Formatting changes. Removed comment length check as we're deferring to OSDF for that.

Author: victor73

cutlass/WgsAssembledSeqSet.py

@@ -35,8 +35,9 @@ class WgsAssembledSeqSet(Base):
 
     def __init__(self):
         """
-        Constructor for the WgsAssembledSeqSet class. This initializes the fields specific
-        to the WgsAssembledSeqSet class, and inherits from the Base class.
+        Constructor for the WgsAssembledSeqSet class. This initializes the
+        fields specific to the WgsAssembledSeqSet class, and inherits from the
+        Base class.
 
         Args:
             None
@@ -159,8 +160,8 @@ def comment(self):
     @enforce_string
     def comment(self, comment):
         """
-        The setter for the WgsAssembledSeqSet comment. The comment must be a string,
-        and less than 512 characters.
+        The setter for the WgsAssembledSeqSet comment. The comment must be a
+        string.
 
         Args:
             comment (str): The new comment to add to the string.
@@ -170,15 +171,14 @@ def comment(self, comment):
         """
         self.logger.debug("In 'comment' setter.")
 
-        if len(comment) > 512:
-            raise Exception("Comment is too long. Max length is 512 characters.")
-
         self._comment = comment
 
     @property
     def format(self):
-        """ str: The file format of the sequence file """
-        self.logger.debug("In format getter.")
+        """
+        str: The file format of the sequence file.
+        """
+        self.logger.debug("In 'format' getter.")
 
         return self._format
 
@@ -194,10 +194,10 @@ def format(self, format_str):
         Returns:
             None
         """
-        self.logger.debug("In format setter.")
+        self.logger.debug("In 'format' setter.")
 
         if type(format_str) != str:
-            raise ValueError("format must be a string.")
+            raise ValueError("Format must be a string.")
 
         formats = ["fasta", "fastq"]
         if format_str in formats:
@@ -230,7 +230,9 @@ def format_doc(self, format_doc):
 
     @property
     def local_file(self):
-        """ str: URL to the local file to upload to the server. """
+        """
+        str: URL to the local file to upload to the server.
+        """
         self.logger.debug("In 'local_file' getter.")
 
         return self._local_file
@@ -671,13 +673,14 @@ def is_valid(self):
 
     def save(self):
         """
-        Saves the data in the current instance. The JSON form of the current data
-        for the instance is validated in the save function. If the data is not valid,
-        then the data will not be saved. If the instance was saved previously, then
-        the node ID is assigned the alpha numeric found in the OSDF instance. If not
-        saved previously, then the node ID is 'None', and upon a successful, will be
-        assigned to the alpha numeric ID found in the OSDF instance. Also, the
-        version is updated as the data is saved in the OSDF instance.
+        Saves the data in the current instance. The JSON form of the current
+        data for the instance is validated in the save function. If the data is
+        not valid, then the data will not be saved. If the instance was saved
+        previously, then the node ID is assigned the alpha numeric found in the
+        OSDF instance. If not saved previously, then the node ID is 'None', and
+        upon a successful, will be assigned to the alpha numeric ID found in
+        the OSDF instance. Also, the version is updated as the data is saved in
+        the OSDF instance.
 
         Args:
             None

cutlass/WgsDnaPrep.py

@@ -132,8 +132,7 @@ def comment(self):
     @enforce_string
     def comment(self, comment):
         """
-        The setter for the comment. The comment must be a string,
-        and less than 512 characters.
+        The setter for the comment. The comment must be a string.
 
         Args:
             comment (str): The new comment to add to the string.
@@ -143,14 +142,13 @@ def comment(self, comment):
         """
         self.logger.debug("In comment setter.")
 
-        if len(comment) > 512:
-            raise Exception("Comment is too long, must be less than 512 characters.")
-
         self._comment = comment
 
     @property
     def frag_size(self):
-        """ int: Target library fragment size after shearing. """
+        """
+        int: Target library fragment size after shearing.
+        """
         self.logger.debug("In frag_size getter.")
 
         return self._frag_size
@@ -177,8 +175,10 @@ def frag_size(self, frag_size):
 
     @property
     def lib_layout(self):
-        """ str: Specification of the layout: fragment/paired, and if paired,
-                 then nominal insert size and standard deviation. """
+        """
+        str: Specification of the layout: fragment/paired, and if paired,
+             then nominal insert size and standard deviation.
+        """
         self.logger.debug("In 'lib_layout' getter.")
 
         return self._lib_layout
@@ -201,9 +201,10 @@ def lib_layout(self, lib_layout):
 
     @property
     def lib_selection(self):
-        """ str: A controlled vocabulary of terms describing selection or reduction
-                 method used in library construction. Terms used by TCGA include
-                 (random, hybrid selection)
+        """
+        str: A controlled vocabulary of terms describing selection or reduction
+             method used in library construction. Terms used by TCGA include
+             (random, hybrid selection)
         """
         self.logger.debug("In 'lib_selection' getter.")
 
@@ -227,7 +228,9 @@ def lib_selection(self, lib_selection):
 
     @property
     def mims(self):
-        """ mimarks: Genomic Standards Consortium MIMS fields. """
+        """
+        mimarks: Genomic Standards Consortium MIMS fields.
+        """
         self.logger.debug("In mims getter.")
 
         return self._mims
@@ -331,7 +334,9 @@ def sequencing_center(self, sequencing_center):
 
     @property
     def sequencing_contact(self):
-        """ str: Name and email of the primary contact at the sequencing center. """
+        """
+        str: Name and email of the primary contact at the sequencing center.
+        """
         self.logger.debug("In 'sequencing_contact' getter.")
 
         return self._sequencing_contact
@@ -354,7 +359,9 @@ def sequencing_contact(self, sequencing_contact):
 
     @property
     def storage_duration(self):
-        """ int: Duration for which sample was stored in days. """
+        """
+        int: Duration for which sample was stored in days.
+        """
         self.logger.debug("In 'storage_duration' getter.")
 
         return self._storage_duration
@@ -381,7 +388,9 @@ def storage_duration(self, storage_duration):
 
     @property
     def srs_id(self):
-        """ str: NCBI Sequence Read Archive sample ID of the form SRS012345. """
+        """
+        str: NCBI Sequence Read Archive sample ID of the form SRS012345.
+        """
         self.logger.debug("In 'srs_id' getter.")
 
         return self._srs_id
@@ -481,10 +490,10 @@ def _get_raw_doc(self):
     @staticmethod
     def search(query = "\"wgs_dna_prep\"[node_type]"):
         """
-        Searches the OSDF database through all WgsDnaPrep node types. Any criteria
-        the user wishes to add is provided by the user in the query language
-        specifications provided in the OSDF documentation. A general format
-        is (including the quotes and brackets):
+        Searches the OSDF database through all WgsDnaPrep node types. Any
+        criteria the user wishes to add is provided by the user in the query
+        language specifications provided in the OSDF documentation. A general
+        format is (including the quotes and brackets):
 
         "search criteria"[field to search]
 
@@ -570,7 +579,6 @@ def load_wgsDnaPrep(prep_data):
     @staticmethod
     def load(prep_id):
         """
-
         Loads the data for the specified input ID from the OSDF instance to
         this object.  If the provided ID does not exist, then an error message
         is provided stating the project does not exist.

cutlass/WgsRawSeqSet.py

@@ -31,8 +31,8 @@ class WgsRawSeqSet(Base):
 
     def __init__(self):
         """
-        Constructor for the WgsRawSeqSet class. This initializes the fields specific
-        to the WgsRawSeqSet class, and inherits from the Base class.
+        Constructor for the WgsRawSeqSet class. This initializes the fields
+        specific to the WgsRawSeqSet class, and inherits from the Base class.
 
         Args:
             None
@@ -176,8 +176,7 @@ def comment(self):
     @enforce_string
     def comment(self, comment):
         """
-        The setter for the comment field. The comment must be a string,
-        and less than 512 characters.
+        The setter for the comment field. The comment must be a string.
 
         Args:
             comment (str): The new comment to add to the string.
@@ -191,8 +190,10 @@ def comment(self, comment):
 
     @property
     def exp_length(self):
-        """ int: The number of raw bases or color space calls expected for the read,
-                 includes both mate pairs and all technical portions. """
+        """
+        int: The number of raw bases or color space calls expected for the read,
+             includes both mate pairs and all technical portions.
+        """
         self.logger.debug("In 'exp_length' getter.")
 
         return self._exp_length
@@ -217,7 +218,9 @@ def exp_length(self, exp_length):
 
     @property
     def format(self):
-        """ str: The file format of the sequence file """
+        """
+        str: The file format of the sequence file.
+        """
         self.logger.debug("In 'format' getter.")
 
         return self._format
@@ -244,7 +247,9 @@ def format(self, format_str):
 
     @property
     def format_doc(self):
-        """ str: URL for documentation of file format. """
+        """
+        str: URL for documentation of file format.
+        """
         self.logger.debug("In 'format_doc' getter.")
 
         return self._format_doc
@@ -267,7 +272,9 @@ def format_doc(self, format_doc):
 
     @property
     def local_file(self):
-        """ str: URL to the local file to upload to the server. """
+        """
+        str: URL to the local file to upload to the server.
+        """
         self.logger.debug("In local_file getter.")
 
         return self._local_file
@@ -423,11 +430,11 @@ def required_fields():
 
     def _get_raw_doc(self):
         """
-        Generates the raw JSON document for the current object. All required fields are
-        filled into the JSON document, regardless they are set or not. Any remaining
-        fields are included only if they are set. This allows the user to visualize
-        the JSON to ensure fields are set appropriately before saving into the
-        database.
+        Generates the raw JSON document for the current object. All required
+        fields are filled into the JSON document, regardless they are set or
+        not. Any remaining fields are included only if they are set. This
+        allows the user to visualize the JSON to ensure fields are set
+        appropriately before saving into the database.
 
         Args:
             None
@@ -478,9 +485,9 @@ def _get_raw_doc(self):
     def search(query = "\"wgs_raw_seq_set\"[node_type]"):
         """
         Searches the OSDF database through all WgsRawSeqSet node types. Any
-        criteria the user wishes to add is provided by the user in the query language
-        specifications provided in the OSDF documentation. A general format
-        is (including the quotes and brackets):
+        criteria the user wishes to add is provided by the user in the query
+        language specifications provided in the OSDF documentation. A general
+        format is (including the quotes and brackets):
 
         "search criteria"[field to search]
 
@@ -492,8 +499,8 @@ def search(query = "\"wgs_raw_seq_set\"[node_type]"):
                          WgsRawSeqSet node type.
 
         Returns:
-            Returns an array of WgsRawSeqSet objects. It returns an empty list if
-            there are no results.
+            Returns an array of WgsRawSeqSet objects. It returns an empty list
+            if there are no results.
         """
         module_logger.debug("In search.")
 
@@ -563,15 +570,16 @@ def load_wgsRawSeqSet(seq_set_data):
     @staticmethod
     def load(seq_set_id):
         """
-        Loads the data for the specified input ID from the OSDF instance to this object.
-        If the provided ID does not exist, then an error message is provided stating the
-        project does not exist.
+        Loads the data for the specified input ID from the OSDF instance to
+        this object.  If the provided ID does not exist, then an error message
+        is provided stating the project does not exist.
 
         Args:
             seq_set_id (str): The OSDF ID for the document to load.
 
         Returns:
-            A WgsRawSeqSet object with all the available OSDF data loaded into it.
+            A WgsRawSeqSet object with all the available OSDF data loaded into
+            it.
         """
         module_logger.debug("In load. Specified ID: %s" % seq_set_id)
 

tests/test_wgs_assembled_seq_set.py

@@ -160,12 +160,6 @@ def testIllegalComment(self):
         with self.assertRaises(Exception):
             seq_set.comment = 1
 
-    def testCommentTooLong(self):
-        seq_set = session.create_object("wgs_assembled_seq_set")
-
-        with self.assertRaises(Exception):
-            seq_set.comment = rand_generator(750)
-
     def testLegalComment(self):
         seq_set = session.create_object("wgs_assembled_seq_set")
         success = False

tests/test_wgs_dna_prep.py

@@ -99,12 +99,6 @@ def testIllegalComment(self):
         with self.assertRaises(Exception):
             wgsDnaPrep.comment = 1
 
-    def testCommentTooLong(self):
-        wgsDnaPrep = session.create_object("wgs_dna_prep")
-
-        with self.assertRaises(Exception):
-            wgsDnaPrep.comment = rand_generator(750)
-
     def testLegalComment(self):
         wgsDnaPrep = session.create_object("wgs_dna_prep")
         success = False

tests/test_wgs_raw_seq_set.py

@@ -103,12 +103,6 @@ def testCommentIllegal(self):
         with self.assertRaises(Exception):
             wgsRawSeqSet.comment = 1
 
-    def testCommentTooLong(self):
-        wgsRawSeqSet = session.create_object("wgs_raw_seq_set")
-
-        with self.assertRaises(Exception):
-            wgsRawSeqSet.comment = rand_generator(750)
-
     def testCommentLegal(self):
         wgsRawSeqSet = session.create_object("wgs_raw_seq_set")
         success = False