Removed deprecated sampletab code.

docs/exportdata.rst

@@ -54,37 +54,6 @@ Note that when subitting SRA XML to ENA, you need to supply broker information a
 To turn off pre-conversion validation, use ``validate_first=False``. By default it is set to ``validate_first=True``.
 
 
------------------------------------
-Converting ISA content to SampleTab
------------------------------------
-To export metadata from SampleTab files (e.g. for EBI BioSamples database), you can do the following to export a
-ISA-Tab to SampleTab:
-
-.. code-block:: python
-
-    from isatools.convert import isatab2sampletab
-    with open('your/path/to/i_investigation.txt', 'r') as input_investigation_file:
-        with open('your/path/to/sampletab.txt', 'w') as output_sampletab_file:
-            isatab2sampletab.convert(input_investigation_file, output_sampletab_file)
-
-To export an ISA JSON file to SampleTab, you can do:
-
-.. code-block:: python
-
-    from isatools.convert import isatab2sampletab
-    with open('your/path/to/i_investigation.txt', 'r') as input_investigation_file:
-        with open('your/path/to/sampletab.txt', 'w') as output_sampletab_file:
-            isatab2sampletab.convert(input_investigation_file, output_sampletab_file)
-
-You can also dump SampleTab content directly from ISA Python objects:
-
-.. code-block:: python
-
-    from isatools import sampletab
-    with open('your/path/to/sampletab.txt', 'w') as output_sampletab:
-        # Note: ISA would be a previously loaded or constructed root Investigation object
-        sampletab.dump(ISA, output_sampletab)
-
 ---------------------------------
 Exporting ISA content to MAGE-TAB
 ---------------------------------
@@ -97,7 +66,7 @@ ISA-Tab to  MAGE-TAB:
     with open('your/path/to/i_investigation.txt', 'r') as input_investigation_file:
         isatab2magetab.convert(input_investigation_file, 'your/output/path/')
 
-To export an ISA JSON file to SampleTab, you can do:
+To export an ISA JSON file to MAGE-TAB, you can do:
 
 .. code-block:: python
 

docs/importdata.rst

@@ -105,35 +105,6 @@ tool from https://github.com/ISA-tools/mzml2isa and can be run as follows:
     from isatools.convert import mzml2isa
     mzml2isa.convert('your/path/to/mzml/files/', 'tmp/', "My Study ID")
 
---------------------------
-Importing SampleTab to ISA
---------------------------
-To import metadata from SampleTab files (e.g. from EBI BioSamples database), you can do the following to import a
-SampleTab to ISA-Tab:
-
-.. code-block:: python
-
-    from isatools.convert import sampletab2isatab
-    with open('your/path/to/sampletab.txt', 'r') as input_sampletab:
-        sampletab2isatab.convert(input_sampletab, 'tmp/')
-
-To import a SampleTab to ISA JSON, you can do:
-
-.. code-block:: python
-
-    from isatools.convert import sampletab2json
-    with open('your/path/to/sampletab.txt', 'r') as input_sampletab:
-        with open('your/path/to/myjson.json', 'w') as output_json:'
-            sampletab2json.convert(input_sampletab, output_json)
-
-You can also load SampleTab content directly into ISA Python objects:
-
-.. code-block:: python
-
-    from isatools import sampletab
-    with open('your/path/to/sampletab.txt', 'r') as input_sampletab:
-        ISA = sampletab.load(input_sampletab)
-
 -------------------------
 Importing MAGE-TAB to ISA
 -------------------------
@@ -144,13 +115,13 @@ MAGE-TAB to ISA-Tab:
 
     from isatools.convert import magetab2isatab
     with open('your/path/to/magetab.idf.txt', 'r') as input_magetab:
-        magetab2isatab.convert(input_sampletab, 'tmp/')
+        magetab2isatab.convert(input_magetab, 'tmp/')
 
 To import a MAGE-TAB to ISA JSON, you can do:
 
 .. code-block:: python
 
-    from isatools.convert import sampletab2json
-    with open('your/path/to/magetab.idf.txt', 'r') as input_sampletab:
-        with open('your/path/to/myjson.json', 'w') as output_json:'
+    from isatools.convert import magetab2json
+    with open('your/path/to/magetab.idf.txt', 'r') as input_magetab:
+        with open('your/path/to/myjson.json', 'w') as output_json:
             magetab2json.convert(input_magetab, output_json)

isa-cookbook/content/exportdata.md

@@ -69,48 +69,6 @@ default it is set to `validate_first=True`.
 
 ***
 
-## Converting ISA content to SampleTab
-
-
-```{warning}
-
-As of July 2020, EBI Biosample has decommissioned SampleTab format and now only accepts submission via a REST API.
-Future releases of the ISA-API will support this mode of data deposition.
-```
-
-To export metadata from SampleTab files (e.g. for EBI BioSamples
-database), you can do the following to export a ISA-Tab to SampleTab:
-
-```python
-from isatools.convert import isatab2sampletab
-
-with open('your/path/to/i_investigation.txt', 'r') as input_investigation_file:
-    with open('your/path/to/sampletab.txt', 'w') as output_sampletab_file:
-        isatab2sampletab.convert(input_investigation_file, output_sampletab_file)
-```
-
-To export an ISA JSON file to SampleTab, you can do:
-
-```python
-from isatools.convert import isatab2sampletab
-
-with open('your/path/to/i_investigation.txt', 'r') as input_investigation_file:
-    with open('your/path/to/sampletab.txt', 'w') as output_sampletab_file:
-        isatab2sampletab.convert(input_investigation_file, output_sampletab_file)
-```
-
-You can also dump SampleTab content directly from ISA Python objects:
-
-```python
-from isatools import sampletab
-
-with open('your/path/to/sampletab.txt', 'w') as output_sampletab:
-    # Note: ISA would be a previously loaded or constructed root Investigation object
-    sampletab.dump(ISA, output_sampletab)
-```
-
-***
-
 ## Exporting ISA content to MAGE-TAB
 
 To export metadata to MAGE-TAB files (e.g. for EBI ArrayExpress
@@ -123,7 +81,7 @@ with open('your/path/to/i_investigation.txt', 'r') as input_investigation_file:
     isatab2magetab.convert(input_investigation_file, 'your/output/path/')
 ```
 
-To export an ISA JSON file to SampleTab, you can do:
+To export an ISA JSON file to MAGE-TAB, you can do:
 
 ```python
 from isatools.convert import json2magetab

isa-cookbook/content/importdata.md

@@ -35,14 +35,14 @@ database), you can do the following to import a MAGE-TAB to ISA-Tab:
 ```python
 from isatools.convert import magetab2isatab
 with open('your/path/to/magetab.idf.txt', 'r') as input_magetab:
-    magetab2isatab.convert(input_sampletab, 'tmp/')
+    magetab2isatab.convert(input_magetab, 'tmp/')
 ```
 
 To import a MAGE-TAB to ISA JSON, you can do:
 
 ```python
-from isatools.convert import sampletab2json
-with open('your/path/to/magetab.idf.txt', 'r') as input_sampletab:
+from isatools.convert import magetab2json
+with open('your/path/to/magetab.idf.txt', 'r') as input_magetab:
     with open('your/path/to/myjson.json', 'w') as output_json:
         magetab2json.convert(input_magetab, output_json)
 ```
@@ -146,39 +146,3 @@ from isatools.convert import mzml2isa
 mzml2isa.convert('your/path/to/mzml/files/', 'tmp/', "My Study ID")
 ```
 
-***
-
-### Importing SampleTab to ISA
-
-```{warning}
-
-As of July 2020, EBI Biosample has decommissioned SampleTab format and now only accepts submission via a REST API.
-Future releases of the ISA-API will support this mode of data deposition.
-```
-
-To import metadata from SampleTab files (e.g. from EBI BioSamples
-database), you can do the following to import a SampleTab to ISA-Tab:
-
-```python
-from isatools.convert import sampletab2isatab
-with open('your/path/to/sampletab.txt', 'r') as input_sampletab:
-    sampletab2isatab.convert(input_sampletab, 'tmp/')
-```
-
-To import a SampleTab to ISA JSON, you can do:
-
-```python
-from isatools.convert import sampletab2json
-with open('your/path/to/sampletab.txt', 'r') as input_sampletab:
-    with open('your/path/to/myjson.json', 'w') as output_json:
-        sampletab2json.convert(input_sampletab, output_json)
-```
-
-You can also load SampleTab content directly into ISA Python objects:
-
-```python
-from isatools import sampletab
-with open('your/path/to/sampletab.txt', 'r') as input_sampletab:
-    ISA = sampletab.load(input_sampletab)
-```
-

isatools/__init__.py

@@ -22,9 +22,6 @@
 from isatools.convert import (
     isatab2json as isatab2json_module,
 )
-from isatools.convert import (
-    isatab2sampletab as isatab2sampletab_module,
-)
 from isatools.convert import (
     isatab2sra as isatab2sra_module,
 )
@@ -37,9 +34,6 @@
 from isatools.convert import (
     json2magetab as json2magetab_module,
 )
-from isatools.convert import (
-    json2sampletab as json2sampletab_module,
-)
 from isatools.convert import (
     json2sra as json2sra_module,
 )
@@ -49,12 +43,6 @@
 from isatools.convert import (
     magetab2json as magetab2json_module,
 )
-from isatools.convert import (
-    sampletab2isatab as sampletab2isatab_module,
-)
-from isatools.convert import (
-    sampletab2json as sampletab2json_module,
-)
 from isatools.net import (
     biocrates2isatab as biocrates2isatab_module,
 )
@@ -78,17 +66,13 @@
 # isatools.convert packages
 isatab2cedar = isatab2cedar_module
 isatab2json = isatab2json_module
-isatab2sampletab = isatab2sampletab_module
 isatab2sra = isatab2sra_module
 isatab2w4m = isatab2w4m_module
 json2isatab = json2isatab_module
 json2magetab = json2magetab_module
-json2sampletab = json2sampletab_module
 json2sra = json2sra_module
 magetab2isatab = magetab2isatab_module
 magetab2json = magetab2json_module
-sampletab2isatab = sampletab2isatab_module
-sampletab2json = sampletab2json_module
 
 # isatools.net packages
 biocrates2isatab = biocrates2isatab_module

isatools/__main__.py

@@ -38,7 +38,7 @@ def main(argv=None):
         dest="cmd",
         help="isatools API command to run",
         required=True,
-        choices=["isatab2json", "json2isatab", "sampletab2isatab", "sampletab2json"],
+        choices=["isatab2json", "json2isatab"],
     )
     p.add_argument("-i", dest="in_path", help="in  (files or directory will be read from here)", required=True)
     p.add_argument(
@@ -69,18 +69,6 @@ def main(argv=None):
         with open(args.in_path) as in_fp:
             json2isatab.convert(in_fp, args.out_path)
 
-    elif args.cmd == "sampletab2isatab":
-        from isatools.convert import sampletab2isatab
-
-        with open(args.in_path) as in_fp:
-            sampletab2isatab.convert(in_fp, args.out_path)
-
-    elif args.cmd == "sampletab2json":
-        from isatools.convert import sampletab2json
-
-        with open(args.in_path) as in_fp, open(args.out_path, "w") as out_fp:
-            sampletab2json.convert(in_fp, out_fp)
-
 
 if __name__ == "__main__":
     main()

isatools/convert/__init__.py

@@ -6,12 +6,10 @@
 #
 # from isatools.convert import isatab2w4m
 # from isatools.convert import isatab2sra
-# from isatools.convert import isatab2sampletab
 # from isatools.convert import json2isatab
 # from isatools.convert import json2magetab
 # from isatools.convert import json2sra
 # from isatools.convert import magetab2isatab
-# from isatools.convert import sampletab2isatab
 # from isatools.convert import mzml2isa
 
 # from isatools.convert.isatab2json import convert

isatools/isatab/graph.py

@@ -22,13 +22,6 @@ def _all_end_to_end_paths(G, start_nodes):
         message = f"Calculating for paths for {num_start_nodes} sources: "
     elif isinstance(start_node, Sample):
         message = f"Calculating for paths for {num_start_nodes} samples: "
-    """if isa_logging.show_pbars:
-        pbar = ProgressBar(
-            min_value=0, max_value=num_start_nodes, widgets=[
-                message, SimpleProgress(), Bar(left=" |", right="| "),
-                ETA()]).start()
-    else:
-        def pbar(x): return x"""
     for start in start_nodes:
         # Find ends
         node = G.indexes[start]