Populating Project/Subproject/Current_Stage in Loris DB

.gitignore

@@ -0,0 +1,3 @@
+**/__pycache__/*
+*.pyc
+.loris_mri/

python/bids_import.py

@@ -181,17 +181,28 @@ def read_and_insert_bids(bids_dir, config_file, verbose, createcand, createvisit
         loris_cand_info = grep_or_create_candidate_db_info(
             bids_reader, bids_id, db, createcand, loris_bids_root_dir, verbose
         )
-        cand_id   = loris_cand_info['CandID']
-        center_id = loris_cand_info['RegistrationCenterID']
+        cand_id    = loris_cand_info['CandID']
+        center_id  = loris_cand_info['RegistrationCenterID']
+        project_id = loris_cand_info['RegistrationProjectID']
+
+        subproject_id = None
+        if 'subproject' in bids_subject_info:
+            subproject = bids_subject_info['subproject']
+            subproject_info = db.pselect(
+                    "SELECT SubprojectID FROM subproject WHERE title = %s",
+                    [subproject,]
+                )
+            if(len(subproject_info) > 0):
+                subproject_id = subproject_info[0]['SubprojectID']
 
         # greps BIDS session's info for the candidate from LORIS (creates the
         # session if it does not exist yet in LORIS and the createvisit is set
         # to true. If no visit in BIDS structure, then use default visit_label
         # stored in the Config module)
         loris_sessions_info = grep_candidate_sessions_info(
-            bids_sessions, bids_id, cand_id, loris_bids_root_dir,
-            createvisit,   verbose, db,      default_bids_vl,
-            center_id
+            bids_sessions, bids_id,    cand_id,       loris_bids_root_dir,
+            createvisit,   verbose,    db,            default_bids_vl,
+            center_id,     project_id, subproject_id
         )
 
     # read list of modalities per session / candidate and register data
@@ -333,35 +344,43 @@ def grep_or_create_candidate_db_info(bids_reader, bids_id,        db,
     return loris_cand_info
 
 
-def grep_or_create_visit_label_db_info(
-        bids_id, cand_id,        visit_label, db, createvisit,
-        verbose, loris_bids_dir, center_id):
+def grep_or_create_session_db_info(
+        bids_id,   cand_id,     visit_label,    
+        db,        createvisit, verbose,       loris_bids_dir,
+        center_id, project_id,  subproject_id):
     """
-    Greps (or creates if candidate does not exist and createcand is true) the
-    BIDS candidate in the LORIS candidate's table and return a list of
-    candidates with their related fields from the database.
+    Greps (or creates if session does not exist and createvisit is true) the
+    BIDS session in the LORIS session's table and return a list of
+    sessions with their related fields from the database.
 
-    :parma bids_id       : BIDS ID of the candidate
+    :parma bids_id       : BIDS ID of the session
      :type bids_id       : str
     :param cand_id       : CandID to use to create the session
      :type cand_id       : int
     :param visit_label   : Visit label to use to create the session
      :type visit_label   : str
     :param db            : database handler object
      :type db            : object
-    :param createvisit   : if true, creates the candidate in LORIS
+    :param createvisit   : if true, creates the session in LORIS
      :type createvisit   : bool
     :param verbose       : if true, prints out information while executing
      :type verbose       : bool
     :param loris_bids_dir: LORIS BIDS import root directory to copy data
      :type loris_bids_dir: str
+    :param center_id     : CenterID  to use to create the session
+     :type center_id     : int
+    :param project_id    : ProjectID  to use to create the session
+     :type project_id    : int
+    :param subproject_id : SubprojectID  to use to create the session
+     :type subproject_id : int
 
     :return: session information grepped from LORIS for cand_id and visit_label
      :rtype: dict
     """
 
     session = Session(
-        verbose, cand_id=cand_id, visit_label=visit_label, center_id=center_id
+        verbose, cand_id, visit_label, 
+        center_id, project_id, subproject_id
     )
     loris_vl_info = session.get_session_info_from_loris(db)
 
@@ -378,9 +397,9 @@ def grep_or_create_visit_label_db_info(
     return loris_vl_info
 
 
-def grep_candidate_sessions_info(bids_ses,    bids_id, cand_id, loris_bids_dir,
-                                 createvisit, verbose, db,      default_vl,
-                                 center_id):
+def grep_candidate_sessions_info(bids_ses,    bids_id,    cand_id,       loris_bids_dir,
+                                 createvisit, verbose,    db,            default_vl,
+                                 center_id,   project_id, subproject_id):
     """
     Greps all session info dictionaries for a given candidate and aggregates
     them into a list, with one entry per session. If the session does not
@@ -413,18 +432,20 @@ def grep_candidate_sessions_info(bids_ses,    bids_id, cand_id, loris_bids_dir,
     loris_sessions_info = []
 
     if not bids_ses:
-        loris_vl_info = grep_or_create_visit_label_db_info(
-            bids_id,     cand_id, default_vl,     db,
-            createvisit, verbose, loris_bids_dir, center_id
+        loris_ses_info = grep_or_create_session_db_info(
+            bids_id,     cand_id,    default_vl,     db,
+            createvisit, verbose,    loris_bids_dir,
+            center_id,   project_id, subproject_id
         )
-        loris_sessions_info.append(loris_vl_info)
+        loris_sessions_info.append(loris_ses_info)
     else:
         for visit_label in bids_ses:
-            loris_vl_info = grep_or_create_visit_label_db_info(
-                bids_id,     cand_id, visit_label,    db,
-                createvisit, verbose, loris_bids_dir, center_id
+            loris_ses_info = grep_or_create_session_db_info(
+                bids_id,     cand_id,    visit_label,    db,
+                createvisit, verbose,    loris_bids_dir,
+                center_id,   project_id, subproject_id
             )
-            loris_sessions_info.append(loris_vl_info)
+            loris_sessions_info.append(loris_ses_info)
 
     return loris_sessions_info
 

python/lib/candidate.py

@@ -49,13 +49,14 @@ def __init__(self, verbose, psc_id=None, cand_id=None, sex=None, dob=None):
         self.verbose = verbose
 
         # create the candidate object
-        self.psc_id    = psc_id
-        self.cand_id   = cand_id
-        self.sex       = sex
-        self.dob       = dob
-        self.age       = None
-        self.site      = None
-        self.center_id = None
+        self.psc_id     = psc_id
+        self.cand_id    = cand_id
+        self.sex        = sex
+        self.dob        = dob
+        self.age        = None
+        self.site       = None
+        self.center_id  = None
+        self.project_id = None
 
     def create_candidate(self, db, participants_info):
         """
@@ -84,13 +85,21 @@ def create_candidate(self, db, participants_info):
                 self.age = row['age']
             if 'site' in row:
                 self.site = row['site']
+            if 'project' in row:
+                project_info = db.pselect(
+                    "SELECT ProjectID FROM Project WHERE Alias = %s",
+                    [row['project'],]
+                )
+                if(len(project_info) > 0):
+                    self.project_id = project_info[0]['ProjectID']
 
             if self.site:
                 site_info = db.pselect(
                     "SELECT CenterID FROM psc WHERE Alias = %s",
                     [self.site,]
                 )
-                self.center_id = site_info[0]['CenterID']
+                if(len(site_info) > 0):
+                    self.center_id = site_info[0]['CenterID']
             else:
                 db_sites = db.pselect("SELECT CenterID, Alias FROM psc")
                 for site in db_sites:
@@ -107,9 +116,10 @@ def create_candidate(self, db, participants_info):
 
         if self.verbose:
             print("Creating candidate with " + \
-                  " PSCID = "    + self.psc_id + "," + \
-                  " CandID = "   + str(self.cand_id) + \
-                  " and Site = " + str(self.site))
+                  "PSCID = "   + self.psc_id + ", " + \
+                  "CandID = "  + str(self.cand_id) + ", " + \
+                  "Site = "    + str(self.site)  + " and " + \
+                  "Project = " + str(self.project_id))
 
         insert_col = ('PSCID', 'CandID', 'RegistrationCenterID')
         insert_val = (self.psc_id, str(self.cand_id), str(self.center_id))
@@ -120,6 +130,9 @@ def create_candidate(self, db, participants_info):
         if self.dob:
             insert_col = insert_col + ('DoB',)
             insert_val = insert_val + (self.dob,)
+        if self.project_id:
+            insert_col = insert_col + ('RegistrationProjectID',)
+            insert_val = insert_val + (str(self.project_id),)
 
         db.insert(
             table_name='candidate',

python/lib/eeg.py

@@ -128,6 +128,21 @@ def __init__(self, bids_reader, bids_sub_id, bids_ses_id, bids_modality, db,
         self.psc_id          = self.loris_cand_info['PSCID']
         self.cand_id         = self.loris_cand_info['CandID']
         self.center_id       = self.loris_cand_info['RegistrationCenterID']
+        self.project_id      = self.loris_cand_info['RegistrationProjectID']
+
+        self.subproject_id   = None 
+        for row in bids_reader.participants_info:
+            if not row['participant_id'] == self.psc_id:
+                continue
+            if 'subproject' in row:
+                subproject_info = db.pselect(
+                    "SELECT SubprojectID FROM subproject WHERE title = %s",
+                    [row['subproject'],]
+                )
+                if(len(subproject_info) > 0):
+                    self.subproject_id = subproject_info[0]['SubprojectID']
+            break
+
         self.session_id      = self.get_loris_session_id()
 
         # grep the channels, electrodes, eeg and events files
@@ -177,10 +192,8 @@ def get_loris_session_id(self):
         visit_label = self.bids_ses_id if self.bids_ses_id else self.default_vl
 
         session = Session(
-            verbose     = self.verbose,
-            cand_id     = self.cand_id,
-            center_id   = self.center_id,
-            visit_label = visit_label
+            self.verbose, self.cand_id, visit_label,
+            self.center_id, self.project_id, self.subproject_id
         )
         loris_vl_info = session.get_session_info_from_loris(self.db)
 

python/lib/mri.py

@@ -119,6 +119,21 @@ def __init__(self, bids_reader, bids_sub_id, bids_ses_id, bids_modality, db,
         self.psc_id          = self.loris_cand_info['PSCID']
         self.cand_id         = self.loris_cand_info['CandID']
         self.center_id       = self.loris_cand_info['RegistrationCenterID']
+        self.project_id      = self.loris_cand_info['RegistrationProjectID']
+
+        self.subproject_id   = None 
+        for row in bids_reader.participants_info:
+            if not row['participant_id'] == self.psc_id:
+                continue
+            if 'subproject' in row:
+                subproject_info = db.pselect(
+                    "SELECT SubprojectID FROM subproject WHERE title = %s",
+                    [row['subproject'],]
+                )
+                if(len(subproject_info) > 0):
+                    self.subproject_id = subproject_info[0]['SubprojectID']
+            break
+
         self.session_id      = self.get_loris_session_id()
 
         # grep all the NIfTI files for the modality
@@ -163,10 +178,8 @@ def get_loris_session_id(self):
         visit_label = self.bids_ses_id if self.bids_ses_id else self.default_vl
 
         session = Session(
-            verbose     = self.verbose,
-            cand_id     = self.cand_id,
-            center_id   = self.center_id,
-            visit_label = visit_label
+            self.verbose, self.cand_id, visit_label,
+            self.center_id, self.project_id, self.subproject_id
         )
         loris_vl_info = session.get_session_info_from_loris(self.db)
 

python/lib/session.py

@@ -19,7 +19,8 @@ class Session:
         db.connect()
 
         session = Session(
-            verbose, cand_id=cand_id, visit_label=visit_label, center_id=center_id
+            verbose, cand_id, visit_label, 
+            center_id, project_id, subproject_id
         )
 
         # grep session information from the database
@@ -32,25 +33,33 @@ class Session:
         db.disconnect()
     """
 
-    def __init__(self, verbose, cand_id, visit_label, center_id):
+    def __init__(self, verbose, cand_id, visit_label,
+                 center_id, project_id, subproject_id):
         """
         Constructor method for the Session class.
 
-        :param verbose    : whether to be verbose
-         :type verbose    : bool
-        :param cand_id    : candidate's CandID
-         :type cand_id    : int
-        :param visit_label: visit label
-         :type visit_label: str
-        :param center_id  : center ID to associate with the session
-         :type center_id  : int
+        :param verbose      : whether to be verbose
+         :type verbose      : bool
+        :param cand_id      : candidate's CandID
+         :type cand_id      : int
+        :param visit_label  : visit label
+         :type visit_label  : str
+        :param center_id    : center ID to associate with the session
+         :type center_id    : int
+        :param project_id   : project ID to associate with the session
+         :type project_id   : int
+        :param subproject_id: subproject ID to associate with the session
+         :type subproject_id: int
         """
         self.verbose = verbose
 
-        self.cand_id     = str(cand_id)
-        self.visit_label = visit_label
-        self.center_id   = center_id
+        self.cand_id       = str(cand_id)
+        self.visit_label   = visit_label
+        self.center_id     = center_id
+        self.project_id    = project_id
+        self.subproject_id = subproject_id
 
+
     def create_session(self, db):
         """
         Creates a session using BIDS information.
@@ -66,10 +75,21 @@ def create_session(self, db):
             print("Creating visit " + self.visit_label \
                   + " for CandID "  + self.cand_id)
 
+        column_names = ('CandID', 'Visit_label', 'CenterID')
+        values = (self.cand_id, self.visit_label, str(self.center_id))
+
+        if self.project_id:
+            column_names = column_names + ('ProjectID',)
+            values = values + (str(self.project_id),)
+
+        if self.subproject_id:
+            column_names = column_names + ('SubprojectID',)
+            values = values + (str(self.subproject_id),)
+
         db.insert(
             table_name='session',
-            column_names=('CandID', 'Visit_label', 'CenterID'),
-            values=(self.cand_id, self.visit_label, str(self.center_id))
+            column_names=column_names,
+            values=values
         )
 
         loris_session_info = self.get_session_info_from_loris(db)