Add OSF io for the hackathon

compSPI · Apr 28, 2022 · 72048df · 72048df
1 parent 9aef412
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diff --git a/notebooks/download_and_upload_with_osf.ipynb b/notebooks/download_and_upload_with_osf.ipynb
@@ -7,13 +7,13 @@
    "source": [
     "# Download and Upload with OSF\n",
     "\n",
-    "This tutorial shows how to download and upload cryo-EM datasets using the `osf` module from `ioSPI`, that interact with the [Open Science Foundation (OSF)](https://osf.io/) framework.\n",
+    "This tutorial shows how to download and upload cryo-EM datasets using the `datasets` module from `ioSPI`, that interact with the [Open Science Foundation (OSF)](https://osf.io/) framework.\n",
     "\n",
     "OSF is an initiative that aims to increase the openness, reproducibility and integrity of scientific research. Among other functionalities, it is possible to upload scientific data which can be accessed by an Application Programming Interface (API). \n",
     "\n",
     "``ioSPI`` offers functionalities that allow uploading and accessing cryo-EM data using:\n",
     "- either, in order to get started: using the class `Project` that leverages the package `osfclient`\n",
-    "- or, if the user requires finer control: using the class `OSFProject` which follows `OSF APIv2`. \n",
+    "- or, if the user requires finer control: using the class `OSFUpload` which follows `OSF APIv2`. \n",
     "\n",
     "This tutorial introduces both options."
    ]
@@ -38,17 +38,17 @@
     "\n",
     "The email address and the token will be needed to connect to different OSF projects.\n",
     "\n",
-    "We import the `osf` module from `ioSPI`:"
+    "We import the `datasets` module from `ioSPI`:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "id": "e74dd634",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ioSPI.ioSPI import osf"
+    "from ioSPI.ioSPI import datasets"
    ]
   },
   {
@@ -87,7 +87,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "id": "febfdedd",
    "metadata": {},
    "outputs": [
@@ -100,7 +100,7 @@
     }
    ],
    "source": [
-    "cryoem_simulated_project = osf.Project(\n",
+    "cryoem_simulated_project = datasets.Project(\n",
     "    username=\"[email protected]\", \n",
     "    token=\"HBGGBOJcLYQfadEKIOyXJiLTum3ydXK4nGP3KmbkYUeBuYkZma9LPBSYennQn92gjP2NHn\",\n",
     "    project_id=\"7g42j\")"
@@ -120,7 +120,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "id": "f4f5b054",
    "metadata": {},
    "outputs": [
@@ -2299,7 +2299,7 @@
      "text": [
       "\r",
       "  0%|          | 0.00/4.22k [00:00<?, ?bytes/s]\r",
-      "100%|██████████| 4.22k/4.22k [00:00<00:00, 8.24Mbytes/s]\n"
+      "100%|██████████| 4.22k/4.22k [00:00<00:00, 9.90Mbytes/s]\n"
      ]
     }
    ],
@@ -2329,7 +2329,7 @@
     "This will create a new project page, as the one we are using here.\n",
     "- Save the project ID of the project you just created!\n",
     "\n",
-    "You should then create a new `my_project` object of the class `osf.Project` with the new project ID.\n",
+    "You should then create a new `my_project` object of the class `datasets.Project` with the new project ID.\n",
     "\n",
     "For the purpose of this tutorial, however, we will stay with our original project cryoEM simulated and use our object `cryoem_simulated_project`.\n",
     "\n",

diff --git a/notebooks/tutorial.ipynb b/notebooks/tutorial.ipynb
@@ -40,11 +40,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ioSPI import particle_metadata\n",
+    "from ioSPI.ioSPI import particle_metadata\n",
     "\n",
     "class Config:\n",
     "    \"\"\"Class to instantiate the config object.\"\"\"\n",
@@ -55,7 +55,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -72,7 +72,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -97,7 +97,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -173,7 +173,7 @@
        "0                      13               14  "
       ]
      },
-     "execution_count": 8,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -192,7 +192,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -210,7 +210,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -226,14 +226,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "# Created by the starfile Python package (version 0.4.11) at 11:16:57 on 09/03/2022\n",
+      "# Created by the starfile Python package (version 0.4.11) at 17:35:08 on 27/04/2022\n",
       "\n",
       "data_\n",
       "\n",
@@ -279,11 +279,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ioSPI import datasets"
+    "from ioSPI.ioSPI import datasets"
    ]
   },
   {
@@ -409,7 +409,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -423,7 +423,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,