update apps

FHIR · Aug 22, 2024 · afe9cbb · afe9cbb
1 parent 7cf2ec8
commit afe9cbb
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Showing 7 changed files with 33 additions and 37 deletions.
diff --git a/genomics-apps/PGxScreening.py b/genomics-apps/PGxScreening.py
@@ -13,7 +13,7 @@
 )
 
 
-@st.cache
+@st.cache_data
 def findSubjectHaplotypes(subject):
     # CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A5, NUDT15, SLCO1B1, TPMP, UGT1A1
     url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-haplotypes?subject='+subject + \
@@ -23,7 +23,7 @@ def findSubjectHaplotypes(subject):
     return r.json()
 
 
-@st.cache
+@st.cache_data
 def findSubjectTxImplications(subject, haplotypes):
     url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/phenotype-operations/$find-subject-tx-implications?subject='+subject+'&haplotypes='+haplotypes
     headers = {'Accept': 'application/json'}
@@ -90,7 +90,8 @@ def getMedicationList(subject):
 if count > 0:
     for i in implications["parameter"]:
         if i["name"] == "implication":
-            # get evidenceLevel, medicationCode, medicationName, implication
+            # get PharmGKBID, evidenceLevel, medicationCode, medicationName, implication
+            PharmGKBID.append("https://www.pharmgkb.org/gene/"+i["resource"]["identifier"][0]["value"])
             for l in i["resource"]["component"]:
                 if l["code"]["coding"][0]["code"] == "93044-6":
                     evidenceLevel.append(l["valueCodeableConcept"]["text"])
@@ -100,11 +101,8 @@ def getMedicationList(subject):
                 elif l["code"]["coding"][0]["code"] == "predicted-therapeutic-implication":
                     implication.append(l["valueCodeableConcept"]["text"])
         elif i["name"] == "genotype":
-            # get genotype, PharmGKBID
+            # get genotype
             genotype.append(i["resource"]["valueCodeableConcept"]["coding"][0]["code"])
-            for l in i["resource"]["component"]:
-                if l["code"]["coding"][0]["code"] == "81252-9":
-                    PharmGKBID.append("https://www.pharmgkb.org/gene/"+l["valueCodeableConcept"]["coding"][0]["code"])
 
 with col2:
     inxData = (pd.DataFrame({
@@ -117,15 +115,16 @@ def getMedicationList(subject):
     if count == 0:
         st.write('### No PGx data')
     else:
-        gb = GridOptionsBuilder.from_dataframe(inxData)
-        gb.configure_column("PharmGKB",
-                            cellRenderer=JsCode("""
-                function (params)
-                {return "<a target='_blank' href=" + params.value + ">" + params.value + "</a>"}
-                """).js_code
-                            )
-        go = gb.build()
-        AgGrid(inxData, gridOptions=go, allow_unsafe_jscode=True, editable=True, enable_enterprise_modules=True, update_mode="value_changed")
+        # gb = GridOptionsBuilder.from_dataframe(inxData)
+        # gb.configure_column("PharmGKB",
+        #                     cellRenderer=JsCode("""
+        #         function (params)
+        #         {return "<a target='_blank' href=" + params.value + ">" + params.value + "</a>"}
+        #         """).js_code
+        #                     )
+        # go = gb.build()
+        # AgGrid(inxData, gridOptions=go, allow_unsafe_jscode=True, editable=True, enable_enterprise_modules=True, update_mode="value_changed")
+        AgGrid(inxData, allow_unsafe_jscode=True, editable=True, enable_enterprise_modules=True, update_mode="value_changed")
     inxData_t = inxData.T
     st.download_button("Download table (json)", inxData_t.to_json())
     st.download_button("Download table (csv)", inxData.to_csv())
@@ -137,7 +136,8 @@ def getMedicationList(subject):
     for i in getMedicationList(subject):
         for j in medicationCode:
             if str(j) == str(i["ing"]):
-                inx = '<a target="_blank" href="https://api.pharmgkb.org/v1/infobutton?mainSearchCriteria.v.c='+str(i["ing"])+'">'+'🧬'+'</a>'
+                # inx = '<a target="_blank" href="https://api.pharmgkb.org/v1/infobutton?mainSearchCriteria.v.c='+str(i["ing"])+'">'+'🧬'+'</a>'
+                inx = '🧬'
                 break
             else:
                 inx = ""

diff --git a/genomics-apps/geneticScreening.py b/genomics-apps/geneticScreening.py
@@ -16,15 +16,15 @@
 )
 
 
-@st.cache
+@st.cache_data
 def findPopulationDxImplications(conditionCode):
     url = 'https://fhir-gen-ops.herokuapp.com/population-operations/phenotype-operations/$find-population-dx-implications?conditions='+conditionCode+'&includePatientList=true'
     headers = {'Accept': 'application/json'}
     r = requests.get(url, headers=headers)
     return r.json()
 
 
-@st.cache
+@st.cache_data
 def findSubjectDxImplications(subject, conditionCode):
     url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/phenotype-operations/$find-subject-dx-implications?subject='+subject+'&conditions='+conditionCode
     headers = {'Accept': 'application/json'}
@@ -120,7 +120,3 @@ def findSubjectDxImplications(subject, conditionCode):
 AgGrid(data, enable_enterprise_modules=True, update_mode="value_changed", allow_unsafe_jscode=True)
 
 st.download_button("Download table", data_t.to_json())
-
-AgGrid(data, enable_enterprise_modules=True, update_mode="value_changed", allow_unsafe_jscode=True)
-
-st.download_button("Download table", data_t.to_json())
diff --git a/genomics-apps/getMolecularConsequences.py b/genomics-apps/getMolecularConsequences.py
@@ -12,14 +12,14 @@
 )
 
 
-@st.cache
+@st.cache_data
 def getFeatureCoordinates(gene):
     url = 'https://fhir-gen-ops.herokuapp.com/utilities/get-feature-coordinates?gene='+gene
     headers = {'Accept': 'application/json'}
     return requests.get(url, headers=headers)
 
 
-@st.cache
+@st.cache_data
 def findSubjectVariants(subject, range, addAnnotationsFlag):
     url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-variants?subject=' + \
         subject+'&ranges='+range+'&includeVariants=true'
@@ -29,7 +29,7 @@ def findSubjectVariants(subject, range, addAnnotationsFlag):
     return requests.get(url, headers=headers)
 
 
-@st.cache
+@st.cache_data
 def findSubjectStructuralIntersectingVariants(subject, range, addAnnotationsFlag):
     url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-structural-intersecting-variants?subject=' + \
         subject+'&ranges='+range+'&includeVariants=true'
@@ -39,7 +39,7 @@ def findSubjectStructuralIntersectingVariants(subject, range, addAnnotationsFlag
     return requests.get(url, headers=headers)
 
 
-@st.cache
+@st.cache_data
 def findSubjectHaplotypes(subject, geneId):
     url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-haplotypes?subject='+subject+'&genes='+geneId
     headers = {'Accept': 'application/json'}
@@ -52,7 +52,7 @@ def _liftOver(chrom, pos):
     return {"chrom": chrom, "pos": newPos[0][1]}
 
 
-@st.cache
+@st.cache_data
 def findSPDI(SPDI):
     url = 'https://api.ncbi.nlm.nih.gov/variation/v0/spdi/' + \
         SPDI + '/canonical_representative'

diff --git a/genomics-apps/getVariants.py b/genomics-apps/getVariants.py
@@ -11,28 +11,28 @@
 )
 
 
-@st.cache
+@st.cache_data
 def getFeatureCoordinates(gene):
     url = 'https://fhir-gen-ops.herokuapp.com/utilities/get-feature-coordinates?gene='+gene
     headers = {'Accept': 'application/json'}
     return requests.get(url, headers=headers)
 
 
-@st.cache
+@st.cache_data
 def findSubjectVariants(subject, range):
     url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-variants?subject='+subject+'&ranges='+range+'&includeVariants=true'
     headers = {'Accept': 'application/json'}
     return requests.get(url, headers=headers)
 
 
-@st.cache
+@st.cache_data
 def findSubjectStructuralIntersectingVariants(subject, range):
     url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-structural-intersecting-variants?subject='+subject+'&ranges='+range+'&includeVariants=true'
     headers = {'Accept': 'application/json'}
     return requests.get(url, headers=headers)
 
 
-@st.cache
+@st.cache_data
 def findSubjectHaplotypes(subject, geneId):
     url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-haplotypes?subject='+subject+'&genes='+geneId
     headers = {'Accept': 'application/json'}

diff --git a/genomics-apps/polygenicScore.py b/genomics-apps/polygenicScore.py
@@ -31,22 +31,22 @@
             :arrow_forward: *population mean* and *standard deviation* are based on Operations reference implementation population.")
 
 
-@st.cache
+@st.cache_data
 def findSubjectVariants(subject, range):
     url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-variants?subject='+subject+'&ranges='+range+'&includeVariants=true'
     headers = {'Accept': 'application/json'}
     return requests.get(url, headers=headers)
 
 
-@st.cache
+@st.cache_data
 def findSubjectSpecificVariants(subject, variant):
     url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-specific-variants?subject='+subject+'&variants='+variant+'&includeVariants=true'
     # url = 'https://fhir-gen-ops-dev-ca42373833b6.herokuapp.com/subject-operations/genotype-operations/$find-subject-specific-variants?subject='+subject+'&variants='+variant+'&includeVariants=true'
     headers = {'Accept': 'application/json'}
     return requests.get(url, headers=headers)
 
 
-@st.cache
+@st.cache_data
 def getPolygenicScoreMetadata(pgs_id):
     url = 'https://www.pgscatalog.org/rest/score/'+pgs_id
     headers = {'Accept': 'application/json'}

diff --git a/genomics-apps/requirements.txt b/genomics-apps/requirements.txt
@@ -1,4 +1,4 @@
-pandas==2.0.3
+pandas==2.2.2
 pyliftover==0.4
 requests==2.32.0
 streamlit==1.34.0

diff --git a/genomics-apps/simpleApp.py b/genomics-apps/simpleApp.py
@@ -11,7 +11,7 @@
 )
 
 
-@st.cache
+@st.cache_data
 def findSubjectVariants(subject, range):
     url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-variants?subject='+subject+'&ranges='+range+'&includeVariants=true'
     headers = {'Accept': 'application/json'}