Adding support to tables

.github/workflows/run_tests_pr.yml

@@ -16,7 +16,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install flake8 pytest
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          pip install .[tables]
       - name: Test with pytest
         run: |
           pytest tests/

.github/workflows/run_tests_push.yml

@@ -1,5 +1,7 @@
 name: Run Tests on push
-on: push
+on: 
+  push:
+    branches: [ main ]
 jobs:
   test:
     runs-on: ubuntu-latest
@@ -16,7 +18,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install flake8 pytest
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          pip install .[tables]
       - name: Test with pytest and generate coverage report/badge
         run: |
           pip install coverage coverage-badge

README.md

@@ -6,7 +6,9 @@ A module with convenience functions for writing Python code that interacts with
 
 # Installation
 
-Just `pip install ezomero` and you should be good to go! The repo contains a `requirements.txt` file with the specific package versions we test `ezomero` with, but any Python>=3.8 and latest `omero-py` and `numpy` _should_ work -  note that this package is in active development!
+Just `pip install ezomero` and you should be good to go! The repo contains the specific package versions we test `ezomero` with in `setup.py`, but any Python>=3.8 and latest `omero-py` and `numpy` _should_ work -  note that this package is in active development!
+
+If you want to use `get_table` and `post_table` to/from Pandas dataframes, you need to install `ezomero[tables]` - that install an optional `pandas` dependency. Installing ezomero without this will default `get_table` and `post_table` to use lists of row lists as their default.
 
 # Usage
 

ezomero/__init__.py

@@ -19,7 +19,8 @@
                      post_file_annotation,
                      post_project,
                      post_screen,
-                     post_roi)
+                     post_roi,
+                     post_table)
 from ._gets import (get_image,
                     get_image_ids,
                     get_project_ids,
@@ -37,6 +38,7 @@
                     get_user_id,
                     get_original_filepaths,
                     get_pyramid_levels,
+                    get_table,
                     get_shape)
 
 __all__ = ['post_dataset',
@@ -46,6 +48,7 @@
            'post_project',
            'post_screen',
            'post_roi',
+           'post_table',
            'get_image',
            'get_image_ids',
            'get_project_ids',
@@ -63,6 +66,7 @@
            'get_user_id',
            'get_original_filepaths',
            'get_pyramid_levels',
+           'get_table',
            'get_shape',
            'put_map_annotation',
            'filter_by_filename',

ezomero/_gets.py

@@ -3,12 +3,19 @@
 import numpy as np
 from ._ezomero import do_across_groups
 from omero.gateway import FileAnnotationWrapper
-from omero import ApiUsageException
+from omero import ApiUsageException, InternalException
 from omero.model import MapAnnotationI, TagAnnotationI
 from omero.rtypes import rint, rlong
 from omero.sys import Parameters
 from omero.model import enums as omero_enums
 from .rois import Point, Line, Rectangle, Ellipse, Polygon, Polyline, Label
+import importlib.util
+# try importing pandas
+if (importlib.util.find_spec('pandas')):
+    import pandas as pd
+    has_pandas = True
+else:
+    has_pandas = False
 
 
 # gets
@@ -863,7 +870,7 @@ def get_file_annotation(conn, file_ann_id, folder_path=None,
     conn : ``omero.gateway.BlitzGateway`` object
         OMERO connection.
     file_ann_id : int
-        ID of map annotation to get.
+        ID of file annotation to get.
     folder_path : str
         Path where file annotation will be saved. Defaults to local script
         directory.
@@ -1077,6 +1084,50 @@ def get_pyramid_levels(conn, image_id, across_groups=True):
     return levels
 
 
+@do_across_groups
+def get_table(conn, file_ann_id, across_groups=True):
+    """Get a table from its FileAnnotation object.
+
+    Parameters
+    ----------
+    conn : ``omero.gateway.BlitzGateway`` object
+        OMERO connection.
+    file_ann_id : int
+        ID of FileAnnotation table to get.
+    across_groups : bool, optional
+        Defines cross-group behavior of function - set to
+        ``False`` to disable it.
+
+    Returns
+    -------
+    table : object
+        Object containing the actual table. It can be either a list of
+        row-lists or a pandas Dataframe in case the optional pandas dependency
+        was installed.
+
+    Examples
+    --------
+    >>> table = get_table(conn, 62)
+    >>> print(table[0])
+    ['ID', 'X', 'Y']
+    """
+    if type(file_ann_id) is not int:
+        raise TypeError('File annotation ID must be an integer')
+    ann = conn.getObject('FileAnnotation', file_ann_id)
+    table = None
+    if ann:
+        orig_table_file = conn.getObject('OriginalFile', ann.getFile().id)
+        resources = conn.c.sf.sharedResources()
+        try:
+            table_obj = resources.openTable(orig_table_file._obj)
+            table = _create_table(table_obj)
+        except InternalException:
+            logging.warning(f" FileAnnotation {file_ann_id} is not a table.")
+    else:
+        logging.warning(f' FileAnnotation {file_ann_id} does not exist.')
+    return table
+
+
 @do_across_groups
 def get_shape(conn, shape_id, across_groups=True):
     """Get an ezomero shape object from an OMERO Shape id
@@ -1112,6 +1163,42 @@ def get_shape(conn, shape_id, across_groups=True):
     return _omero_shape_to_shape(omero_shape)
 
 
+def _create_table(table_obj):
+    if importlib.util.find_spec('pandas'):
+        columns = []
+        for col in table_obj.getHeaders():
+            columns.append(col.name)
+        table = pd.DataFrame(columns=columns)
+        rowCount = table_obj.getNumberOfRows()
+        data = table_obj.read(list(range(len(columns))), 0, rowCount)
+        for col in data.columns:
+            col_data = []
+            for v in col.values:
+                col_data.append(v)
+            table[col.name] = col_data
+
+    else:
+        table = []
+        columns = []
+        data_lists = []
+        for col in table_obj.getHeaders():
+            columns.append(col.name)
+        table.append(columns)
+        rowCount = table_obj.getNumberOfRows()
+        data = table_obj.read(list(range(len(columns))), 0, rowCount)
+        for col in data.columns:
+            col_data = []
+            for v in col.values:
+                col_data.append(v)
+            data_lists.append(col_data)
+        # transpose data_lists
+        data_lists = [list(i) for i in zip(*data_lists)]
+        for row in data_lists:
+            table.append(row)
+
+    return table
+
+
 def _omero_shape_to_shape(omero_shape):
     """ Helper function to convert ezomero shapes into omero shapes"""
     shape_type = omero_shape.ice_id().split("::omero::model::")[1]