Merge remote-tracking branch 'uliege/master'

README.md

@@ -19,17 +19,28 @@ See [documentation](http://doc.cytomine.be/display/ALGODOC/%5BDOC%5D+Data+access
 
 **To install *official* release of Cytomine-python-client, see @cytomine. Follow this guide to install forked version by ULiege.** 
 
-### Manual installation
-To download and install manually the package, see [manual installation procedure](http://doc.cytomine.be/display/ALGODOC/Data+access+using+Python+client#DataaccessusingPythonclient-Installation).
-
 ### Automatic installation
 To retrieve package using `pip`:
 
+    pip install --extra-index-url=https://packagecloud.io/cytomine-uliege/Cytomine-python-client/pypi/simple cytomine-python-client
+
+or, to add the extra index permanently to your `pip` configuration:
+
     curl -s https://packagecloud.io/install/repositories/cytomine-uliege/Cytomine-python-client/script.python.sh | bash
     pip install cytomine-python-client
 
 See [package repository](https://packagecloud.io/cytomine-uliege/Cytomine-python-client) for details.
 
+### Manual installation
+To download and install manually the package in a Python env, run (here for version 2.7.3):
+
+    wget https://github.com/Cytomine-ULiege/Cytomine-python-client/releases/download/v2.7.3/Cytomine-Python-Client-2.7.3.zip 
+    unzip Cytomine-Python-Client-2.7.3.zip 
+    cd Cytomine-Python-Client-2.7.3
+    pip install .
+
+For more details and manual installation with Miniconda, see [manual installation procedure](http://doc.cytomine.be/display/ALGODOC/Data+access+using+Python+client#DataaccessusingPythonclient-Installation).
+
 ### In a Docker container
 To ease developpement of new Cytomine software, the Cytomine-python-client package is available in Docker containers:
 * [cytomineuliege/software-python3-base](https://hub.docker.com/r/cytomineuliege/software-python3-base/) provides a Python 3.5 environment with client already installed.
@@ -84,4 +95,4 @@ When using our software, we kindly ask you to cite our website url and related p
 
 ## License
 
-Apache 2.0
+Apache 2.0

cytomine/utilities/descriptor_reader.py

@@ -27,7 +27,14 @@
 __author__ = "Rubens Ulysse <urubens@uliege.be>"
 
 
-def read_descriptor(filename, schema_version="cytomine-0.1"):
+def _format_type(type):
+    if type.lower() == "listdomain":
+        return "ListDomain"
+    else:
+        return type.lower().capitalize()
+
+
+def read_descriptor(filename, schema_version="cytomine-0.1", delete_missing=False):
     """
     Read a software descriptor and add a not executable version of it to Cytomine.
     It should be used only for software development or testing purpose.
@@ -45,6 +52,8 @@ def read_descriptor(filename, schema_version="cytomine-0.1"):
         The descriptor file path.
     schema_version: String
         The version of descriptor schema.
+    delete_missing: Bool
+        If set to True, deletes the registered parameters missing from the descriptor file.
 
     Returns
     -------
@@ -66,6 +75,7 @@ def read_descriptor(filename, schema_version="cytomine-0.1"):
             software = existing_software[0]
 
         existing_software_parameters = SoftwareParameterCollection().fetch_with_filter("software", software.id)
+        processed_parameters = set()
 
         for parameter_descriptor in descriptor["inputs"]:
             if "id" not in parameter_descriptor.keys():
@@ -87,13 +97,9 @@ def read_descriptor(filename, schema_version="cytomine-0.1"):
                          .replace("@id", parameter_descriptor["id"].lower()) if isinstance(v, str) else v
                      for k, v in parameter_descriptor.items()}
 
-            type = param["type"].lower().capitalize()
-            if type == 'Listdomain':
-                type = 'ListDomain'
-
             sp = SoftwareParameter(
                 name=param["id"],
-                type=type,
+                type=_format_type(param["type"]),
                 id_software=software.id,
                 default_value=(param["default-value"] if "default-value" in param.keys() else ""),
                 required=(not param["optional"] if "optional" in param.keys() else False),
@@ -113,6 +119,13 @@ def read_descriptor(filename, schema_version="cytomine-0.1"):
             else:
                 sp.update(existing_software_parameter[0].id)
 
+            processed_parameters.add(param["id"])
+
+        if delete_missing:
+            for parameter in existing_software_parameters:
+                if parameter.name not in processed_parameters:
+                    parameter.delete()
+
         return software