make all _id params int instead of str

abretaud · abretaud · commit 1362bd062fcd · 2019-08-20T17:20:18.000+02:00
diff --git a/chado/expression/__init__.py b/chado/expression/__init__.py
@@ -28,19 +28,19 @@ def get_biomaterials(self, provider_id="", biomaterial_id="", organism_id="", bi
         """
         List biomaterials in the database
 
-        :type organism_id: str
+        :type organism_id: int
         :param organism_id: Limit query to the selected organism
 
-        :type biomaterial_id: str
+        :type biomaterial_id: int
         :param biomaterial_id: Limit query to the selected biomaterial id
 
-        :type provider_id: str
+        :type provider_id: int
         :param provider_id: Limit query to the selected provider
 
         :type biomaterial_name: str
         :param biomaterial_name: Limit query to the selected biomaterial name
 
-        :type analysis_id: str
+        :type analysis_id: int
         :param analysis_id: Limit query to the selected analysis_id
 
         :rtype: list
@@ -87,7 +87,7 @@ def add_biomaterial(self, biomaterial_name, organism_id,
         :type biomaterial_name: str
         :param biomaterial_name: Biomaterial name
 
-        :type organism_id: str
+        :type organism_id: int
         :param organism_id: The id of the associated organism
 
         :type description: str
@@ -157,10 +157,10 @@ def add_expression(self, organism_id, analysis_id, file_path, separator="\t", un
         """
         Add an expression matrix file to the database
 
-        :type organism_id: str
+        :type organism_id: int
         :param organism_id: The id of the associated organism
 
-        :type analysis_id: str
+        :type analysis_id: int
         :param analysis_id: The id of the associated analysis
 
         :type file_path: str
@@ -226,10 +226,10 @@ def delete_biomaterials(self, names=None, ids=None, organism_id="", analysis_id=
         :type ids: str
         :param ids: JSON list of biomaterial ids to delete.
 
-        :type organism_id: str
+        :type organism_id: int
         :param organism_id: Delete all biomaterial associated with this organism id.
 
-        :type analysis_id: str
+        :type analysis_id: int
         :param analysis_id: Delete all biomaterial associated with this analysis id.
 
         :rtype: str
@@ -623,7 +623,7 @@ def _expression_create_biomaterial_structure(self, biomaterial, organism_id, ana
         channel_id = self._create_generic_channel()
         self._create_assay_biomaterial(assay_id, biomaterial_id, channel_id)
         # Try to add the unit to cvterm list
-        if(unit):
+        if (unit):
             try:
                 cvterm_id = self.ci.get_cvterm_id('unit_of_measure', 'sep')
             except chado.RecordNotFoundError:
diff --git a/chado/feature/__init__.py b/chado/feature/__init__.py
@@ -43,10 +43,10 @@ def get_features(self, organism_id=None, analysis_id=None, name=None, uniquename
         """
         Get all or some features
 
-        :type organism_id: str
+        :type organism_id: int
         :param organism_id: organism_id filter
 
-        :type analysis_id: str
+        :type analysis_id: int
         :param analysis_id: analysis_id filter
 
         :type name: str
@@ -94,7 +94,7 @@ def get_feature_cvterms(self, feature_id):
         """
         Get cvterms associated with a feature
 
-        :type feature_id: str
+        :type feature_id: int
         :param feature_id: Id of the feature
 
         :rtype: list
@@ -128,7 +128,7 @@ def get_feature_analyses(self, feature_id):
         """
         Get analyses associated with a feature
 
-        :type feature_id: str
+        :type feature_id: int
         :param feature_id: Id of the feature
 
         :rtype: list
@@ -190,10 +190,10 @@ def delete_features(self, organism_id=None, analysis_id=None, name=None, uniquen
         """
         Get all or some features
 
-        :type organism_id: str
+        :type organism_id: int
         :param organism_id: organism_id filter
 
-        :type analysis_id: str
+        :type analysis_id: int
         :param analysis_id: analysis_id filter
 
         :type name: str
diff --git a/chado/load/__init__.py b/chado/load/__init__.py
@@ -52,7 +52,7 @@ def blast(self, analysis_id, organism_id, input, blastdb=None, blastdb_id=None,
         :type blastdb: str
         :param blastdb: Name of the database blasted against (must be in the Chado db table)
 
-        :type blastdb_id: str
+        :type blastdb_id: int
         :param blastdb_id: ID of the database blasted against (must be in the Chado db table)
 
         :type query_type: str
diff --git a/chakin/commands/expression/add_biomaterial.py b/chakin/commands/expression/add_biomaterial.py
@@ -5,7 +5,7 @@
 
 @click.command('add_biomaterial')
 @click.argument("biomaterial_name", type=str)
-@click.argument("organism_id", type=str)
+@click.argument("organism_id", type=int)
 @click.option(
     "--description",
     help="Description of the biomaterial",
diff --git a/chakin/commands/expression/add_expression.py b/chakin/commands/expression/add_expression.py
@@ -4,8 +4,8 @@
 
 
 @click.command('add_expression')
-@click.argument("organism_id", type=str)
-@click.argument("analysis_id", type=str)
+@click.argument("organism_id", type=int)
+@click.argument("analysis_id", type=int)
 @click.argument("file_path", type=str)
 @click.option(
     "--separator",
diff --git a/chakin/commands/expression/delete_biomaterials.py b/chakin/commands/expression/delete_biomaterials.py
@@ -17,12 +17,12 @@
 @click.option(
     "--organism_id",
     help="Delete all biomaterial associated with this organism id.",
-    type=str
+    type=int
 )
 @click.option(
     "--analysis_id",
     help="Delete all biomaterial associated with this analysis id.",
-    type=str
+    type=int
 )
 @pass_context
 @custom_exception
diff --git a/chakin/commands/expression/get_biomaterials.py b/chakin/commands/expression/get_biomaterials.py
@@ -7,17 +7,17 @@
 @click.option(
     "--provider_id",
     help="Limit query to the selected provider",
-    type=str
+    type=int
 )
 @click.option(
     "--biomaterial_id",
     help="Limit query to the selected biomaterial id",
-    type=str
+    type=int
 )
 @click.option(
     "--organism_id",
     help="Limit query to the selected organism",
-    type=str
+    type=int
 )
 @click.option(
     "--biomaterial_name",
@@ -27,7 +27,7 @@
 @click.option(
     "--analysis_id",
     help="Limit query to the selected analysis_id",
-    type=str
+    type=int
 )
 @pass_context
 @custom_exception
diff --git a/chakin/commands/feature/delete_features.py b/chakin/commands/feature/delete_features.py
@@ -7,12 +7,12 @@
 @click.option(
     "--organism_id",
     help="organism_id filter",
-    type=str
+    type=int
 )
 @click.option(
     "--analysis_id",
     help="analysis_id filter",
-    type=str
+    type=int
 )
 @click.option(
     "--name",
diff --git a/chakin/commands/feature/get_feature_analyses.py b/chakin/commands/feature/get_feature_analyses.py
@@ -4,7 +4,7 @@
 
 
 @click.command('get_feature_analyses')
-@click.argument("feature_id", type=str)
+@click.argument("feature_id", type=int)
 @pass_context
 @custom_exception
 @list_output
diff --git a/chakin/commands/feature/get_feature_cvterms.py b/chakin/commands/feature/get_feature_cvterms.py
@@ -4,7 +4,7 @@
 
 
 @click.command('get_feature_cvterms')
-@click.argument("feature_id", type=str)
+@click.argument("feature_id", type=int)
 @pass_context
 @custom_exception
 @list_output
diff --git a/chakin/commands/feature/get_features.py b/chakin/commands/feature/get_features.py
@@ -7,12 +7,12 @@
 @click.option(
     "--organism_id",
     help="organism_id filter",
-    type=str
+    type=int
 )
 @click.option(
     "--analysis_id",
     help="analysis_id filter",
-    type=str
+    type=int
 )
 @click.option(
     "--name",
diff --git a/chakin/commands/load/blast.py b/chakin/commands/load/blast.py
@@ -15,7 +15,7 @@
 @click.option(
     "--blastdb_id",
     help="ID of the database blasted against (must be in the Chado db table)",
-    type=str
+    type=int
 )
 @click.option(
     "--re_name",
diff --git a/docs/commands/expression.rst b/docs/commands/expression.rst
@@ -140,11 +140,13 @@ Will delete biomaterials based on selector. Only one selector will be used.
 **Options**::
 
 
-      --names TEXT        JSON list of biomaterial names to delete.
-      --ids TEXT          JSON list of biomaterial ids to delete.
-      --organism_id TEXT  Delete all biomaterial associated with this organism id.
-      --analysis_id TEXT  Delete all biomaterial associated with this analysis id.
-      -h, --help          Show this message and exit.
+      --names TEXT           JSON list of biomaterial names to delete.
+      --ids TEXT             JSON list of biomaterial ids to delete.
+      --organism_id INTEGER  Delete all biomaterial associated with this organism
+                             id.
+      --analysis_id INTEGER  Delete all biomaterial associated with this analysis
+                             id.
+      -h, --help             Show this message and exit.
     
 
 ``get_biomaterials`` command
@@ -167,10 +169,10 @@ List biomaterials in the database
 **Options**::
 
 
-      --provider_id TEXT       Limit query to the selected provider
-      --biomaterial_id TEXT    Limit query to the selected biomaterial id
-      --organism_id TEXT       Limit query to the selected organism
-      --biomaterial_name TEXT  Limit query to the selected biomaterial name
-      --analysis_id TEXT       Limit query to the selected analysis_id
-      -h, --help               Show this message and exit.
+      --provider_id INTEGER     Limit query to the selected provider
+      --biomaterial_id INTEGER  Limit query to the selected biomaterial id
+      --organism_id INTEGER     Limit query to the selected organism
+      --biomaterial_name TEXT   Limit query to the selected biomaterial name
+      --analysis_id INTEGER     Limit query to the selected analysis_id
+      -h, --help                Show this message and exit.
     
diff --git a/docs/commands/feature.rst b/docs/commands/feature.rst
@@ -25,11 +25,11 @@ Get all or some features
 **Options**::
 
 
-      --organism_id TEXT  organism_id filter
-      --analysis_id TEXT  analysis_id filter
-      --name TEXT         name filter
-      --uniquename TEXT   uniquename filter
-      -h, --help          Show this message and exit.
+      --organism_id INTEGER  organism_id filter
+      --analysis_id INTEGER  analysis_id filter
+      --name TEXT            name filter
+      --uniquename TEXT      uniquename filter
+      -h, --help             Show this message and exit.
     
 
 ``get_feature_analyses`` command
@@ -98,11 +98,11 @@ Get all or some features
 **Options**::
 
 
-      --organism_id TEXT  organism_id filter
-      --analysis_id TEXT  analysis_id filter
-      --name TEXT         name filter
-      --uniquename TEXT   uniquename filter
-      -h, --help          Show this message and exit.
+      --organism_id INTEGER  organism_id filter
+      --analysis_id INTEGER  analysis_id filter
+      --name TEXT            name filter
+      --uniquename TEXT      uniquename filter
+      -h, --help             Show this message and exit.
     
 
 ``load_fasta`` command
diff --git a/docs/commands/load.rst b/docs/commands/load.rst
@@ -25,19 +25,20 @@ Load a blast analysis, in the same way as does the tripal_analysis_blast module
 **Options**::
 
 
-      --blastdb TEXT     Name of the database blasted against (must be in the Chado
-                         db table)
-      --blastdb_id TEXT  ID of the database blasted against (must be in the Chado db
-                         table)
-      --re_name TEXT     Regular expression to extract the feature name from the
-                         input file (first capturing group will be used).
-      --query_type TEXT  The feature type (e.g. 'gene', 'mRNA', 'polypeptide',
-                         'contig') of the query. It must be a valid Sequence
-                         Ontology term.  [default: polypeptide]
-      --match_on_name    Match features using their name instead of their uniquename
-      --skip_missing     Skip lines with unknown features or GO id instead of
-                         aborting everything.
-      -h, --help         Show this message and exit.
+      --blastdb TEXT        Name of the database blasted against (must be in the
+                            Chado db table)
+      --blastdb_id INTEGER  ID of the database blasted against (must be in the Chado
+                            db table)
+      --re_name TEXT        Regular expression to extract the feature name from the
+                            input file (first capturing group will be used).
+      --query_type TEXT     The feature type (e.g. 'gene', 'mRNA', 'polypeptide',
+                            'contig') of the query. It must be a valid Sequence
+                            Ontology term.  [default: polypeptide]
+      --match_on_name       Match features using their name instead of their
+                            uniquename
+      --skip_missing        Skip lines with unknown features or GO id instead of
+                            aborting everything.
+      -h, --help            Show this message and exit.
     
 
 ``go`` command
diff --git a/galaxy/expression_add_biomaterial.xml b/galaxy/expression_add_biomaterial.xml
@@ -34,7 +34,7 @@ chakin expression add_biomaterial
 	<inputs>
     <!-- arguments -->
 	<param name="biomaterial_name" label="Biomaterial Name" argument="biomaterial_name" type="text" help="Biomaterial name" />
-	<param name="organism_id" label="Organism Id" argument="organism_id" type="text" help="The id of the associated organism" />
+	<param name="organism_id" label="Organism Id" argument="organism_id" type="integer" value="0" help="The id of the associated organism" />
 
     <!-- options -->
 	<param name="description" label="Description" argument="description" type="text" help="Description of the biomaterial" />
diff --git a/galaxy/expression_add_expression.xml b/galaxy/expression_add_expression.xml
@@ -34,8 +34,8 @@ chakin expression add_expression
 </command>
 	<inputs>
     <!-- arguments -->
-	<param name="organism_id" label="Organism Id" argument="organism_id" type="text" help="The id of the associated organism" />
-	<param name="analysis_id" label="Analysis Id" argument="analysis_id" type="text" help="The id of the associated analysis" />
+	<param name="organism_id" label="Organism Id" argument="organism_id" type="integer" value="0" help="The id of the associated organism" />
+	<param name="analysis_id" label="Analysis Id" argument="analysis_id" type="integer" value="0" help="The id of the associated analysis" />
 	<param name="file_path" label="File Path" argument="file_path" type="text" help="File path" />
 
     <!-- options -->
diff --git a/galaxy/expression_delete_biomaterials.xml b/galaxy/expression_delete_biomaterials.xml
@@ -29,8 +29,8 @@ chakin expression delete_biomaterials
     <!-- options -->
 	<param name="names" label="Names" argument="names" type="text" help="JSON list of biomaterial names to delete." />
 	<param name="ids" label="Ids" argument="ids" type="text" help="JSON list of biomaterial ids to delete." />
-	<param name="organism_id" label="Organism Id" argument="organism_id" type="text" help="Delete all biomaterial associated with this organism id." />
-	<param name="analysis_id" label="Analysis Id" argument="analysis_id" type="text" help="Delete all biomaterial associated with this analysis id." />
+	<param name="organism_id" label="Organism Id" argument="organism_id" type="integer" value="0" help="Delete all biomaterial associated with this organism id." />
+	<param name="analysis_id" label="Analysis Id" argument="analysis_id" type="integer" value="0" help="Delete all biomaterial associated with this analysis id." />
 
 	</inputs>
 	<outputs>
diff --git a/galaxy/expression_get_biomaterials.xml b/galaxy/expression_get_biomaterials.xml
@@ -30,11 +30,11 @@ chakin expression get_biomaterials
     <!-- arguments -->
 
     <!-- options -->
-	<param name="provider_id" label="Provider Id" argument="provider_id" type="text" help="Limit query to the selected provider" />
-	<param name="biomaterial_id" label="Biomaterial Id" argument="biomaterial_id" type="text" help="Limit query to the selected biomaterial id" />
-	<param name="organism_id" label="Organism Id" argument="organism_id" type="text" help="Limit query to the selected organism" />
+	<param name="provider_id" label="Provider Id" argument="provider_id" type="integer" value="0" help="Limit query to the selected provider" />
+	<param name="biomaterial_id" label="Biomaterial Id" argument="biomaterial_id" type="integer" value="0" help="Limit query to the selected biomaterial id" />
+	<param name="organism_id" label="Organism Id" argument="organism_id" type="integer" value="0" help="Limit query to the selected organism" />
 	<param name="biomaterial_name" label="Biomaterial Name" argument="biomaterial_name" type="text" help="Limit query to the selected biomaterial name" />
-	<param name="analysis_id" label="Analysis Id" argument="analysis_id" type="text" help="Limit query to the selected analysis_id" />
+	<param name="analysis_id" label="Analysis Id" argument="analysis_id" type="integer" value="0" help="Limit query to the selected analysis_id" />
 
 	</inputs>
 	<outputs>
diff --git a/galaxy/feature_delete_features.xml b/galaxy/feature_delete_features.xml
diff --git a/galaxy/feature_get_feature_analyses.xml b/galaxy/feature_get_feature_analyses.xml
diff --git a/galaxy/feature_get_feature_cvterms.xml b/galaxy/feature_get_feature_cvterms.xml
diff --git a/galaxy/feature_get_features.xml b/galaxy/feature_get_features.xml
diff --git a/galaxy/load_blast.xml b/galaxy/load_blast.xml
