adjusting bh23 workbook, and model class

ISA-tools · Aug 5, 2024 · 339db38 · 339db38
1 parent 00c2f63
commit 339db38
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Showing 4 changed files with 86 additions and 204 deletions.
diff --git a/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb b/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb
diff --git a/isa-cookbook/content/notebooks/isa-api-programmatic-rebuild-of-BII-S-3.ipynb b/isa-cookbook/content/notebooks/isa-api-programmatic-rebuild-of-BII-S-3.ipynb
@@ -4,15 +4,13 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "    ### Loading the ISA-API"
+    "### Loading the ISA-API"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from isatools.model import (\n",
@@ -53,9 +51,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "investigation = Investigation()\n",
@@ -223,9 +219,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "study.sources = [Source(name=\"GSM255770\"), Source(name=\"GSM255771\"),Source(name=\"GSM255772\"),Source(name=\"GSM255773\")]\n",
@@ -268,9 +262,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# Starting by declaring the 2 types of assays used in BII-S-3 as coded with ISAcreator tool\n",
@@ -308,9 +300,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "\n",
@@ -435,9 +425,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "study.assays.append(assay)\n",
@@ -447,9 +435,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# assay_g = investigation.studies[0].assays[1]\n",
@@ -506,9 +492,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from isatools.isatab import dump\n",
@@ -527,9 +511,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from isatools.isatab import load\n",
@@ -581,9 +563,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# import hashlib\n",
@@ -594,9 +574,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import filecmp\n",
@@ -607,9 +585,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "filecmp.cmp('./output/BII-S-3-synth/s_BII-S-3-synthesis.txt', './notebook-output/BII-S-3-roundtrip/s_BII-S-3-synthesis.txt')"
@@ -618,9 +594,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "filecmp.cmp('./output/BII-S-3-synth/a_gilbert-assay-Gx.txt', './notebook-output/BII-S-3-roundtrip/a_gilbert-assay-Gx.txt')"
@@ -629,9 +603,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "filecmp.cmp('./output/BII-S-3-synth/a_gilbert-assay-Tx.txt', './notebook-output/BII-S-3-roundtrip/a_gilbert-assay-Tx.txt')"

diff --git a/isatools/model/utils.py b/isatools/model/utils.py
@@ -1,7 +1,5 @@
 import itertools
-
 import networkx as nx
-import os
 
 from isatools.model.datafile import DataFile
 from isatools.model.process import Process
@@ -60,7 +58,6 @@ def _expand_path(path, identifiers_to_objects, dead_end_outputs):
     path_modified = False
     for i, identifier in enumerate(path):
         node = identifiers_to_objects[identifier]
-
         # If the node is a process at beginning of the path, add a path for each of its inputs.
         if i == 0 and isinstance(node, Process):
             identifier_list = [input_.sequence_identifier for input_ in node.inputs]
@@ -90,7 +87,7 @@ def _expand_path(path, identifiers_to_objects, dead_end_outputs):
             output_sequence_identifiers = {output.sequence_identifier for output in node.outputs}
             input_sequence_identifiers = {input_.sequence_identifier for input_ in
                                           identifiers_to_objects[path[i + 1]].inputs}
-            identifier_intersection = output_sequence_identifiers.intersection(input_sequence_identifiers)
+            identifier_intersection = list(output_sequence_identifiers.intersection(input_sequence_identifiers))
 
             combinations = _compute_combinations(identifier_intersection, identifiers_to_objects)
             for combo in combinations:
@@ -206,6 +203,7 @@ def _build_paths_and_indexes(process_sequence=None):
 
     return paths, identifiers_to_objects
 
+
 def _build_assay_graph(process_sequence=None):
     """:obj:`networkx.DiGraph` Returns a directed graph object based on a
     given ISA process sequence."""
@@ -289,7 +287,7 @@ def batch_create_assays(*args, n=1):
     from a prototype sequence (currently works only as flat end-to-end
     processes of Material->Process->Material->...)
 
-    :param *args: An argument list representing the process sequence prototype
+    # :param *args: An argument list representing the process sequence prototype
     :param n: Number of process sequences to create in the batch
     :returns: List of process sequences replicating the prototype sequence
 
@@ -376,13 +374,13 @@ def batch_create_assays(*args, n=1):
                     if isinstance(material_a, list):
                         process.inputs = material_a
                     else:
-                        process.inputs.append(material_a)
+                        process.inputs = [material_a]  # /.append(material_a)
                     if isinstance(material_b, list):
                         process.outputs = material_b
                         for material in material_b:
                             material.derives_from = [material_a]
                     else:
-                        process.outputs.append(material_b)
+                        process.outputs = [material_b]  # .append(material_b)
                         material_b.derives_from = [material_a]
                     process_sequence.append(process)
                 material_a = material_b
@@ -402,4 +400,3 @@ def _deep_copy(isa_object):
     if isinstance(isa_object, ProcessSequenceNode):
         new_obj.assign_identifier()
     return new_obj
-
diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json
@@ -1,4 +1,4 @@
-{
+                {
     "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "ISA Comment schema - it corresponds to ISA Comment[] construct",