=""),
+                    ],
+                    className="mb-3",
+                ),
+                html.Hr(),
+                dbc.InputGroup(
+                    [
+                        dbc.InputGroupAddon("JGI Username", addon_type="prepend"),
+                        dbc.Input(id='jgi_username', placeholder="Enter Username Password", value=""),
+                    ],
+                    className="mb-3",
+                ),
+                dbc.InputGroup(
+                    [
+                        dbc.InputGroupAddon("JGI Password", addon_type="prepend"),
+                        dbc.Input(id='jgi_password', placeholder="Enter Dataset Password", type="password", value=""),
+                    ],
+                    className="mb-3",
+                ),
+            ]),
+            dbc.ModalFooter(
+                dbc.Button("Close", id="credentials_modal_close", className="ml-auto")
+            ),
+        ],
+        id="credentials_modal",
+        size="xl",
+    ),
+]
+
 BODY = dbc.Container(
     [
         dbc.Row([
             dbc.Col(
                 dbc.Card(DASHBOARD)
             ),
         ], style={"marginTop": 30}),
+        dbc.Row(
+            PRIVATE_CREDENTIALS_MODAL
+        )
     ],
     className="mt-12",
 )
@@ -447,7 +482,7 @@ def create_link(accession, dataset_password, file_table_data, selected_table_dat
             download_button = dbc.Button("Download First Selected File", color="primary", className="mr-1")
             download_link = dcc.Link(download_button, href=download_url, target="_blank")
         else:
-            download_link = html.Br()    
+            download_link = html.Br()
     else:
         download_link = html.Br()
 
@@ -563,6 +598,17 @@ def dataset_information(accession, dataset_password):
 def set_page_size(page_size):
     return [int(page_size), int(page_size)]
 
+# Helping to toggle the modals
+def toggle_modal(n1, n2, is_open):
+    if n1 or n2:
+        return not is_open
+    return is_open
+
+app.callback(
+    Output("credentials_modal", "is_open"),
+    [Input("credentials_modal_button", "n_clicks"), Input("credentials_modal_close", "n_clicks")],
+    [State("credentials_modal", "is_open")],
+)(toggle_modal)
 
 
 if __name__ == "__main__":

utils.py

@@ -40,6 +40,12 @@ def get_dataset_files(accession, metadata_source, dataset_password="", metadata_
     elif "ST" in accession:
         files_df, dataset_accession = _get_metabolomicsworkbench_files(accession)
 
+    elif "JGI:" in accession:
+        all_files = _get_jgi_files(accession)
+        temp_df = pd.DataFrame(all_files)
+        files_df = pd.DataFrame()
+        files_df["filename"] = temp_df["filename"]
+
     elif len(accession) == 32:
         # We're likely looking at a uuid from GNPS, lets hit the API
         all_files = _get_gnps_task_files(accession)
@@ -238,6 +244,37 @@ def _get_metabolomicsworkbench_dataset_information(dataset_accession):
     return metabolomics_workbench_data["study_title"], metabolomics_workbench_data["study_summary"]
 
 
+def _get_jgi_files(dataset_accession):
+    url = "https://genome.jgi.doe.gov/portal/ext-api/downloads/get-directory?organism={}&organizedByFileType=false".format(dataset_accession.replace("JGI:", ""))
+    session = requests.Session()
+    r = session.post('https://signon.jgi.doe.gov/signon/create', params={"login": "", "password": ''})
+    cookies = session.cookies.get_dict()
+
+    r = session.get(url, cookies=cookies)
+
+    acceptable_extensions = [".raw", ".mzML", ".mzXML", ".CDF", ".RAW", "cdf"]
+
+    output_list = []
+
+    import xmltodict as xtd
+    import json
+    dataset_list = xtd.parse(r.text)
+    all_folders = dataset_list["organismDownloads"]["folder"]["folder"][0]["folder"][0]["folder"]
+
+    for folder in all_folders:
+        file_url = "https://genome.jgi.doe.gov{}".format(folder["file"]["@url"])
+        filename = folder["file"]["@filename"]
+
+        _, extension = os.path.splitext(filename)
+
+        if extension in acceptable_extensions:
+            output_dict = {}
+            output_dict["filename"] = filename
+            output_dict["remote_link"] = file_url
+            output_list.append(output_dict)
+
+    return output_list 
+
 
 def _get_pxd_files(dataset_accession):
     url = "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID={}&outputMode=json&test=no".format(dataset_accession)