[ALS-7658] Add json file for code blocks

hms-dbmi · Oct 21, 2024 · ae75a39 · ae75a39
1 parent 07adea3
commit ae75a39
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Showing 3 changed files with 16 additions and 78 deletions.
diff --git a/src/lib/assets/codeBlocks.json b/src/lib/assets/codeBlocks.json
@@ -0,0 +1,10 @@
+{
+  "bdcPythonExport": "# Requires python 3.7 or later\nimport sys\nimport pandas as pd\nimport matplotlib.pyplot as plt\n\n# BDC Powered by Terra users uncomment the following line to specify package install location\n# sys.path.insert(0, r\"/home/jupyter/.local/lib/python3.7/site-packages\")\n!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-python-client.git\n!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-python-adapter-hpds.git\n!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-biodatacatalyst-python-adapter-hpds.git\n\nimport PicSureClient\nimport PicSureBdcAdapter\n\ntoken_file = \"token.txt\"\nwith open(token_file, \"r\") as f:\n  my_token = f.read()\n\nbdc = PicSureBdcAdapter.Adapter(\"https://picsure.biodatacatalyst.nhlbi.nih.gov/picsure\", my_token)\n\nresource = bdc.useResource('02e23f52-f354-4e8b-992c-d37c8b9ba140')\n\nqueryID = <<QUERY ID GENERATED SHOULD GO HERE!!>>\n\nresults = resource.retrieveQueryResults(queryID)\n\nfrom io import StringIO\ndf_UI = pd.read_csv(StringIO(results), low_memory=False)\ndf_UI.head() # View top 5 rows of dataframe",
+  "bdcRExport": "# Requires R 3.4 or later\n### Uncomment this code if you are not using the PIC-SURE environment in *BDC-Seven Bridges*, or if you do not have all the necessary dependencies installed.\n#install.packages(\"devtools\")\n\nSys.setenv(TAR = \"/bin/tar\")\noptions(unzip = \"internal\")\ndevtools::install_github(\"hms-dbmi/pic-sure-r-adapter-hpds\", ref=\"main\", force=T, quiet=FALSE)\nlibrary(dplyr)\n\ntoken_file <- \"token.txt\"\ntoken <- scan(token_file, what = \"character\")\n\nsession <- picsure::bdc.initializeSession(\"https://picsure.biodatacatalyst.nhlbi.nih.gov/picsure\", token)\nsession <- picsure::bdc.setResource(session = session, resourceName = \"AUTH\")\n\nqueryID <- \"526c318d-4a0c-4937-9baa-e21042a0e444\"\nresults <- picsure::getResultByQueryUUID(session, queryID)\nhead(results) # View top 5 rows of dataframe",
+  "bdcPythonAPI": "# Requires python 3.6 or later\nimport sys\nimport pandas as pd\nimport matplotlib.pyplot as plt\n# BDC Powered by Terra users uncomment the following line to specify package install location\n# sys.path.insert(0, r\"/home/jupyter/.local/lib/python3.7/site-packages\")\n!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-python-client.git\n!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-python-adapter-hpds.git\n!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-biodatacatalyst-python-adapter-hpds.git\nimport PicSureClient\nimport PicSureBdcAdapter\n# Set up connection to PIC-SURE API\nPICSURE_network_URL = \"https://picsure.biodatacatalyst.nhlbi.nih.gov/picsure\"\ntoken_file = \"token.txt\"\n\nwith open(token_file, \"r\") as f:\n    my_token = f.read()\n\nbdc = PicSureBdcAdapter.Adapter(PICSURE_network_URL, my_token)",
+  "bdcRAPI": "# Requires R 3.4 or later\n### Uncomment this code if you are not using the PIC-SURE environment in *BDC-Seven Bridges*, or if you do not have all the necessary dependencies installed.\n#install.packages(\"devtools\")\nSys.setenv(TAR = \"/bin/tar\")\noptions(unzip = \"internal\")\ndevtools::install_github(\"hms-dbmi/pic-sure-r-adapter-hpds\", ref=\"main\", force=T, quiet=FALSE)\nlibrary(dplyr)\nPICSURE_network_URL = \"https://picsure.biodatacatalyst.nhlbi.nih.gov/picsure\"\ntoken_file <- \"token.txt\"\ntoken <- scan(token_file, what = \"character\")\nsession <- picsure::bdc.initializeSession(PICSURE_network_URL, token)\nsession <- picsure::bdc.setResource(session = session,  resourceName = \"AUTH\")",
+  "basePythonExport": "Code not set",
+  "baseRExport": "Code not set",
+  "basePythonAPI": "Code not set",
+  "baseRAPI": "Code not set"
+}
diff --git a/src/lib/components/explorer/export/ExportStepper.svelte b/src/lib/components/explorer/export/ExportStepper.svelte
@@ -20,6 +20,7 @@
   import { createDatasetName } from '$lib/services/datasets';
   import CardButton from '$lib/components/buttons/CardButton.svelte';
   import type { ExpectedResultType } from '$lib/models/query/Query.ts';
+  import codeBlocks from '$lib/assets/codeBlocks.json';
 
   export let query: QueryRequestInterface;
   export let showTreeStep = false;
@@ -321,55 +322,13 @@
                         language="python"
                         lineNumbers={true}
                         buttonCopied="Copied!"
-                        code={`# Requires python 3.7 or later
-import sys
-import pandas as pd
-import matplotlib.pyplot as plt
-# BDC Powered by Terra users uncomment the following line to specify package install location
-# sys.path.insert(0, r"/home/jupyter/.local/lib/python3.7/site-packages")
-!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-python-client.git
-!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-python-adapter-hpds.git
-!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-biodatacatalyst-python-adapter-hpds.git
-import PicSureHpdsLib
-import PicSureClient
-
-PICSURE_network_URL = "https://picsure.biodatacatalyst.nhlbi.nih.gov/picsure"
-
-token_file = "token.txt"
-with open(token_file, "r") as f:
-    my_token = f.read()
-
-connection = PicSureClient.Client.connect(url = PICSURE_network_URL, token = my_token)
-
-queryID = "${datasetId}"
-
-results = resource.retrieveQueryResults(queryID)
-
-from io import StringIO
-df_UI = pd.read_csv(StringIO(results), low_memory=False)`}
+                        code={codeBlocks?.bdcPythonExport || 'Code not set'}
                       ></CodeBlock>
                     {:else if tabSet === 1}
                       <CodeBlock
                         language="r"
                         lineNumbers={true}
-                        code={`# Requires R 3.4 or later
-### Uncomment this code if you are not using the PIC-SURE environment in *BDC-Seven Bridges*, or if you do not have all the necessary dependencies installed.
-#install.packages("devtools")
-
-Sys.setenv(TAR = "/bin/tar")
-options(unzip = "internal")
-devtools::install_github("hms-dbmi/pic-sure-r-adapter-hpds", ref="main", force=T, quiet=FALSE)
-library(dplyr)
-
-PICSURE_network_URL = "https://picsure.biodatacatalyst.nhlbi.nih.gov/picsure"
-token_file <- "token.txt"
-token <- scan(token_file, what = "character")
-session <- picsure::bdc.initializeSession(PICSURE_network_URL, token)
-session <- picsure::bdc.setResource(session = session)
-
-queryID <- "${datasetId}"
-
-results <- picsure::getResultByQueryUUID(session, queryID)`}
+                        code={codeBlocks?.bdcRExport || 'Code not set'}
                       ></CodeBlock>
                     {:else if tabSet === 2}
                       <div>

diff --git a/src/routes/(picsure)/(authorized)/analyze/+page.svelte b/src/routes/(picsure)/(authorized)/analyze/+page.svelte
@@ -3,6 +3,7 @@
   import UserToken from '$lib/components/UserToken.svelte';
   import { branding } from '$lib/configuration';
   import { CodeBlock, Tab, TabGroup } from '@skeletonlabs/skeleton';
+  import codeBlocks from '$lib/assets/codeBlocks.json';
 
   let tabSet: number = 0;
 </script>
@@ -53,42 +54,10 @@
             language="python"
             lineNumbers={true}
             buttonCopied="Copied!"
-            code={`# Requires python 3.6 or later
-import sys
-import pandas as pd
-import matplotlib.pyplot as plt
-# BDC Powered by Terra users uncomment the following line to specify package install location
-# sys.path.insert(0, r"/home/jupyter/.local/lib/python3.7/site-packages")
-!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-python-client.git
-!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-python-adapter-hpds.git
-!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-biodatacatalyst-python-adapter-hpds.git
-import PicSureClient
-import PicSureBdcAdapter
-# Set up connection to PIC-SURE API
-PICSURE_network_URL = "https://picsure.biodatacatalyst.nhlbi.nih.gov/picsure"
-token_file = "token.txt"
-
-with open(token_file, "r") as f:
-    my_token = f.read()
-
-bdc = PicSureBdcAdapter.Adapter(PICSURE_network_URL, my_token)`}
+            code={codeBlocks?.bdcPythonAPI || 'Code not set'}
           ></CodeBlock>
         {:else if tabSet === 1}
-          <CodeBlock
-            language="r"
-            lineNumbers={true}
-            code={`# Requires R 3.4 or later
-### Uncomment this code if you are not using the PIC-SURE environment in *BDC-Seven Bridges*, or if you do not have all the necessary dependencies installed.
-#install.packages("devtools")
-Sys.setenv(TAR = "/bin/tar")
-options(unzip = "internal")
-devtools::install_github("hms-dbmi/pic-sure-r-adapter-hpds", ref="main", force=T, quiet=FALSE)
-library(dplyr)
-PICSURE_network_URL = "https://picsure.biodatacatalyst.nhlbi.nih.gov/picsure"
-token_file <- "token.txt"
-token <- scan(token_file, what = "character")
-session <- picsure::bdc.initializeSession(PICSURE_network_URL, token)
-session <- picsure::bdc.setResource(session = session,  resourceName = "AUTH")`}
+          <CodeBlock language="r" lineNumbers={true} code={codeBlocks?.bdcRAPI || 'Code not set'}
           ></CodeBlock>
         {/if}
       </svelte:fragment>