add conversion script

.gitignore

@@ -82,3 +82,5 @@ bower_components
 .bower-cache
 .bower-registry
 .bower-tmp
+
+cell-lines

scripts/convert_cell_catalog.py

@@ -0,0 +1,103 @@
+import json
+import os
+
+
+def sort_media_data(media_list):
+    new_media_dict = {"videos": []}
+    for media in media_list:
+        if media["type"] == "movie":
+            new_media_dict["videos"].append(
+                {"video": media["link"], "caption": f'"{media["caption"]}"'}
+            )
+    return new_media_dict
+
+def check_status(status):
+    try:
+        if status == "In Progress":
+            return "in progress"
+        elif status == "Yes":
+            return "released"
+    except KeyError:
+        return "no status found"
+
+
+with open("./data/cell_line_catalog.json", "r") as f:
+    data = cell_line_catalog = json.load(f)
+
+for cell_line in data:
+    # gene data
+    gene_symbols = cell_line["Main_gene_symbol"]
+    gene_symbol = gene_symbols[0]
+    protein = cell_line["Main_protein"]
+    gene_id = cell_line["Main_gene_id"]
+    gene_name = cell_line["Main_gene_name"]
+    isoform = cell_line["Main_isoforms"]
+    structure = cell_line["Main_structure"]
+
+    # print(f"{gene_symbol} {protein} {gene_id} {gene_name} {isoform} {structure}")
+    if len(gene_symbols) > 1:
+        print(f"Multiple gene symbols found for {gene_symbols}")
+        continue
+    # with open(f"./genes/{gene_symbol.lower()}.md", "w") as f:
+    #     f.write("---\n")
+    #     f.write("templateKey: gene-name\n")
+    #     f.write(f"symbol: {gene_symbol}\n")
+    #     f.write(f"name: {gene_name}\n")
+    #     f.write(f"protein: {protein}\n")
+    #     f.write(f"structure: {structure}\n")
+    #     if len(isoform) > 0:
+    #         f.write(f"isoforms:\n")
+    #         for iso in isoform:
+    #             gene_name = iso["gene_name"]
+    #             gene_isoforms = iso["gene_isoforms"]
+    #             f.write(f"  - name: {gene_name}\n")
+    #             if len(gene_isoforms) > 0:
+    #                 f.write(f"    ids:\n")
+    #                 for key in gene_isoforms:
+    #                     f.write(f"      - {key}\n")
+    #     f.write("---")
+
+    # Main cell line data
+    directory = "./cell-lines"
+    if not os.path.exists(directory):
+        os.mkdir(directory)
+    cell_line_id = int(cell_line["cell_line_id"].split("-")[1])
+    if cell_line['clone_number']:
+        cell_line_name = f"AICS-{cell_line_id}-{cell_line['clone_number']}"
+    else:
+        cell_line_name = f"AICS-{cell_line_id}-in-progress"
+    path = f"./cell-lines/{cell_line_name}"
+    if not os.path.exists(path):
+        os.mkdir(path)  # create directory
+    new_media_data = sort_media_data(cell_line["Main_media"])
+    with open(f"./cell-lines/{cell_line_name}/index.md", "w") as f:
+        f.write("---\n")
+        f.write("templateKey: cell-line\n")
+        f.write(f"cell_line_id: {cell_line_id}\n")
+        f.write(f"status: {check_status(cell_line['status'])}\n")
+        # handle parental line thumbnail image
+        if cell_line_id == 13:
+            f.write(f"thumbnail_image: aics-{cell_line_id}.jpg\n")
+        elif cell_line_id == 75:
+            f.write(
+                "thumbnail_image: 20181023_m02_001_s13_cl85_cropped_scalebar20_withinset_rgb.jpg\n"
+            )
+        f.write(f"clone_number: {cell_line['clone_number']}\n")
+        f.write(f"allele_count: {cell_line['alleleCount']}\n")
+        f.write(f"parental_line: 0\n")
+        f.write(f"gene: {gene_symbol}\n")
+        f.write("tag_location:\n")
+        f.write(f"  - {cell_line['Main_terminal_tagged']}\n")
+        f.write("fluorescent_tag:\n")
+        f.write(f"  - {cell_line['Main_fluorescent_tag']}\n")
+        f.write(f"order_link: {cell_line['Main_order_link']}\n")
+        f.write(f"cofa: {cell_line['Main_cofa']}\n")
+        # In progress cell lines (AICS 70 and 122) have only limited data, check the keys before accessing
+        f.write(f"donor_plasmid: {cell_line.get('Main_donor_plasmid', '')}\n")
+        f.write(f"eu_hpsc_reg: {cell_line.get('Main_eu_hpsc_reg', '')}\n")
+        f.write(f"images_and_videos:\n")
+        f.write(f"  videos:\n")
+        for video in new_media_data["videos"]:
+            f.write(f"    - video: {video['video']}\n")
+            f.write(f"      caption: {video['caption']}\n")
+        f.write("---")